2021��� 05��� 08��� ��������� 13:59:19 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC /usr/local/freesurfer/bin/recon-all -i T1.nii -s pd_struc_recon -all subjid pd_struc_recon setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Linux yelab-Precision-5820-Tower 5.4.0-72-generic #80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 191191 maxlocks unlimited maxsignal 191191 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 46G 3.9G 17G 550M 25G 41G Swap: 31G 460M 31G ######################################## program versions used 7.1.1 (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551) 7.1.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/08-05:59:19-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: yelab Machine: yelab-Precision-5820-Tower Platform: Linux PlatformVersion: 5.4.0-72-generic CompilerName: GCC CompilerVersion: 4.9.2 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_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/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon mri_convert /media/yelab/data/PD/PD_Nii/sub1/STRUC/T1.nii /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig/001.mgz mri_convert /media/yelab/data/PD/PD_Nii/sub1/STRUC/T1.nii /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig/001.mgz INFO: using NIfTI-1 qform reading from /media/yelab/data/PD/PD_Nii/sub1/STRUC/T1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00783747, -0.998485, -0.0544653) j_ras = (0.100148, -0.0534094, 0.993538) k_ras = (0.994942, 0.0132414, -0.0995776) writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig/001.mgz... @#@FSTIME 2021:05:08:13:59:19 mri_convert N 2 e 1.95 S 0.03 U 1.92 P 100% M 31536 F 0 R 6495 W 0 c 5 w 1 I 0 O 34384 L 0.70 1.27 1.65 @#@FSLOADPOST 2021:05:08:13:59:21 mri_convert N 2 0.70 1.27 1.65 #-------------------------------------------- #@# MotionCor 2021��� 05��� 08��� ��������� 13:59:22 CST Found 1 runs /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig/001.mgz /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon mri_convert /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz --conform mri_convert /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz --conform reading from /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00783747, -0.998485, -0.0544653) j_ras = (0.100148, -0.0534094, 0.993538) k_ras = (0.994942, 0.0132414, -0.0995776) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 8368 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz... @#@FSTIME 2021:05:08:13:59:25 mri_convert N 3 e 3.55 S 0.07 U 3.47 P 100% M 43724 F 0 R 17779 W 0 c 26 w 1 I 0 O 14624 L 0.73 1.27 1.64 @#@FSLOADPOST 2021:05:08:13:59:28 mri_convert N 3 0.75 1.26 1.64 mri_add_xform_to_header -c /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/transforms/talairach.xfm /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2021:05:08:13:59:29 mri_add_xform_to_header N 4 e 1.15 S 0.01 U 1.12 P 99% M 23400 F 0 R 4583 W 0 c 5 w 2 I 0 O 14624 L 0.75 1.26 1.64 @#@FSLOADPOST 2021:05:08:13:59:30 mri_add_xform_to_header N 4 0.75 1.26 1.64 #-------------------------------------------- #@# Talairach 2021��� 05��� 08��� ��������� 13:59:30 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri /usr/local/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 yelab-Precision-5820-Tower 5.4.0-72-generic #80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 2021��� 05��� 08��� ��������� 13:59:30 CST Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.9078 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.9078/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.9078/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.9078/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.9078/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (7.45058e-09, -2.32831e-10, -1) k_ras = (0, 1, -1.16415e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... 2021��� 05��� 08��� ��������� 14:01:30 CST mri_nu_correct.mni done @#@FSTIME 2021:05:08:13:59:30 mri_nu_correct.mni N 12 e 120.34 S 0.13 U 120.22 P 100% M 489040 F 0 R 149318 W 0 c 384 w 101 I 0 O 10592 L 0.75 1.26 1.64 @#@FSLOADPOST 2021:05:08:14:01:30 mri_nu_correct.mni N 12 1.58 1.43 1.65 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at 2021��� 05��� 08��� ��������� 14:01:30 CST Ended at 2021��� 05��� 08��� ��������� 14:01:49 CST talairach_avi done @#@FSTIME 2021:05:08:14:01:30 talairach_avi N 4 e 18.79 S 0.86 U 11.93 P 68% M 255728 F 0 R 396529 W 0 c 272 w 142 I 0 O 295256 L 1.58 1.43 1.65 @#@FSLOADPOST 2021:05:08:14:01:49 talairach_avi N 4 1.56 1.44 1.65 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.1.1 --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/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 0.99203 0.01798 -0.07498 5.16978; 0.01856 1.04876 0.22862 -29.46085; 0.07487 -0.19407 1.10586 -3.56892; 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 2021��� 05��� 08��� ��������� 14:01:51 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7624, pval=0.6675 >= threshold=0.0050) @#@FSTIME 2021:05:08:14:01:51 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 6088 F 0 R 215 W 0 c 0 w 1 I 0 O 0 L 1.56 1.44 1.65 @#@FSLOADPOST 2021:05:08:14:01:51 talairach_afd N 4 1.56 1.44 1.65 awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/transforms/talairach_avi.log tal_QC_AZS /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/transforms/talairach_avi.log TalAviQA: 0.97884 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction 2021��� 05��� 08��� ��������� 14:01:51 CST mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri /usr/local/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 yelab-Precision-5820-Tower 5.4.0-72-generic #80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 2021��� 05��� 08��� ��������� 14:01:51 CST Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.9329 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.9329/ones.mgz 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.9329/ones.mgz sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab input /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.9329/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.9329/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.9329/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.9329/input.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.9329/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.9329/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.9329/input.mean.dat sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.9329/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.9329/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.9329/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.9329/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.9329/output.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.9329/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.9329/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.9329/output.mean.dat sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.9329/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.9329/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.9329/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz mul 2.33240173639494877329 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.9329/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (7.45058e-09, -2.32831e-10, -1) k_ras = (0, 1, -1.16415e-09) 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 4 seconds. mapping (16, 131) to ( 3, 110) 2021��� 05��� 08��� ��������� 14:04:10 CST mri_nu_correct.mni done @#@FSTIME 2021:05:08:14:01:51 mri_nu_correct.mni N 9 e 139.13 S 0.57 U 138.56 P 100% M 614468 F 0 R 510036 W 0 c 1171 w 173 I 0 O 22800 L 1.56 1.44 1.65 @#@FSLOADPOST 2021:05:08:14:04:10 mri_nu_correct.mni N 9 2.16 1.65 1.69 mri_add_xform_to_header -c /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2021:05:08:14:04:10 mri_add_xform_to_header N 4 e 0.61 S 0.01 U 0.59 P 99% M 23488 F 0 R 4588 W 0 c 1 w 1 I 0 O 6960 L 2.16 1.65 1.69 @#@FSLOADPOST 2021:05:08:14:04:11 mri_add_xform_to_header N 4 2.16 1.65 1.69 #-------------------------------------------- #@# Intensity Normalization 2021��� 05��� 08��� ��������� 14:04:11 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 0.99203 0.01798 -0.07498 5.16978; 0.01856 1.04876 0.22862 -29.46085; 0.07487 -0.19407 1.10586 -3.56892; 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 = 17 Starting OpenSpline(): npoints = 17 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 63 (63), valley at 46 (46) csf peak at 32, setting threshold to 52 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 63 (63), valley at 45 (45) csf peak at 19, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 21 seconds. @#@FSTIME 2021:05:08:14:04:11 mri_normalize N 7 e 81.14 S 0.31 U 80.82 P 99% M 584216 F 0 R 267376 W 0 c 198 w 1 I 0 O 7848 L 2.16 1.65 1.69 @#@FSLOADPOST 2021:05:08:14:05:32 mri_normalize N 7 1.80 1.64 1.68 #-------------------------------------------- #@# Skull Stripping 2021��� 05��� 08��� ��������� 14:05:32 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/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/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=12.0 skull bounding box = (39, 45, 30) --> (223, 255, 224) finding center of left hemi white matter using (100, 115, 127) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (77,89,103) --> (122, 140,150) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 4.6 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.439 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.352462 @ (-10.526, -10.526, -10.526) max log p = -4.144608 @ (5.263, 5.263, -5.263) max log p = -4.103214 @ (2.632, -2.632, -2.632) max log p = -4.080557 @ (1.316, 3.947, 3.947) max log p = -4.068923 @ (-0.658, -0.658, -1.974) max log p = -4.057186 @ (0.987, -3.618, 0.987) max log p = -4.057186 @ (0.000, 0.000, 0.000) max log p = -4.057186 @ (0.000, 0.000, 0.000) Found translation: (-1.0, -8.2, -15.5): log p = -4.057 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.935, old_max_log_p =-4.057 (thresh=-4.1) 1.00000 0.00000 0.00000 -0.98685; 0.00000 1.07125 0.11999 -26.62859; 0.00000 -0.15634 1.04996 1.71615; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 20 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.881, old_max_log_p =-3.935 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.98685; 0.00000 1.13954 0.12763 -37.38567; 0.00000 -0.15634 1.04996 1.71615; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.881, old_max_log_p =-3.881 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.98685; 0.00000 1.13954 0.12763 -37.38567; 0.00000 -0.15634 1.04996 1.71615; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.819, old_max_log_p =-3.881 (thresh=-3.9) 0.98002 -0.03591 -0.00747 5.55774; 0.03087 1.07082 0.15034 -37.70702; 0.00202 -0.19982 1.06360 4.06238; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 12 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.810, old_max_log_p =-3.819 (thresh=-3.8) 0.97848 -0.07043 -0.01465 11.72181; 0.06298 1.05372 0.21922 -46.26359; -0.00000 -0.26943 1.05149 16.05230; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 12 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.810, old_max_log_p =-3.810 (thresh=-3.8) 0.97848 -0.07043 -0.01465 11.72181; 0.06298 1.05372 0.21922 -46.26359; -0.00000 -0.26943 1.05149 16.05230; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 12 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.803, old_max_log_p =-3.810 (thresh=-3.8) 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 5 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.803, old_max_log_p =-3.803 (thresh=-3.8) 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 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 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 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: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.803 (old=-4.439) transform before final EM align: 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 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 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 0.97848 -0.07043 -0.01465 11.72181; 0.06284 1.05125 0.21871 -45.82209; -0.00000 -0.26975 1.05272 15.94084; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 805060 FSRUNTIME@ mri_em_register 0.1768 hours 1 threads registration took 10 minutes and 37 seconds. @#@FSTIME 2021:05:08:14:05:32 mri_em_register N 4 e 636.63 S 0.65 U 635.96 P 99% M 629404 F 0 R 166646 W 0 c 1234 w 1 I 0 O 16 L 1.80 1.64 1.68 @#@FSLOADPOST 2021:05:08:14:16:09 mri_em_register N 4 1.81 1.67 1.66 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/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=128 y=122 z=122 r=85 first estimation of the main basin volume: 2661947 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=145, y=112, z=83, Imax=255 CSF=16, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9784746897 voxels, voxel volume =1.000 = 9784746897 mmm3 = 9784747.008 cm3 done. PostAnalyze...Basin Prior 89 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=127, z=118, r=9354 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 43938 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 3330 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 2916 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 18324 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 18972 OTHER CSF_MIN=3, CSF_intensity=23, CSF_MAX=37 , nb = 396 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 6, 9, 33, 62 after analyzing : 6, 25, 33, 34 RIGHT_CER before analyzing : 5, 5, 18, 76 after analyzing : 5, 18, 25, 32 LEFT_CER before analyzing : 5, 7, 35, 67 after analyzing : 5, 25, 35, 35 RIGHT_BRAIN before analyzing : 6, 9, 32, 60 after analyzing : 6, 24, 32, 33 LEFT_BRAIN before analyzing : 6, 10, 36, 62 after analyzing : 6, 27, 36, 35 OTHER before analyzing : 37, 5, 0, 2 after analyzing : 5, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 72.751, std = 6.218 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.70, sigma = 5.11 after rotation: sse = 3.70, sigma = 5.11 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.49, its var is 5.55 before Erosion-Dilatation 1.65% 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...32 iterations mri_strip_skull: done peeling brain Brain Size = 1703188 voxels, voxel volume = 1.000 mm3 = 1703188 mmm3 = 1703.188 cm3 MRImask(): AllowDiffGeom = 1 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 11.674018 mri_watershed stimesec 0.175970 mri_watershed ru_maxrss 809904 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 205131 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2600 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 0 mri_watershed ru_nivcsw 31 mri_watershed done @#@FSTIME 2021:05:08:14:16:09 mri_watershed N 6 e 11.87 S 0.19 U 11.67 P 100% M 809904 F 0 R 205132 W 0 c 31 w 1 I 0 O 2600 L 1.81 1.67 1.66 @#@FSLOADPOST 2021:05:08:14:16:21 mri_watershed N 6 1.84 1.69 1.67 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration 2021��� 05��� 08��� ��������� 14:16:22 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/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/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=17.0 skull bounding box = (50, 64, 44) --> (201, 195, 205) finding center of left hemi white matter using (100, 108, 125) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (81,92,105) --> (118, 124,144) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 5.1 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.151 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.054555 @ (-10.526, -10.526, -10.526) max log p = -3.691751 @ (5.263, 5.263, -5.263) max log p = -3.633458 @ (2.632, -2.632, -2.632) max log p = -3.633458 @ (0.000, 0.000, 0.000) max log p = -3.598211 @ (-0.658, 0.658, 3.289) max log p = -3.598211 @ (0.000, 0.000, 0.000) max log p = -3.598211 @ (0.000, 0.000, 0.000) max log p = -3.598211 @ (0.000, 0.000, 0.000) Found translation: (-3.3, -7.2, -15.1): log p = -3.598 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.414, old_max_log_p =-3.598 (thresh=-3.6) 1.00000 0.00000 0.00000 -3.28948; 0.00000 1.13509 0.16902 -44.70533; 0.00000 -0.11999 1.07125 -8.53962; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 9 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.413, old_max_log_p =-3.414 (thresh=-3.4) 1.00000 0.00000 0.00000 -3.28948; 0.00000 1.13509 0.16902 -44.70533; 0.00000 -0.11099 0.99091 0.00741; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 7 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.287, old_max_log_p =-3.413 (thresh=-3.4) 0.97915 -0.07285 -0.01085 11.82277; 0.06659 1.14945 0.20599 -57.76701; -0.00218 -0.15500 1.04116 1.67674; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 2 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.280, old_max_log_p =-3.287 (thresh=-3.3) 0.96010 -0.07143 -0.01064 14.05948; 0.06659 1.14945 0.20599 -57.76701; -0.00222 -0.15791 1.06068 -0.26846; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 2 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.280, old_max_log_p =-3.280 (thresh=-3.3) 0.96010 -0.07143 -0.01064 14.05948; 0.06659 1.14945 0.20599 -57.76701; -0.00222 -0.15791 1.06068 -0.26846; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 2 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.251, old_max_log_p =-3.280 (thresh=-3.3) 0.95772 -0.09131 -0.00545 15.77490; 0.08205 1.14544 0.21435 -60.25035; -0.01062 -0.16671 1.05901 2.57047; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 57 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.238, old_max_log_p =-3.251 (thresh=-3.2) 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 57 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.238, old_max_log_p =-3.238 (thresh=-3.2) 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 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 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.238 (old=-4.151) transform before final EM align: 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 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 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 792508 FSRUNTIME@ mri_em_register 0.1490 hours 1 threads registration took 8 minutes and 57 seconds. @#@FSTIME 2021:05:08:14:16:22 mri_em_register N 7 e 536.55 S 0.56 U 535.97 P 99% M 616872 F 0 R 166667 W 0 c 942 w 1 I 0 O 16 L 1.84 1.69 1.67 @#@FSLOADPOST 2021:05:08:14:25:18 mri_em_register N 7 1.74 1.72 1.68 #-------------------------------------- #@# CA Normalize 2021��� 05��� 08��� ��������� 14:25:18 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/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/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=17.0 skull bounding box = (50, 64, 44) --> (201, 195, 205) finding center of left hemi white matter using (100, 108, 125) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (81,92,105) --> (118, 124,144) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 5.1 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 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82955; -0.01059 -0.16632 1.05653 2.81153; 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 (127, 67, 46) --> (198, 166, 201) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 3901 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (60, 70, 45) --> (129, 170, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 2 of 3918 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (132, 143, 71) --> (184, 181, 121) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 88 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 143, 68) --> (132, 184, 122) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 86 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 135, 105) --> (150, 195, 132) Brain_Stem: limiting intensities to 90.0 --> 132.0 0 of 283 (0.0%) samples deleted using 8276 total control points for intensity normalization... bias field = 0.985 +- 0.058 58 of 8274 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 67, 46) --> (198, 166, 201) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 4007 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (60, 70, 45) --> (129, 170, 202) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 3 of 4179 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (132, 143, 71) --> (184, 181, 121) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 94 (1.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 143, 68) --> (132, 184, 122) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 137 (0.7%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 135, 105) --> (150, 195, 132) Brain_Stem: limiting intensities to 88.0 --> 132.0 40 of 327 (12.2%) samples deleted using 8744 total control points for intensity normalization... bias field = 1.028 +- 0.049 50 of 8620 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 67, 46) --> (198, 166, 201) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 3880 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (60, 70, 45) --> (129, 170, 202) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 3 of 4181 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (132, 143, 71) --> (184, 181, 121) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 145 (6.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 143, 68) --> (132, 184, 122) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 159 (9.4%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 135, 105) --> (150, 195, 132) Brain_Stem: limiting intensities to 88.0 --> 132.0 123 of 351 (35.0%) samples deleted using 8716 total control points for intensity normalization... bias field = 1.023 +- 0.042 14 of 8428 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 50 seconds. @#@FSTIME 2021:05:08:14:25:18 mri_ca_normalize N 8 e 49.68 S 0.32 U 49.35 P 99% M 705880 F 0 R 408251 W 0 c 163 w 1 I 0 O 3912 L 1.74 1.72 1.68 @#@FSLOADPOST 2021:05:08:14:26:08 mri_ca_normalize N 8 1.69 1.71 1.68 #-------------------------------------- #@# CA Reg 2021��� 05��� 08��� ��������� 14:26:08 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/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/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 0.834032 #FOTS# QuadFit found better minimum quadopt=(dt=241.653,rms=0.786268) vs oldopt=(dt=92.48,rms=0.803486) #GCMRL# 0 dt 241.652747 rms 0.786 5.727% neg 0 invalid 762 tFOTS 13.1190 tGradient 5.9800 tsec 20.0660 #FOTS# QuadFit found better minimum quadopt=(dt=149.433,rms=0.776896) vs oldopt=(dt=92.48,rms=0.778559) #GCMRL# 1 dt 149.432558 rms 0.777 1.192% neg 0 invalid 762 tFOTS 13.1710 tGradient 6.1020 tsec 20.2410 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.762142) vs oldopt=(dt=369.92,rms=0.764608) #GCMRL# 2 dt 517.888000 rms 0.762 1.899% neg 0 invalid 762 tFOTS 13.1980 tGradient 5.9890 tsec 20.1530 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.759352) vs oldopt=(dt=92.48,rms=0.759752) #GCMRL# 3 dt 129.472000 rms 0.759 0.366% neg 0 invalid 762 tFOTS 13.9610 tGradient 5.9600 tsec 20.8930 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.741853) vs oldopt=(dt=1479.68,rms=0.742604) #GCMRL# 4 dt 1775.616000 rms 0.742 2.304% neg 0 invalid 762 tFOTS 13.1920 tGradient 6.0430 tsec 20.1980 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.738964) vs oldopt=(dt=92.48,rms=0.73935) #GCMRL# 5 dt 129.472000 rms 0.739 0.389% neg 0 invalid 762 tFOTS 13.9590 tGradient 5.9100 tsec 20.8360 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.735615) vs oldopt=(dt=369.92,rms=0.735949) #GCMRL# 6 dt 517.888000 rms 0.736 0.453% neg 0 invalid 762 tFOTS 13.1720 tGradient 5.9000 tsec 20.0410 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.735008) vs oldopt=(dt=92.48,rms=0.735032) #GCMRL# 7 dt 110.976000 rms 0.735 0.000% neg 0 invalid 762 tFOTS 13.1670 tGradient 5.9860 tsec 20.1400 #GCMRL# 8 dt 110.976000 rms 0.734 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9760 tsec 6.9520 #GCMRL# 9 dt 110.976000 rms 0.734 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0320 tsec 7.0000 #GCMRL# 10 dt 110.976000 rms 0.732 0.178% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0200 tsec 6.9910 #GCMRL# 11 dt 110.976000 rms 0.731 0.247% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0790 tsec 7.0530 #GCMRL# 12 dt 110.976000 rms 0.728 0.299% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9760 tsec 6.9540 #GCMRL# 13 dt 110.976000 rms 0.726 0.318% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2320 tsec 7.2300 #GCMRL# 14 dt 110.976000 rms 0.724 0.306% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2680 tsec 7.2460 #GCMRL# 15 dt 110.976000 rms 0.722 0.302% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9680 tsec 6.9330 #GCMRL# 16 dt 110.976000 rms 0.720 0.275% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9740 tsec 6.9370 #GCMRL# 17 dt 110.976000 rms 0.718 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0520 tsec 7.0170 #GCMRL# 18 dt 110.976000 rms 0.716 0.241% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1730 tsec 7.1690 #GCMRL# 19 dt 110.976000 rms 0.714 0.230% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1820 tsec 7.1780 #GCMRL# 20 dt 110.976000 rms 0.713 0.226% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1470 tsec 7.1510 #GCMRL# 21 dt 110.976000 rms 0.711 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0770 tsec 7.0410 #GCMRL# 22 dt 110.976000 rms 0.710 0.191% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9440 tsec 6.9120 #GCMRL# 23 dt 110.976000 rms 0.709 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9490 tsec 6.9150 #GCMRL# 24 dt 110.976000 rms 0.708 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0200 tsec 6.9960 #GCMRL# 25 dt 110.976000 rms 0.707 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9900 tsec 6.9670 #GCMRL# 26 dt 110.976000 rms 0.706 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9890 tsec 6.9600 #GCMRL# 27 dt 110.976000 rms 0.705 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0360 tsec 7.0120 #GCMRL# 28 dt 110.976000 rms 0.704 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9860 tsec 6.9850 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.704284) vs oldopt=(dt=92.48,rms=0.704289) #GCMRL# 29 dt 129.472000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 14.0830 tGradient 5.9930 tsec 21.0800 #GCMRL# 30 dt 129.472000 rms 0.704 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0130 tsec 6.9920 #GCMRL# 31 dt 129.472000 rms 0.704 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9810 tsec 6.9570 #GCMRL# 32 dt 129.472000 rms 0.704 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0120 tsec 6.9850 #GCMRL# 33 dt 129.472000 rms 0.704 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9890 tsec 6.9710 #GCMRL# 34 dt 129.472000 rms 0.704 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0050 tsec 6.9810 #GCMRL# 35 dt 129.472000 rms 0.704 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0050 tsec 6.9740 #GCMRL# 36 dt 129.472000 rms 0.704 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9900 tsec 6.9620 #GCAMreg# pass 0 level1 5 level2 1 tsec 390.776 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 0.703903 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.702688) vs oldopt=(dt=369.92,rms=0.702741) #GCMRL# 38 dt 295.936000 rms 0.703 0.173% neg 0 invalid 762 tFOTS 13.3240 tGradient 6.0320 tsec 20.3300 #GCMRL# 39 dt 369.920000 rms 0.702 0.000% neg 0 invalid 762 tFOTS 14.1160 tGradient 5.9790 tsec 21.0950 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 0.714148 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.713083) vs oldopt=(dt=25.92,rms=0.713104) #GCMRL# 41 dt 31.104000 rms 0.713 0.149% neg 0 invalid 762 tFOTS 13.2900 tGradient 4.6160 tsec 18.8830 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.712751) vs oldopt=(dt=25.92,rms=0.712792) #GCMRL# 42 dt 36.288000 rms 0.713 0.000% neg 0 invalid 762 tFOTS 12.5640 tGradient 4.5290 tsec 18.0860 #GCMRL# 43 dt 36.288000 rms 0.712 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6620 tsec 5.6470 #GCMRL# 44 dt 36.288000 rms 0.712 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5630 tsec 5.5420 #GCAMreg# pass 0 level1 4 level2 1 tsec 57.365 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 0.712288 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.711413) vs oldopt=(dt=25.92,rms=0.71149) #GCMRL# 46 dt 36.288000 rms 0.711 0.123% neg 0 invalid 762 tFOTS 14.0910 tGradient 4.5950 tsec 19.6690 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.711227) vs oldopt=(dt=25.92,rms=0.71126) #GCMRL# 47 dt 36.288000 rms 0.711 0.000% neg 0 invalid 762 tFOTS 14.0720 tGradient 4.5910 tsec 19.6550 #GCMRL# 48 dt 36.288000 rms 0.711 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6110 tsec 5.5910 #GCMRL# 49 dt 36.288000 rms 0.711 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7140 tsec 5.6880 #GCMRL# 50 dt 36.288000 rms 0.711 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6310 tsec 5.6000 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 0.727509 #GCMRL# 52 dt 0.000000 rms 0.727 0.070% neg 0 invalid 762 tFOTS 12.5910 tGradient 3.8730 tsec 17.4420 #GCAMreg# pass 0 level1 3 level2 1 tsec 39.395 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 0.727509 #GCMRL# 54 dt 0.000000 rms 0.727 0.070% neg 0 invalid 762 tFOTS 12.5290 tGradient 3.9350 tsec 17.4320 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 0.777881 #FOTS# QuadFit found better minimum quadopt=(dt=2.40889,rms=0.767382) vs oldopt=(dt=2.88,rms=0.76777) #GCMRL# 56 dt 2.408889 rms 0.767 1.350% neg 0 invalid 762 tFOTS 12.4390 tGradient 3.3000 tsec 16.7070 #GCMRL# 57 dt 0.150000 rms 0.767 0.000% neg 0 invalid 762 tFOTS 11.6770 tGradient 3.3020 tsec 15.9630 #GCAMreg# pass 0 level1 2 level2 1 tsec 41.451 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 0.767844 #GCMRL# 59 dt 0.000000 rms 0.767 0.062% neg 0 invalid 762 tFOTS 11.6540 tGradient 3.3010 tsec 15.9240 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 0.831407 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.827176) vs oldopt=(dt=0.32,rms=0.827692) #GCMRL# 61 dt 0.448000 rms 0.827 0.509% neg 0 invalid 762 tFOTS 12.4550 tGradient 3.1700 tsec 16.5980 #FOTS# QuadFit found better minimum quadopt=(dt=0.67,rms=0.820122) vs oldopt=(dt=0.32,rms=0.822541) #GCMRL# 62 dt 0.670000 rms 0.820 0.853% neg 0 invalid 762 tFOTS 12.4400 tGradient 3.2830 tsec 16.6900 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.817966) vs oldopt=(dt=0.32,rms=0.818147) #GCMRL# 63 dt 0.256000 rms 0.818 0.263% neg 0 invalid 762 tFOTS 12.4510 tGradient 3.1770 tsec 16.5940 #FOTS# QuadFit found better minimum quadopt=(dt=0.508621,rms=0.815001) vs oldopt=(dt=0.32,rms=0.815742) #GCMRL# 64 dt 0.508621 rms 0.815 0.362% neg 0 invalid 762 tFOTS 12.4400 tGradient 3.1830 tsec 16.5870 #GCMRL# 65 dt 0.320000 rms 0.813 0.000% neg 0 invalid 762 tFOTS 12.4430 tGradient 3.1360 tsec 16.5630 #GCMRL# 66 dt 0.320000 rms 0.812 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1910 tsec 4.1560 #GCMRL# 67 dt 0.320000 rms 0.809 0.276% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1860 tsec 4.1590 #GCMRL# 68 dt 0.320000 rms 0.807 0.255% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1600 tsec 4.1280 #GCMRL# 69 dt 0.320000 rms 0.806 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2290 tsec 4.1920 #GCMRL# 70 dt 0.320000 rms 0.806 -0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1810 tsec 5.0450 #GCMRL# 71 dt 0.320000 rms 0.805 0.097% neg 0 invalid 762 tFOTS 12.4370 tGradient 3.1830 tsec 16.5850 #GCAMreg# pass 0 level1 1 level2 1 tsec 141.504 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 0.805307 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.804042) vs oldopt=(dt=0.32,rms=0.804049) #GCMRL# 73 dt 0.384000 rms 0.804 0.157% neg 0 invalid 762 tFOTS 12.4050 tGradient 3.1410 tsec 16.5170 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.803814) vs oldopt=(dt=0.08,rms=0.803864) #GCMRL# 74 dt 0.112000 rms 0.804 0.000% neg 0 invalid 762 tFOTS 12.4440 tGradient 3.2130 tsec 16.6450 #GCMRL# 75 dt 0.112000 rms 0.804 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1740 tsec 4.1410 #GCMRL# 76 dt 0.112000 rms 0.804 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1700 tsec 4.1380 #GCMRL# 77 dt 0.112000 rms 0.803 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1710 tsec 4.1390 #GCMRL# 78 dt 0.112000 rms 0.803 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1380 tsec 4.1070 #GCMRL# 79 dt 0.112000 rms 0.803 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2170 tsec 4.1850 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 0.779719 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.773049) vs oldopt=(dt=0.32,rms=0.773499) #GCMRL# 81 dt 0.256000 rms 0.773 0.855% neg 0 invalid 762 tFOTS 12.4460 tGradient 2.6580 tsec 16.0680 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.772712) vs oldopt=(dt=0.02,rms=0.772728) #GCMRL# 82 dt 0.024000 rms 0.773 0.000% neg 0 invalid 762 tFOTS 12.4410 tGradient 2.5670 tsec 15.9930 #GCAMreg# pass 0 level1 0 level2 1 tsec 40.116 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 0.773235 #FOTS# QuadFit found better minimum quadopt=(dt=0.012,rms=0.772661) vs oldopt=(dt=0.02,rms=0.77268) #GCMRL# 84 dt 0.012000 rms 0.773 0.074% neg 0 invalid 762 tFOTS 12.4660 tGradient 2.5580 tsec 15.9950 #FOTS# QuadFit found better minimum quadopt=(dt=0.0004375,rms=0.772659) vs oldopt=(dt=0.0003125,rms=0.772659) #GCMRL# 85 dt 0.000438 rms 0.773 0.000% neg 0 invalid 762 tFOTS 12.4910 tGradient 2.5830 tsec 16.0700 GCAMregister done in 16.7 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.16729 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (1529 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1529 voxels, peak = 5), gca=6.4 gca peak = 0.17690 (16) mri peak = 0.17831 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.37 x + 0.0 (839 voxels, overlap=0.005) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (839 voxels, peak = 6), gca=6.4 gca peak = 0.28275 (96) mri peak = 0.15843 (101) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (942 voxels, overlap=0.848) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (942 voxels, peak = 101), gca=101.3 gca peak = 0.18948 (93) mri peak = 0.09910 (96) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (816 voxels, overlap=0.736) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (816 voxels, peak = 97), gca=97.2 gca peak = 0.20755 (55) mri peak = 0.13430 (61) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (823 voxels, overlap=0.495) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (823 voxels, peak = 60), gca=60.2 gca peak = 0.31831 (58) mri peak = 0.09985 (64) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (728 voxels, overlap=0.978) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (728 voxels, peak = 61), gca=60.6 gca peak = 0.11957 (102) mri peak = 0.11535 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (61409 voxels, overlap=0.706) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (61409 voxels, peak = 106), gca=105.6 gca peak = 0.11429 (102) mri peak = 0.09838 (107) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (65389 voxels, overlap=0.729) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (65389 voxels, peak = 107), gca=106.6 gca peak = 0.14521 (59) mri peak = 0.04368 (57) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19188 voxels, overlap=0.862) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19188 voxels, peak = 60), gca=60.5 gca peak = 0.14336 (58) mri peak = 0.03963 (53) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (17936 voxels, overlap=0.971) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (17936 voxels, peak = 56), gca=56.0 gca peak = 0.13305 (70) mri peak = 0.15315 (75) Right_Caudate (50): linear fit = 1.05 x + 0.0 (585 voxels, overlap=0.634) Right_Caudate (50): linear fit = 1.05 x + 0.0 (585 voxels, peak = 74), gca=73.8 gca peak = 0.15761 (71) mri peak = 0.09495 (77) Left_Caudate (11): linear fit = 1.04 x + 0.0 (971 voxels, overlap=0.740) Left_Caudate (11): linear fit = 1.04 x + 0.0 (971 voxels, peak = 74), gca=74.2 gca peak = 0.13537 (57) mri peak = 0.04611 (54) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (21486 voxels, overlap=0.918) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (21486 voxels, peak = 57), gca=57.0 gca peak = 0.13487 (56) mri peak = 0.04711 (64) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (25742 voxels, overlap=0.879) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (25742 voxels, peak = 60), gca=59.6 gca peak = 0.19040 (84) mri peak = 0.09446 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8744 voxels, overlap=0.400) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8744 voxels, peak = 89), gca=89.5 gca peak = 0.18871 (83) mri peak = 0.11049 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8431 voxels, overlap=0.205) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8431 voxels, peak = 93), gca=92.5 gca peak = 0.24248 (57) mri peak = 0.11295 (67) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (352 voxels, overlap=0.559) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (352 voxels, peak = 66), gca=66.4 gca peak = 0.35833 (56) mri peak = 0.10728 (63) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (540 voxels, overlap=0.546) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (540 voxels, peak = 65), gca=64.7 gca peak = 0.12897 (85) mri peak = 0.06277 (92) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (5539 voxels, overlap=0.829) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (5539 voxels, peak = 87), gca=87.1 gca peak = 0.13127 (83) mri peak = 0.06534 (90) Right_Thalamus (49): linear fit = 1.08 x + 0.0 (4468 voxels, overlap=0.836) Right_Thalamus (49): linear fit = 1.08 x + 0.0 (4468 voxels, peak = 89), gca=89.2 gca peak = 0.12974 (78) mri peak = 0.10481 (80) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2433 voxels, overlap=0.639) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2433 voxels, peak = 82), gca=81.5 gca peak = 0.17796 (79) mri peak = 0.07694 (81) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2468 voxels, overlap=0.885) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2468 voxels, peak = 82), gca=81.8 gca peak = 0.10999 (80) mri peak = 0.09776 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12928 voxels, overlap=0.416) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12928 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.10368 (94) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1209 voxels, overlap=0.491) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1209 voxels, peak = 99), gca=99.0 gca peak = 0.11941 (89) mri peak = 0.10333 (94) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1321 voxels, overlap=0.547) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1321 voxels, peak = 97), gca=96.6 gca peak = 0.20775 (25) mri peak = 0.13585 (13) gca peak = 0.13297 (21) mri peak = 0.15627 (13) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (266 voxels, overlap=0.283) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (266 voxels, peak = 12), gca=12.1 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_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 estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 3.08902 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 0.799553 #FOTS# QuadFit found better minimum quadopt=(dt=230.221,rms=0.779354) vs oldopt=(dt=369.92,rms=0.784653) #GCMRL# 87 dt 230.221126 rms 0.779 2.526% neg 0 invalid 762 tFOTS 13.4570 tGradient 5.8880 tsec 20.3180 #FOTS# QuadFit found better minimum quadopt=(dt=190.316,rms=0.773146) vs oldopt=(dt=92.48,rms=0.775222) #GCMRL# 88 dt 190.315789 rms 0.773 0.797% neg 0 invalid 762 tFOTS 13.1560 tGradient 5.8420 tsec 19.9660 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.766507) vs oldopt=(dt=369.92,rms=0.767371) #GCMRL# 89 dt 295.936000 rms 0.767 0.859% neg 0 invalid 762 tFOTS 12.4460 tGradient 6.0250 tsec 19.4360 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.762406) vs oldopt=(dt=92.48,rms=0.762657) #GCMRL# 90 dt 129.472000 rms 0.762 0.535% neg 0 invalid 762 tFOTS 13.1790 tGradient 5.8800 tsec 20.0300 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.755935) vs oldopt=(dt=369.92,rms=0.756547) #GCMRL# 91 dt 517.888000 rms 0.756 0.849% neg 0 invalid 762 tFOTS 13.1970 tGradient 5.9660 tsec 20.1320 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.752568) vs oldopt=(dt=92.48,rms=0.752656) #GCMRL# 92 dt 110.976000 rms 0.753 0.445% neg 0 invalid 762 tFOTS 13.2180 tGradient 5.9310 tsec 20.1270 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.740521) vs oldopt=(dt=1479.68,rms=0.740879) #GCMRL# 93 dt 1775.616000 rms 0.741 1.601% neg 0 invalid 762 tFOTS 13.1620 tGradient 5.9580 tsec 20.0860 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.736817) vs oldopt=(dt=92.48,rms=0.736873) #GCMRL# 94 dt 110.976000 rms 0.737 0.500% neg 0 invalid 762 tFOTS 13.1710 tGradient 5.8780 tsec 20.0180 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.734159) vs oldopt=(dt=369.92,rms=0.734566) #GCMRL# 95 dt 517.888000 rms 0.734 0.361% neg 0 invalid 762 tFOTS 13.2280 tGradient 5.9530 tsec 20.1500 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.732822) vs oldopt=(dt=92.48,rms=0.732999) #GCMRL# 96 dt 129.472000 rms 0.733 0.182% neg 0 invalid 762 tFOTS 13.1720 tGradient 5.9330 tsec 20.0780 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.731215) vs oldopt=(dt=369.92,rms=0.731364) #GCMRL# 97 dt 517.888000 rms 0.731 0.219% neg 0 invalid 762 tFOTS 13.1850 tGradient 5.9130 tsec 20.0740 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.729897) vs oldopt=(dt=92.48,rms=0.729955) #GCMRL# 98 dt 110.976000 rms 0.730 0.180% neg 0 invalid 762 tFOTS 13.9910 tGradient 5.9010 tsec 20.8570 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.728262) vs oldopt=(dt=369.92,rms=0.72857) #GCMRL# 99 dt 517.888000 rms 0.728 0.224% neg 0 invalid 762 tFOTS 13.1660 tGradient 5.9230 tsec 20.0600 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.727355) vs oldopt=(dt=92.48,rms=0.727484) #GCMRL# 100 dt 129.472000 rms 0.727 0.125% neg 0 invalid 762 tFOTS 13.1820 tGradient 5.9040 tsec 20.0580 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.726363) vs oldopt=(dt=369.92,rms=0.726393) #GCMRL# 101 dt 443.904000 rms 0.726 0.136% neg 0 invalid 762 tFOTS 13.2190 tGradient 5.8440 tsec 20.0380 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.725365) vs oldopt=(dt=92.48,rms=0.725456) #GCMRL# 102 dt 129.472000 rms 0.725 0.137% neg 0 invalid 762 tFOTS 13.1810 tGradient 5.9020 tsec 20.0540 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.724689) vs oldopt=(dt=369.92,rms=0.724718) #GCMRL# 103 dt 295.936000 rms 0.725 0.093% neg 0 invalid 762 tFOTS 13.1930 tGradient 5.8850 tsec 20.0520 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.723919) vs oldopt=(dt=92.48,rms=0.724054) #GCMRL# 104 dt 129.472000 rms 0.724 0.106% neg 0 invalid 762 tFOTS 13.1980 tGradient 5.8660 tsec 20.0370 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.723001) vs oldopt=(dt=369.92,rms=0.723088) #GCMRL# 105 dt 517.888000 rms 0.723 0.127% neg 0 invalid 762 tFOTS 13.1330 tGradient 5.8360 tsec 19.9330 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.721864) vs oldopt=(dt=92.48,rms=0.721999) #GCMRL# 106 dt 129.472000 rms 0.722 0.157% neg 0 invalid 762 tFOTS 13.2010 tGradient 5.8670 tsec 20.0380 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.721397) vs oldopt=(dt=369.92,rms=0.721455) #GCMRL# 107 dt 295.936000 rms 0.721 0.065% neg 0 invalid 762 tFOTS 13.1470 tGradient 5.8290 tsec 19.9370 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.720574) vs oldopt=(dt=92.48,rms=0.720722) #GCMRL# 108 dt 129.472000 rms 0.721 0.114% neg 0 invalid 762 tFOTS 13.2020 tGradient 5.8360 tsec 20.0060 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.719908) vs oldopt=(dt=369.92,rms=0.719935) #GCMRL# 109 dt 443.904000 rms 0.720 0.092% neg 0 invalid 762 tFOTS 14.0070 tGradient 5.8470 tsec 20.8220 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.718956) vs oldopt=(dt=92.48,rms=0.719099) #GCMRL# 110 dt 129.472000 rms 0.719 0.132% neg 0 invalid 762 tFOTS 13.2780 tGradient 5.9120 tsec 20.1600 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.718534) vs oldopt=(dt=369.92,rms=0.718556) #GCMRL# 111 dt 295.936000 rms 0.719 0.059% neg 0 invalid 762 tFOTS 13.9940 tGradient 5.8740 tsec 20.8310 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.717807) vs oldopt=(dt=92.48,rms=0.717953) #GCMRL# 112 dt 129.472000 rms 0.718 0.101% neg 0 invalid 762 tFOTS 13.2000 tGradient 5.8580 tsec 20.0270 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.717206) vs oldopt=(dt=369.92,rms=0.717238) #GCMRL# 113 dt 443.904000 rms 0.717 0.084% neg 0 invalid 762 tFOTS 13.9500 tGradient 5.8530 tsec 20.7650 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.716325) vs oldopt=(dt=92.48,rms=0.716481) #GCMRL# 114 dt 129.472000 rms 0.716 0.123% neg 0 invalid 762 tFOTS 13.1690 tGradient 5.8700 tsec 20.0030 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.715983) vs oldopt=(dt=369.92,rms=0.716012) #GCMRL# 115 dt 295.936000 rms 0.716 0.000% neg 0 invalid 762 tFOTS 13.9880 tGradient 5.8830 tsec 20.8600 #GCMRL# 116 dt 295.936000 rms 0.715 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8810 tsec 6.8430 #GCMRL# 117 dt 295.936000 rms 0.714 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0150 tsec 6.9790 #GCMRL# 118 dt 295.936000 rms 0.712 0.338% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8720 tsec 6.8380 #GCMRL# 119 dt 295.936000 rms 0.710 0.287% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8770 tsec 6.8550 #GCMRL# 120 dt 295.936000 rms 0.708 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8660 tsec 6.8380 #GCMRL# 121 dt 295.936000 rms 0.705 0.483% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8710 tsec 6.8400 #GCMRL# 122 dt 295.936000 rms 0.702 0.343% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8630 tsec 6.8290 #GCMRL# 123 dt 295.936000 rms 0.701 0.228% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7900 tsec 6.7590 #GCMRL# 124 dt 295.936000 rms 0.698 0.415% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8740 tsec 6.8420 #GCMRL# 125 dt 295.936000 rms 0.696 0.256% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8080 tsec 6.7860 #GCMRL# 126 dt 295.936000 rms 0.695 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8220 tsec 6.8010 #GCMRL# 127 dt 295.936000 rms 0.693 0.280% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9150 tsec 6.8910 #GCMRL# 128 dt 295.936000 rms 0.692 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8640 tsec 6.8310 #GCMRL# 129 dt 295.936000 rms 0.690 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8570 tsec 6.8270 #GCMRL# 130 dt 295.936000 rms 0.689 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9590 tsec 6.9250 #GCMRL# 131 dt 295.936000 rms 0.688 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8890 tsec 6.8570 #GCMRL# 132 dt 295.936000 rms 0.686 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9350 tsec 6.9070 #GCMRL# 133 dt 295.936000 rms 0.686 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8170 tsec 6.7830 #GCMRL# 134 dt 295.936000 rms 0.685 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8420 tsec 6.8110 #GCMRL# 135 dt 295.936000 rms 0.684 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9820 tsec 6.9510 #GCMRL# 136 dt 295.936000 rms 0.683 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8410 tsec 6.8150 #GCMRL# 137 dt 295.936000 rms 0.682 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8000 tsec 6.7730 #GCMRL# 138 dt 295.936000 rms 0.681 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9200 tsec 6.8900 #GCMRL# 139 dt 295.936000 rms 0.681 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9280 tsec 6.9010 #GCMRL# 140 dt 295.936000 rms 0.680 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9560 tsec 6.9300 #GCMRL# 141 dt 295.936000 rms 0.679 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8920 tsec 6.8560 #GCMRL# 142 dt 295.936000 rms 0.679 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8920 tsec 6.8570 #GCMRL# 143 dt 295.936000 rms 0.678 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8990 tsec 6.8650 #GCMRL# 144 dt 295.936000 rms 0.678 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8710 tsec 6.8430 #GCMRL# 145 dt 295.936000 rms 0.678 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9010 tsec 6.8720 #GCMRL# 146 dt 295.936000 rms 0.677 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8950 tsec 6.8660 #GCMRL# 147 dt 295.936000 rms 0.677 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8810 tsec 6.8490 #GCMRL# 148 dt 295.936000 rms 0.676 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8710 tsec 6.8420 #GCMRL# 149 dt 295.936000 rms 0.676 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9010 tsec 6.8640 #GCMRL# 150 dt 295.936000 rms 0.675 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9410 tsec 6.9070 #GCMRL# 151 dt 295.936000 rms 0.675 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9160 tsec 6.8900 #GCMRL# 152 dt 295.936000 rms 0.674 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9510 tsec 6.9300 #GCMRL# 153 dt 295.936000 rms 0.674 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9310 tsec 6.9040 #GCMRL# 154 dt 295.936000 rms 0.674 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9270 tsec 6.8980 #GCMRL# 155 dt 295.936000 rms 0.673 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9590 tsec 6.9340 #GCMRL# 156 dt 295.936000 rms 0.673 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0230 tsec 6.9990 #GCMRL# 157 dt 295.936000 rms 0.673 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0100 tsec 6.9820 #GCMRL# 158 dt 295.936000 rms 0.673 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8720 tsec 6.8470 #GCMRL# 159 dt 295.936000 rms 0.672 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9760 tsec 6.9450 #GCMRL# 160 dt 295.936000 rms 0.672 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9120 tsec 6.8930 #GCMRL# 161 dt 295.936000 rms 0.672 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8760 tsec 6.8500 #GCMRL# 162 dt 295.936000 rms 0.671 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9960 tsec 6.9690 #GCMRL# 163 dt 295.936000 rms 0.671 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8830 tsec 6.8500 #GCMRL# 164 dt 295.936000 rms 0.671 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8890 tsec 6.8640 #GCMRL# 165 dt 295.936000 rms 0.671 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9180 tsec 6.8900 #GCMRL# 166 dt 295.936000 rms 0.670 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9210 tsec 6.8960 #GCMRL# 167 dt 295.936000 rms 0.670 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9960 tsec 6.9720 #GCMRL# 168 dt 295.936000 rms 0.670 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9340 tsec 6.9060 #GCMRL# 169 dt 295.936000 rms 0.670 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1530 tsec 7.1560 #GCMRL# 170 dt 295.936000 rms 0.669 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9710 tsec 6.9440 #GCMRL# 171 dt 295.936000 rms 0.669 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9610 tsec 6.9360 #GCMRL# 172 dt 295.936000 rms 0.669 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9390 tsec 6.9130 #GCMRL# 173 dt 295.936000 rms 0.669 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0280 tsec 7.0020 #GCMRL# 174 dt 295.936000 rms 0.668 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9510 tsec 6.9240 #GCMRL# 175 dt 295.936000 rms 0.668 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9550 tsec 6.9350 #GCMRL# 176 dt 295.936000 rms 0.668 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9830 tsec 6.9540 #GCMRL# 177 dt 295.936000 rms 0.668 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9560 tsec 6.9370 #GCMRL# 178 dt 295.936000 rms 0.668 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0070 tsec 6.9870 #GCMRL# 179 dt 295.936000 rms 0.667 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0070 tsec 6.9780 #GCMRL# 180 dt 295.936000 rms 0.667 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9580 tsec 6.9370 #GCMRL# 181 dt 295.936000 rms 0.667 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0260 tsec 6.9940 #GCMRL# 182 dt 295.936000 rms 0.667 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9120 tsec 6.8920 #GCMRL# 183 dt 295.936000 rms 0.667 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9480 tsec 6.9200 #GCMRL# 184 dt 295.936000 rms 0.666 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0170 tsec 7.0000 #GCMRL# 185 dt 295.936000 rms 0.666 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9550 tsec 6.9280 #GCMRL# 186 dt 295.936000 rms 0.666 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0240 tsec 7.0020 #GCMRL# 187 dt 295.936000 rms 0.666 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0200 tsec 6.9930 #GCMRL# 188 dt 295.936000 rms 0.666 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9800 tsec 6.9610 #GCMRL# 189 dt 295.936000 rms 0.665 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9790 tsec 6.9640 #GCMRL# 190 dt 295.936000 rms 0.665 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9620 tsec 6.9410 #GCMRL# 191 dt 295.936000 rms 0.665 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9690 tsec 6.9430 #GCMRL# 192 dt 295.936000 rms 0.665 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0480 tsec 7.0240 #GCMRL# 193 dt 295.936000 rms 0.665 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9660 tsec 6.9560 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.664818) vs oldopt=(dt=1479.68,rms=0.66482) #GCMRL# 194 dt 1183.744000 rms 0.665 0.000% neg 0 invalid 762 tFOTS 14.0390 tGradient 5.9660 tsec 21.0000 #GCAMreg# pass 0 level1 5 level2 1 tsec 1156.08 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 0.665362 #GCMRL# 196 dt 369.920000 rms 0.664 0.213% neg 0 invalid 762 tFOTS 13.3350 tGradient 6.0280 tsec 20.3390 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.663326) vs oldopt=(dt=369.92,rms=0.66342) #GCMRL# 197 dt 295.936000 rms 0.663 0.093% neg 0 invalid 762 tFOTS 13.2710 tGradient 5.9560 tsec 20.1980 #FOTS# QuadFit found better minimum quadopt=(dt=55.488,rms=0.663281) vs oldopt=(dt=92.48,rms=0.663298) #GCMRL# 198 dt 55.488000 rms 0.663 0.000% neg 0 invalid 762 tFOTS 13.2850 tGradient 5.9790 tsec 20.2570 #GCMRL# 199 dt 55.488000 rms 0.663 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9680 tsec 6.9430 #GCMRL# 200 dt 55.488000 rms 0.663 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9780 tsec 6.9540 #GCMRL# 201 dt 55.488000 rms 0.663 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0710 tsec 7.0590 #GCMRL# 202 dt 55.488000 rms 0.663 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9710 tsec 6.9410 #GCMRL# 203 dt 55.488000 rms 0.663 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9810 tsec 6.9580 #GCMRL# 204 dt 55.488000 rms 0.663 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9720 tsec 6.9490 #GCMRL# 205 dt 55.488000 rms 0.663 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9860 tsec 6.9620 #GCMRL# 206 dt 55.488000 rms 0.662 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9940 tsec 6.9950 #FOTS# QuadFit found better minimum quadopt=(dt=0.0180625,rms=0.66242) vs oldopt=(dt=0.0225781,rms=0.66242) 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 0.666222 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.662032) vs oldopt=(dt=103.68,rms=0.662582) #GCMRL# 208 dt 145.152000 rms 0.662 0.629% neg 0 invalid 762 tFOTS 12.5400 tGradient 4.5730 tsec 18.0920 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.65359) vs oldopt=(dt=414.72,rms=0.654318) #GCMRL# 209 dt 331.776000 rms 0.654 1.275% neg 0 invalid 762 tFOTS 13.2890 tGradient 4.6410 tsec 18.9050 #FOTS# QuadFit found better minimum quadopt=(dt=64.4211,rms=0.649261) vs oldopt=(dt=25.92,rms=0.65051) #GCMRL# 210 dt 64.421053 rms 0.649 0.662% neg 0 invalid 762 tFOTS 13.3040 tGradient 4.5370 tsec 18.8130 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.646305) vs oldopt=(dt=103.68,rms=0.646821) #GCMRL# 211 dt 145.152000 rms 0.646 0.455% neg 0 invalid 762 tFOTS 12.5060 tGradient 4.5190 tsec 18.0010 #FOTS# QuadFit found better minimum quadopt=(dt=88.939,rms=0.644594) vs oldopt=(dt=103.68,rms=0.644638) #GCMRL# 212 dt 88.938967 rms 0.645 0.265% neg 0 invalid 762 tFOTS 14.0880 tGradient 4.4950 tsec 19.5600 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.642222) vs oldopt=(dt=103.68,rms=0.642308) #GCMRL# 213 dt 124.416000 rms 0.642 0.368% neg 0 invalid 762 tFOTS 13.2990 tGradient 4.4370 tsec 18.7170 #FOTS# QuadFit found better minimum quadopt=(dt=62.8148,rms=0.640817) vs oldopt=(dt=103.68,rms=0.641311) #GCMRL# 214 dt 62.814815 rms 0.641 0.219% neg 0 invalid 762 tFOTS 13.3030 tGradient 4.5060 tsec 18.7830 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.637264) vs oldopt=(dt=414.72,rms=0.63744) #GCMRL# 215 dt 331.776000 rms 0.637 0.554% neg 0 invalid 762 tFOTS 12.5180 tGradient 4.4810 tsec 17.9810 #FOTS# QuadFit found better minimum quadopt=(dt=59.7736,rms=0.634832) vs oldopt=(dt=25.92,rms=0.63531) #GCMRL# 216 dt 59.773585 rms 0.635 0.382% neg 0 invalid 762 tFOTS 13.3430 tGradient 4.5510 tsec 18.8770 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.633248) vs oldopt=(dt=103.68,rms=0.633343) #GCMRL# 217 dt 145.152000 rms 0.633 0.250% neg 0 invalid 762 tFOTS 13.3180 tGradient 4.4760 tsec 18.7680 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.632227) vs oldopt=(dt=25.92,rms=0.632425) #GCMRL# 218 dt 36.288000 rms 0.632 0.161% neg 0 invalid 762 tFOTS 12.5040 tGradient 4.4580 tsec 17.9370 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.630043) vs oldopt=(dt=414.72,rms=0.630104) #GCMRL# 219 dt 331.776000 rms 0.630 0.345% neg 0 invalid 762 tFOTS 13.3890 tGradient 4.4660 tsec 18.8250 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.628143) vs oldopt=(dt=25.92,rms=0.628507) #GCMRL# 220 dt 36.288000 rms 0.628 0.302% neg 0 invalid 762 tFOTS 13.3200 tGradient 4.4810 tsec 18.7750 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.626759) vs oldopt=(dt=103.68,rms=0.627013) #GCMRL# 221 dt 145.152000 rms 0.627 0.220% neg 0 invalid 762 tFOTS 13.2990 tGradient 4.5290 tsec 18.7980 #FOTS# QuadFit found better minimum quadopt=(dt=63.5259,rms=0.626113) vs oldopt=(dt=103.68,rms=0.62632) #GCMRL# 222 dt 63.525926 rms 0.626 0.103% neg 0 invalid 762 tFOTS 14.0840 tGradient 4.4560 tsec 19.5100 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.624953) vs oldopt=(dt=103.68,rms=0.625149) #GCMRL# 223 dt 145.152000 rms 0.625 0.185% neg 0 invalid 762 tFOTS 13.2890 tGradient 4.4480 tsec 18.7110 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.624454) vs oldopt=(dt=25.92,rms=0.624562) #GCMRL# 224 dt 36.288000 rms 0.624 0.080% neg 0 invalid 762 tFOTS 12.5690 tGradient 4.4650 tsec 18.0070 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.621674) vs oldopt=(dt=414.72,rms=0.622046) #GCMRL# 225 dt 580.608000 rms 0.622 0.445% neg 0 invalid 762 tFOTS 13.3160 tGradient 4.4570 tsec 18.7490 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.619801) vs oldopt=(dt=25.92,rms=0.620134) #GCMRL# 226 dt 36.288000 rms 0.620 0.301% neg 0 invalid 762 tFOTS 13.3340 tGradient 4.5000 tsec 18.8120 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.618976) vs oldopt=(dt=103.68,rms=0.619049) #GCMRL# 227 dt 145.152000 rms 0.619 0.133% neg 0 invalid 762 tFOTS 13.3000 tGradient 4.4910 tsec 18.7640 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.618513) vs oldopt=(dt=25.92,rms=0.618607) #GCMRL# 228 dt 36.288000 rms 0.619 0.075% neg 0 invalid 762 tFOTS 12.5490 tGradient 4.4800 tsec 17.9980 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.617585) vs oldopt=(dt=414.72,rms=0.617692) #GCMRL# 229 dt 331.776000 rms 0.618 0.150% neg 0 invalid 762 tFOTS 13.3280 tGradient 4.4740 tsec 18.7820 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.616452) vs oldopt=(dt=25.92,rms=0.616664) #GCMRL# 230 dt 36.288000 rms 0.616 0.184% neg 0 invalid 762 tFOTS 13.2920 tGradient 4.5440 tsec 18.8150 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.615647) vs oldopt=(dt=103.68,rms=0.615776) #GCMRL# 231 dt 145.152000 rms 0.616 0.130% neg 0 invalid 762 tFOTS 13.3270 tGradient 4.4670 tsec 18.7690 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.615298) vs oldopt=(dt=103.68,rms=0.615436) #GCMRL# 232 dt 62.208000 rms 0.615 0.057% neg 0 invalid 762 tFOTS 12.5370 tGradient 4.4920 tsec 18.0080 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.614592) vs oldopt=(dt=103.68,rms=0.614719) #GCMRL# 233 dt 145.152000 rms 0.615 0.115% neg 0 invalid 762 tFOTS 13.2910 tGradient 4.4610 tsec 18.7260 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.614325) vs oldopt=(dt=25.92,rms=0.614383) #GCMRL# 234 dt 36.288000 rms 0.614 0.000% neg 0 invalid 762 tFOTS 14.1300 tGradient 4.4870 tsec 19.6190 #GCMRL# 235 dt 36.288000 rms 0.614 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4730 tsec 5.4590 #GCMRL# 236 dt 36.288000 rms 0.614 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4810 tsec 5.4580 #GCMRL# 237 dt 36.288000 rms 0.613 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4710 tsec 5.4470 #GCMRL# 238 dt 36.288000 rms 0.613 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4950 tsec 5.4760 #GCMRL# 239 dt 36.288000 rms 0.612 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5300 tsec 5.5040 #GCMRL# 240 dt 36.288000 rms 0.611 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4770 tsec 5.4470 #GCMRL# 241 dt 36.288000 rms 0.611 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4700 tsec 5.4500 #GCMRL# 242 dt 36.288000 rms 0.610 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5080 tsec 5.4830 #GCMRL# 243 dt 36.288000 rms 0.609 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4770 tsec 5.4530 #GCMRL# 244 dt 36.288000 rms 0.608 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4770 tsec 5.4560 #GCMRL# 245 dt 36.288000 rms 0.607 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4240 tsec 5.3990 #GCMRL# 246 dt 36.288000 rms 0.606 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4630 tsec 5.4360 #GCMRL# 247 dt 36.288000 rms 0.606 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4080 tsec 5.3880 #GCMRL# 248 dt 36.288000 rms 0.605 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5080 tsec 5.4840 #GCMRL# 249 dt 36.288000 rms 0.604 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5050 tsec 5.4840 #GCMRL# 250 dt 36.288000 rms 0.604 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4180 tsec 5.3930 #GCMRL# 251 dt 36.288000 rms 0.603 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4290 tsec 5.4060 #GCMRL# 252 dt 36.288000 rms 0.602 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5120 tsec 5.4870 #GCMRL# 253 dt 36.288000 rms 0.602 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4040 tsec 5.3790 #GCMRL# 254 dt 36.288000 rms 0.601 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4140 tsec 5.3930 #GCMRL# 255 dt 36.288000 rms 0.600 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4560 tsec 5.4310 #GCMRL# 256 dt 36.288000 rms 0.599 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4650 tsec 5.4400 #GCMRL# 257 dt 36.288000 rms 0.599 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4440 tsec 5.4200 #GCMRL# 258 dt 36.288000 rms 0.598 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5140 tsec 5.4920 #GCMRL# 259 dt 36.288000 rms 0.598 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4450 tsec 5.8480 #GCMRL# 260 dt 36.288000 rms 0.598 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4910 tsec 5.4620 #GCMRL# 261 dt 36.288000 rms 0.598 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4830 tsec 5.4590 #GCMRL# 262 dt 36.288000 rms 0.598 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4640 tsec 5.4350 #GCMRL# 263 dt 36.288000 rms 0.597 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5000 tsec 5.4740 #GCMRL# 264 dt 36.288000 rms 0.597 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4880 tsec 5.4580 #GCMRL# 265 dt 36.288000 rms 0.597 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4940 tsec 5.4680 #GCMRL# 266 dt 36.288000 rms 0.596 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4440 tsec 5.4150 #GCMRL# 267 dt 36.288000 rms 0.596 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6660 tsec 6.1080 #GCMRL# 268 dt 36.288000 rms 0.596 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4510 tsec 5.4310 #GCMRL# 269 dt 36.288000 rms 0.596 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4970 tsec 5.4750 #GCMRL# 270 dt 36.288000 rms 0.596 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5090 tsec 5.4860 #GCMRL# 271 dt 36.288000 rms 0.596 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5100 tsec 5.5040 #GCMRL# 272 dt 36.288000 rms 0.596 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4570 tsec 5.4500 #GCMRL# 273 dt 36.288000 rms 0.595 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5010 tsec 5.5120 #GCMRL# 274 dt 36.288000 rms 0.595 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4980 tsec 5.4850 #GCMRL# 275 dt 36.288000 rms 0.595 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5230 tsec 5.5330 #GCMRL# 276 dt 36.288000 rms 0.594 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6610 tsec 5.6700 #GCMRL# 277 dt 36.288000 rms 0.594 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7160 tsec 5.7100 #GCMRL# 278 dt 36.288000 rms 0.594 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4550 tsec 5.4280 #GCMRL# 279 dt 36.288000 rms 0.593 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4770 tsec 5.4510 #GCMRL# 280 dt 36.288000 rms 0.593 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4360 tsec 5.8420 #GCMRL# 281 dt 36.288000 rms 0.593 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4370 tsec 5.8590 #GCMRL# 282 dt 36.288000 rms 0.593 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4680 tsec 5.9080 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.593267) vs oldopt=(dt=1.62,rms=0.593267) #GCMRL# 283 dt 2.268000 rms 0.593 0.000% neg 0 invalid 762 tFOTS 10.3280 tGradient 4.4630 tsec 15.8110 #GCMRL# 284 dt 2.268000 rms 0.593 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4410 tsec 5.4240 #GCMRL# 285 dt 1.134000 rms 0.593 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6290 tsec 6.4630 #GCAMreg# pass 0 level1 4 level2 1 tsec 810.334 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 0.593879 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.591062) vs oldopt=(dt=103.68,rms=0.591357) #GCMRL# 287 dt 145.152000 rms 0.591 0.474% neg 0 invalid 762 tFOTS 13.6490 tGradient 4.6010 tsec 19.2450 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.590657) vs oldopt=(dt=103.68,rms=0.590768) #GCMRL# 288 dt 62.208000 rms 0.591 0.069% neg 0 invalid 762 tFOTS 13.0890 tGradient 4.6070 tsec 18.7040 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.590222) vs oldopt=(dt=103.68,rms=0.590297) #GCMRL# 289 dt 145.152000 rms 0.590 0.074% neg 0 invalid 762 tFOTS 13.6760 tGradient 4.5240 tsec 19.1970 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.589972) vs oldopt=(dt=103.68,rms=0.590035) #GCMRL# 290 dt 62.208000 rms 0.590 0.000% neg 0 invalid 762 tFOTS 12.8570 tGradient 4.4870 tsec 18.3580 #GCMRL# 291 dt 62.208000 rms 0.590 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5070 tsec 5.5200 #GCMRL# 292 dt 62.208000 rms 0.590 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7080 tsec 5.7380 #GCMRL# 293 dt 62.208000 rms 0.589 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5790 tsec 5.5840 #GCMRL# 294 dt 62.208000 rms 0.589 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5100 tsec 5.5080 #GCMRL# 295 dt 62.208000 rms 0.589 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4890 tsec 5.4710 #GCMRL# 296 dt 62.208000 rms 0.588 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4830 tsec 5.4730 #GCMRL# 297 dt 62.208000 rms 0.588 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5130 tsec 5.5150 #GCMRL# 298 dt 62.208000 rms 0.587 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6830 tsec 5.6690 #GCMRL# 299 dt 62.208000 rms 0.587 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4790 tsec 5.4880 #GCMRL# 300 dt 62.208000 rms 0.586 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5380 tsec 5.5210 #GCMRL# 301 dt 62.208000 rms 0.586 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4180 tsec 5.3970 #GCMRL# 302 dt 62.208000 rms 0.585 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4130 tsec 5.3940 #GCMRL# 303 dt 62.208000 rms 0.585 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4000 tsec 5.3800 #GCMRL# 304 dt 62.208000 rms 0.584 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4060 tsec 5.3820 #GCMRL# 305 dt 62.208000 rms 0.584 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4280 tsec 5.4010 #GCMRL# 306 dt 62.208000 rms 0.583 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4480 tsec 5.4250 #GCMRL# 307 dt 62.208000 rms 0.583 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4220 tsec 5.4120 #GCMRL# 308 dt 62.208000 rms 0.582 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4630 tsec 5.4450 #GCMRL# 309 dt 62.208000 rms 0.582 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4190 tsec 5.3990 #GCMRL# 310 dt 62.208000 rms 0.581 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4480 tsec 5.4290 #GCMRL# 311 dt 62.208000 rms 0.581 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4190 tsec 5.4010 #GCMRL# 312 dt 62.208000 rms 0.580 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4220 tsec 5.3940 #GCMRL# 313 dt 62.208000 rms 0.580 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3820 tsec 5.3590 #GCMRL# 314 dt 62.208000 rms 0.579 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4710 tsec 5.4360 #GCMRL# 315 dt 62.208000 rms 0.579 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2860 tsec 5.2440 #GCMRL# 316 dt 62.208000 rms 0.579 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2820 tsec 5.2380 #GCMRL# 317 dt 62.208000 rms 0.578 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2810 tsec 5.2390 #GCMRL# 318 dt 62.208000 rms 0.578 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3040 tsec 5.2590 #GCMRL# 319 dt 62.208000 rms 0.577 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2980 tsec 5.2580 #GCMRL# 320 dt 62.208000 rms 0.577 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3110 tsec 5.2710 #GCMRL# 321 dt 62.208000 rms 0.577 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3020 tsec 5.2580 #GCMRL# 322 dt 62.208000 rms 0.576 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3140 tsec 5.2690 #GCMRL# 323 dt 62.208000 rms 0.576 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3330 tsec 5.2980 #GCMRL# 324 dt 62.208000 rms 0.576 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3360 tsec 5.2940 #GCMRL# 325 dt 62.208000 rms 0.575 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3230 tsec 5.2810 #GCMRL# 326 dt 62.208000 rms 0.575 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3510 tsec 5.3090 #GCMRL# 327 dt 62.208000 rms 0.575 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3690 tsec 5.3300 #GCMRL# 328 dt 62.208000 rms 0.575 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3360 tsec 5.3030 #GCMRL# 329 dt 62.208000 rms 0.574 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3170 tsec 5.2800 #GCMRL# 330 dt 62.208000 rms 0.574 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3500 tsec 5.3100 #GCMRL# 331 dt 62.208000 rms 0.574 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3290 tsec 5.2850 #GCMRL# 332 dt 62.208000 rms 0.574 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3160 tsec 5.2730 #GCMRL# 333 dt 62.208000 rms 0.574 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3270 tsec 5.2890 #GCMRL# 334 dt 62.208000 rms 0.573 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3420 tsec 5.3030 #GCMRL# 335 dt 62.208000 rms 0.573 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3750 tsec 5.3340 #GCMRL# 336 dt 62.208000 rms 0.573 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3530 tsec 5.3090 #GCMRL# 337 dt 62.208000 rms 0.573 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3350 tsec 5.2920 #GCMRL# 338 dt 62.208000 rms 0.573 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3430 tsec 5.3050 #GCMRL# 339 dt 62.208000 rms 0.572 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3580 tsec 5.3250 #GCMRL# 340 dt 62.208000 rms 0.572 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3390 tsec 5.3020 #GCMRL# 341 dt 62.208000 rms 0.572 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3280 tsec 5.2980 #GCMRL# 342 dt 62.208000 rms 0.572 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3370 tsec 5.2880 #GCMRL# 343 dt 62.208000 rms 0.572 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3400 tsec 5.3100 #GCMRL# 344 dt 62.208000 rms 0.571 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4200 tsec 5.3770 #GCMRL# 345 dt 62.208000 rms 0.571 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3400 tsec 5.3020 #GCMRL# 346 dt 62.208000 rms 0.571 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3470 tsec 5.3100 #GCMRL# 347 dt 62.208000 rms 0.571 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3340 tsec 5.2950 #GCMRL# 348 dt 62.208000 rms 0.571 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3430 tsec 5.3060 #GCMRL# 349 dt 62.208000 rms 0.571 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3610 tsec 5.3230 #GCMRL# 350 dt 62.208000 rms 0.570 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3400 tsec 5.2990 #GCMRL# 351 dt 62.208000 rms 0.570 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3390 tsec 5.3200 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.570166) vs oldopt=(dt=414.72,rms=0.5702) #GCMRL# 352 dt 580.608000 rms 0.570 0.030% neg 0 invalid 762 tFOTS 13.8390 tGradient 4.3620 tsec 19.1550 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.570126) vs oldopt=(dt=25.92,rms=0.570134) #GCMRL# 353 dt 36.288000 rms 0.570 0.000% neg 0 invalid 762 tFOTS 13.3300 tGradient 4.3320 tsec 18.6410 #GCMRL# 354 dt 36.288000 rms 0.570 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3250 tsec 5.2830 #GCMRL# 355 dt 36.288000 rms 0.570 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3510 tsec 5.3190 #GCMRL# 356 dt 36.288000 rms 0.570 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3900 tsec 5.3500 #GCMRL# 357 dt 36.288000 rms 0.570 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3860 tsec 5.3460 #GCMRL# 358 dt 36.288000 rms 0.570 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3570 tsec 5.3210 #GCMRL# 359 dt 36.288000 rms 0.570 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3520 tsec 5.3240 #GCMRL# 360 dt 36.288000 rms 0.570 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3690 tsec 5.3310 #GCMRL# 361 dt 36.288000 rms 0.570 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3490 tsec 5.3100 #GCMRL# 362 dt 36.288000 rms 0.570 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3540 tsec 5.3160 #GCMRL# 363 dt 36.288000 rms 0.570 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3610 tsec 5.3280 #GCMRL# 364 dt 36.288000 rms 0.570 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3380 tsec 5.3040 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 0.581972 #FOTS# QuadFit found better minimum quadopt=(dt=25.1777,rms=0.580496) vs oldopt=(dt=32,rms=0.580618) #GCMRL# 366 dt 25.177665 rms 0.580 0.254% neg 0 invalid 762 tFOTS 12.3210 tGradient 3.5890 tsec 16.8740 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.578847) vs oldopt=(dt=32,rms=0.579121) #GCMRL# 367 dt 44.800000 rms 0.579 0.284% neg 0 invalid 762 tFOTS 13.0620 tGradient 3.5940 tsec 17.6140 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.576288) vs oldopt=(dt=32,rms=0.576955) #GCMRL# 368 dt 44.800000 rms 0.576 0.442% neg 0 invalid 762 tFOTS 11.5390 tGradient 3.5760 tsec 16.0770 #GCMRL# 369 dt 128.000000 rms 0.571 0.909% neg 0 invalid 762 tFOTS 12.2890 tGradient 3.5530 tsec 16.7980 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.570097) vs oldopt=(dt=8,rms=0.570351) #GCMRL# 370 dt 11.200000 rms 0.570 0.167% neg 0 invalid 762 tFOTS 11.5610 tGradient 3.5530 tsec 16.0770 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.569838) vs oldopt=(dt=2,rms=0.569887) #GCMRL# 371 dt 2.800000 rms 0.570 0.000% neg 0 invalid 762 tFOTS 10.8040 tGradient 3.5610 tsec 15.3480 #GCMRL# 372 dt 2.800000 rms 0.570 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5490 tsec 4.5110 #GCMRL# 373 dt 2.800000 rms 0.570 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5750 tsec 4.9540 #GCMRL# 374 dt 0.700000 rms 0.569 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5930 tsec 5.7720 #GCMRL# 375 dt 0.175000 rms 0.569 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5760 tsec 5.7880 #FOTS# QuadFit found better minimum quadopt=(dt=0.04375,rms=0.569464) vs oldopt=(dt=0.03125,rms=0.569465) #GCMRL# 376 dt 0.043750 rms 0.569 0.000% neg 0 invalid 762 tFOTS 8.5120 tGradient 3.5820 tsec 13.0710 #GCMRL# 377 dt 0.043750 rms 0.569 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5790 tsec 4.5410 #GCMRL# 378 dt 0.021875 rms 0.569 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5790 tsec 5.3580 #GCAMreg# pass 0 level1 3 level2 1 tsec 151.771 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 0.570062 #GCMRL# 380 dt 0.000000 rms 0.569 0.106% neg 0 invalid 762 tFOTS 5.4420 tGradient 3.5730 tsec 9.9780 #GCMRL# 381 dt 0.250000 rms 0.569 0.000% neg 0 invalid 762 tFOTS 5.4540 tGradient 3.5680 tsec 10.8670 #GCMRL# 382 dt 0.000061 rms 0.569 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5760 tsec 9.7820 #GCMRL# 383 dt 0.000008 rms 0.569 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5670 tsec 6.1420 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 0.599258 #FOTS# QuadFit found better minimum quadopt=(dt=9.99385,rms=0.594687) vs oldopt=(dt=11.52,rms=0.594781) #GCMRL# 385 dt 9.993846 rms 0.595 0.763% neg 0 invalid 762 tFOTS 12.2770 tGradient 3.1510 tsec 16.3940 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.593218) vs oldopt=(dt=2.88,rms=0.593612) #GCMRL# 386 dt 4.032000 rms 0.593 0.247% neg 0 invalid 762 tFOTS 11.5250 tGradient 3.0630 tsec 15.5510 #FOTS# QuadFit found better minimum quadopt=(dt=16.128,rms=0.589758) vs oldopt=(dt=11.52,rms=0.590435) #GCMRL# 387 dt 16.128000 rms 0.590 0.583% neg 0 invalid 762 tFOTS 12.3890 tGradient 3.0580 tsec 16.4100 #FOTS# QuadFit found better minimum quadopt=(dt=13.824,rms=0.587454) vs oldopt=(dt=11.52,rms=0.587785) #GCMRL# 388 dt 13.824000 rms 0.587 0.391% neg 0 invalid 762 tFOTS 12.3400 tGradient 3.0730 tsec 16.3750 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.587024) vs oldopt=(dt=2.88,rms=0.587145) #GCMRL# 389 dt 4.032000 rms 0.587 0.073% neg 0 invalid 762 tFOTS 11.5550 tGradient 3.0870 tsec 15.6050 #FOTS# QuadFit found better minimum quadopt=(dt=13.824,rms=0.585835) vs oldopt=(dt=11.52,rms=0.586017) #GCMRL# 390 dt 13.824000 rms 0.586 0.203% neg 0 invalid 762 tFOTS 12.3240 tGradient 3.0910 tsec 16.3820 #FOTS# QuadFit found better minimum quadopt=(dt=16.128,rms=0.585207) vs oldopt=(dt=11.52,rms=0.58534) #GCMRL# 391 dt 16.128000 rms 0.585 0.107% neg 0 invalid 762 tFOTS 12.3340 tGradient 3.0890 tsec 16.3980 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.58498) vs oldopt=(dt=2.88,rms=0.585049) #GCMRL# 392 dt 4.032000 rms 0.585 0.000% neg 0 invalid 762 tFOTS 10.8440 tGradient 3.0670 tsec 14.8890 #GCMRL# 393 dt 4.032000 rms 0.585 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0720 tsec 4.0360 #GCMRL# 394 dt 4.032000 rms 0.585 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0630 tsec 4.4510 #GCMRL# 395 dt 4.032000 rms 0.584 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0960 tsec 4.0610 #GCMRL# 396 dt 4.032000 rms 0.584 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0670 tsec 4.0310 #GCMRL# 397 dt 4.032000 rms 0.583 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0540 tsec 4.0150 #GCMRL# 398 dt 4.032000 rms 0.583 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0490 tsec 4.0180 #GCMRL# 399 dt 4.032000 rms 0.582 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0750 tsec 4.0470 #GCMRL# 400 dt 4.032000 rms 0.582 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0750 tsec 4.4580 #GCMRL# 401 dt 4.032000 rms 0.582 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0600 tsec 4.0170 #GCMRL# 402 dt 4.032000 rms 0.582 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0900 tsec 4.4970 #GCMRL# 403 dt 46.080000 rms 0.582 0.098% neg 0 invalid 762 tFOTS 12.3200 tGradient 3.0590 tsec 16.3360 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.581563) vs oldopt=(dt=11.52,rms=0.581591) #GCMRL# 404 dt 19.200000 rms 0.582 0.000% neg 0 invalid 762 tFOTS 12.3090 tGradient 3.0580 tsec 16.3460 #GCMRL# 405 dt 9.600000 rms 0.581 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0840 tsec 4.8800 #GCMRL# 406 dt 9.600000 rms 0.581 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0750 tsec 4.4610 #GCMRL# 407 dt 9.600000 rms 0.581 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0730 tsec 4.0380 #GCMRL# 408 dt 9.600000 rms 0.581 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0650 tsec 4.0330 #GCMRL# 409 dt 9.600000 rms 0.580 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0680 tsec 4.0380 #GCMRL# 410 dt 9.600000 rms 0.580 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0070 tsec 4.3790 #GCMRL# 411 dt 9.600000 rms 0.580 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9990 tsec 4.3830 #GCMRL# 412 dt 9.600000 rms 0.580 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0120 tsec 3.9800 #GCMRL# 413 dt 9.600000 rms 0.580 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9990 tsec 3.9720 #GCMRL# 414 dt 9.600000 rms 0.579 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0110 tsec 3.9710 #GCMRL# 415 dt 9.600000 rms 0.579 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0040 tsec 3.9710 #GCMRL# 416 dt 9.600000 rms 0.579 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9980 tsec 3.9560 #GCMRL# 417 dt 9.600000 rms 0.578 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0130 tsec 3.9770 #GCMRL# 418 dt 9.600000 rms 0.578 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0110 tsec 3.9750 #GCMRL# 419 dt 9.600000 rms 0.578 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9820 tsec 4.3600 #GCMRL# 420 dt 9.600000 rms 0.578 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9990 tsec 3.9840 #FOTS# QuadFit found better minimum quadopt=(dt=20,rms=0.577611) vs oldopt=(dt=11.52,rms=0.577642) #GCMRL# 421 dt 20.000000 rms 0.578 0.012% neg 0 invalid 762 tFOTS 12.3090 tGradient 2.9720 tsec 16.2310 #GCMRL# 422 dt 11.520000 rms 0.578 0.000% neg 0 invalid 762 tFOTS 12.2890 tGradient 2.9630 tsec 16.2310 #GCMRL# 423 dt 11.520000 rms 0.578 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9800 tsec 3.9480 #GCMRL# 424 dt 11.520000 rms 0.577 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9900 tsec 3.9530 #GCMRL# 425 dt 11.520000 rms 0.577 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9810 tsec 3.9480 #GCMRL# 426 dt 11.520000 rms 0.577 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0140 tsec 3.9790 #GCMRL# 427 dt 11.520000 rms 0.577 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9840 tsec 3.9500 #GCMRL# 428 dt 11.520000 rms 0.577 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9860 tsec 4.3580 #GCMRL# 429 dt 11.520000 rms 0.577 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9800 tsec 3.9360 #GCMRL# 430 dt 11.520000 rms 0.576 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0040 tsec 3.9660 #GCMRL# 431 dt 11.520000 rms 0.576 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9630 tsec 3.9180 #GCMRL# 432 dt 11.520000 rms 0.576 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9680 tsec 3.9230 #GCMRL# 433 dt 11.520000 rms 0.576 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9670 tsec 3.9240 #GCMRL# 434 dt 11.520000 rms 0.575 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0140 tsec 3.9810 #GCMRL# 435 dt 11.520000 rms 0.575 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9990 tsec 3.9640 #GCMRL# 436 dt 11.520000 rms 0.575 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0080 tsec 3.9730 #GCMRL# 437 dt 11.520000 rms 0.575 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0140 tsec 3.9850 #GCMRL# 438 dt 11.520000 rms 0.574 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0140 tsec 3.9920 #GCMRL# 439 dt 11.520000 rms 0.574 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 3.9640 #GCMRL# 440 dt 11.520000 rms 0.574 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0150 tsec 3.9840 #GCMRL# 441 dt 11.520000 rms 0.574 -0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0120 tsec 5.3040 #FOTS# QuadFit found better minimum quadopt=(dt=2.304,rms=0.573861) vs oldopt=(dt=2.88,rms=0.573861) #GCMRL# 442 dt 2.304000 rms 0.574 0.000% neg 0 invalid 762 tFOTS 11.6660 tGradient 3.0100 tsec 15.6460 #GCAMreg# pass 0 level1 2 level2 1 tsec 413.771 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 0.574336 #GCMRL# 444 dt 0.000000 rms 0.574 0.083% neg 0 invalid 762 tFOTS 12.4140 tGradient 2.9940 tsec 16.3680 #GCMRL# 445 dt 0.150000 rms 0.574 0.000% neg 0 invalid 762 tFOTS 12.5920 tGradient 2.9930 tsec 17.4690 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 0.603815 #FOTS# QuadFit found better minimum quadopt=(dt=0,rms=0.603363) vs oldopt=(dt=0,rms=0.603363) #GCMRL# 447 dt 0.000000 rms 0.603 0.075% neg 0 invalid 762 tFOTS 11.8200 tGradient 2.9350 tsec 15.7220 #GCMRL# 448 dt 0.100000 rms 0.603 0.000% neg 0 invalid 762 tFOTS 11.8740 tGradient 2.8800 tsec 16.6480 #GCAMreg# pass 0 level1 1 level2 1 tsec 40.794 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 0.603815 #GCMRL# 450 dt 0.000000 rms 0.603 0.075% neg 0 invalid 762 tFOTS 11.6100 tGradient 2.9890 tsec 15.5610 #GCMRL# 451 dt 0.100000 rms 0.603 0.000% neg 0 invalid 762 tFOTS 11.6760 tGradient 2.8590 tsec 16.3920 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 0.553812 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.538438) vs oldopt=(dt=0.32,rms=0.540829) #GCMRL# 453 dt 0.384000 rms 0.538 2.776% neg 0 invalid 762 tFOTS 11.7140 tGradient 2.2780 tsec 14.9610 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.536836) vs oldopt=(dt=0.08,rms=0.537285) #GCMRL# 454 dt 0.112000 rms 0.537 0.298% neg 0 invalid 762 tFOTS 10.9130 tGradient 2.3230 tsec 14.2180 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.532182) vs oldopt=(dt=0.32,rms=0.532948) #GCMRL# 455 dt 0.384000 rms 0.532 0.867% neg 0 invalid 762 tFOTS 12.1790 tGradient 2.3360 tsec 15.4770 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.529779) vs oldopt=(dt=0.32,rms=0.53017) #GCMRL# 456 dt 0.384000 rms 0.530 0.452% neg 0 invalid 762 tFOTS 12.0850 tGradient 2.3430 tsec 15.4110 #GCMRL# 457 dt 0.320000 rms 0.528 0.254% neg 0 invalid 762 tFOTS 11.7800 tGradient 2.4480 tsec 15.2070 #GCMRL# 458 dt 0.320000 rms 0.527 0.199% neg 0 invalid 762 tFOTS 11.8110 tGradient 2.4180 tsec 15.2060 #GCMRL# 459 dt 0.320000 rms 0.527 0.162% neg 0 invalid 762 tFOTS 11.6940 tGradient 2.3800 tsec 15.0440 #GCMRL# 460 dt 0.320000 rms 0.526 0.133% neg 0 invalid 762 tFOTS 11.6860 tGradient 2.3120 tsec 14.9680 #GCMRL# 461 dt 0.320000 rms 0.525 0.117% neg 0 invalid 762 tFOTS 11.8480 tGradient 2.3070 tsec 15.1230 #GCMRL# 462 dt 0.320000 rms 0.525 0.096% neg 0 invalid 762 tFOTS 11.6620 tGradient 2.3120 tsec 14.9380 #GCMRL# 463 dt 0.320000 rms 0.524 0.090% neg 0 invalid 762 tFOTS 11.7000 tGradient 2.3430 tsec 15.0240 #GCMRL# 464 dt 0.320000 rms 0.524 0.073% neg 0 invalid 762 tFOTS 11.7620 tGradient 2.3220 tsec 15.0590 #GCMRL# 465 dt 0.320000 rms 0.523 0.072% neg 0 invalid 762 tFOTS 11.9250 tGradient 2.3660 tsec 15.2850 #GCMRL# 466 dt 0.320000 rms 0.523 0.058% neg 0 invalid 762 tFOTS 11.7720 tGradient 2.3990 tsec 15.1470 #GCMRL# 467 dt 0.320000 rms 0.523 0.058% neg 0 invalid 762 tFOTS 11.8150 tGradient 2.3340 tsec 15.1480 #GCMRL# 468 dt 0.320000 rms 0.523 0.000% neg 0 invalid 762 tFOTS 12.0450 tGradient 2.3500 tsec 15.4020 #GCMRL# 469 dt 0.320000 rms 0.522 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3470 tsec 3.3320 #GCMRL# 470 dt 0.320000 rms 0.522 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3200 tsec 3.2940 #GCMRL# 471 dt 0.320000 rms 0.522 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3850 tsec 3.7940 #GCMRL# 472 dt 0.320000 rms 0.521 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3300 tsec 3.3050 #GCMRL# 473 dt 0.320000 rms 0.521 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3330 tsec 3.7430 #GCMRL# 474 dt 0.320000 rms 0.521 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3350 tsec 3.3270 #GCMRL# 475 dt 0.320000 rms 0.521 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4050 tsec 3.8260 #GCMRL# 476 dt 0.320000 rms 0.521 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3770 tsec 3.8150 #GCMRL# 477 dt 0.320000 rms 0.521 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3420 tsec 3.7640 #GCMRL# 478 dt 0.320000 rms 0.521 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4340 tsec 3.8940 #GCMRL# 479 dt 0.320000 rms 0.520 0.020% neg 0 invalid 762 tFOTS 11.9080 tGradient 2.4230 tsec 15.3050 #GCMRL# 480 dt 0.320000 rms 0.520 0.000% neg 0 invalid 762 tFOTS 11.9140 tGradient 2.3390 tsec 15.2580 #GCMRL# 481 dt 0.320000 rms 0.520 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3520 tsec 3.3360 #GCMRL# 482 dt 0.320000 rms 0.520 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3260 tsec 3.3090 #GCMRL# 483 dt 0.320000 rms 0.520 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3500 tsec 3.7530 #GCMRL# 484 dt 0.320000 rms 0.520 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3790 tsec 3.3600 #GCMRL# 485 dt 0.320000 rms 0.520 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3340 tsec 3.7710 #GCMRL# 486 dt 0.320000 rms 0.520 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4250 tsec 3.4720 #GCMRL# 487 dt 0.320000 rms 0.520 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4600 tsec 3.9110 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.519565) vs oldopt=(dt=0.32,rms=0.519568) #GCMRL# 488 dt 0.256000 rms 0.520 0.000% neg 0 invalid 762 tFOTS 12.0600 tGradient 2.3870 tsec 15.5210 #GCMRL# 489 dt 0.256000 rms 0.520 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3660 tsec 3.3550 #GCMRL# 490 dt 0.256000 rms 0.519 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3540 tsec 3.3680 #GCMRL# 491 dt 0.256000 rms 0.519 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3710 tsec 3.7810 #GCMRL# 492 dt 0.256000 rms 0.519 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5450 tsec 3.5270 #GCMRL# 493 dt 0.256000 rms 0.519 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3490 tsec 3.3340 #GCAMreg# pass 0 level1 0 level2 1 tsec 373.48 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 0.519739 #FOTS# QuadFit found better minimum quadopt=(dt=0.28125,rms=0.516214) vs oldopt=(dt=0.08,rms=0.518324) #GCMRL# 495 dt 0.281250 rms 0.516 0.678% neg 0 invalid 762 tFOTS 11.0640 tGradient 2.3660 tsec 14.4070 #GCMRL# 496 dt 0.320000 rms 0.515 0.277% neg 0 invalid 762 tFOTS 12.1410 tGradient 2.3710 tsec 15.4930 #FOTS# QuadFit found better minimum quadopt=(dt=0.35,rms=0.514219) vs oldopt=(dt=0.32,rms=0.514261) #GCMRL# 497 dt 0.350000 rms 0.514 0.110% neg 0 invalid 762 tFOTS 11.9690 tGradient 2.3520 tsec 15.3090 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.514039) vs oldopt=(dt=0.32,rms=0.514053) #GCMRL# 498 dt 0.384000 rms 0.514 0.000% neg 0 invalid 762 tFOTS 11.8850 tGradient 2.3890 tsec 15.2780 #GCMRL# 499 dt 0.384000 rms 0.514 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4050 tsec 3.3920 #GCMRL# 500 dt 0.384000 rms 0.514 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3850 tsec 3.3790 GCAMregister done in 63.317 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 0.511834 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.511053) vs oldopt=(dt=92.48,rms=0.511055) #GCMRL# 502 dt 110.976000 rms 0.511 0.152% neg 0 invalid 762 tFOTS 13.9640 tGradient 5.6500 tsec 20.5920 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.510848) vs oldopt=(dt=92.48,rms=0.510875) #GCMRL# 503 dt 129.472000 rms 0.511 0.000% neg 0 invalid 762 tFOTS 13.9320 tGradient 5.7090 tsec 20.6220 #GCAMreg# pass 0 level1 5 level2 1 tsec 52.323 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 0.511414 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.509743) vs oldopt=(dt=369.92,rms=0.510041) #GCMRL# 505 dt 221.952000 rms 0.510 0.327% neg 0 invalid 762 tFOTS 14.0320 tGradient 5.6240 tsec 20.6260 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.509549) vs oldopt=(dt=92.48,rms=0.50958) #GCMRL# 506 dt 73.984000 rms 0.510 0.000% neg 0 invalid 762 tFOTS 13.9590 tGradient 5.6220 tsec 20.5620 #GCMRL# 507 dt 73.984000 rms 0.509 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6900 tsec 6.6600 #GCMRL# 508 dt 73.984000 rms 0.509 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6340 tsec 6.5920 #GCMRL# 509 dt 73.984000 rms 0.509 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5850 tsec 6.5550 #GCMRL# 510 dt 73.984000 rms 0.509 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5360 tsec 6.5080 #GCMRL# 511 dt 73.984000 rms 0.509 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6080 tsec 6.5770 #GCMRL# 512 dt 73.984000 rms 0.508 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6020 tsec 6.5900 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.508387) vs oldopt=(dt=369.92,rms=0.508408) 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 0.509006 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.507854) vs oldopt=(dt=25.92,rms=0.507936) #GCMRL# 514 dt 36.288000 rms 0.508 0.226% neg 0 invalid 762 tFOTS 13.9700 tGradient 4.2840 tsec 19.2440 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.507357) vs oldopt=(dt=103.68,rms=0.507506) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 515 dt 62.208000 rms 0.507 0.000% neg 0 invalid 762 tFOTS 14.0430 tGradient 4.2740 tsec 20.6330 #GCMRL# 516 dt 62.208000 rms 0.507 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2370 tsec 5.2010 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 517 dt 62.208000 rms 0.507 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2080 tsec 7.3000 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 65.999 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 0.507054 #FOTS# QuadFit found better minimum quadopt=(dt=166.029,rms=0.502991) vs oldopt=(dt=103.68,rms=0.503413) #GCMRL# 519 dt 166.028986 rms 0.503 0.801% neg 0 invalid 762 tFOTS 14.8600 tGradient 4.2430 tsec 20.0750 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.502313) vs oldopt=(dt=25.92,rms=0.502413) #GCMRL# 520 dt 36.288000 rms 0.502 0.000% neg 0 invalid 762 tFOTS 14.0240 tGradient 4.1760 tsec 19.1940 #GCMRL# 521 dt 36.288000 rms 0.502 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4840 tsec 5.4790 #GCMRL# 522 dt 36.288000 rms 0.502 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3080 tsec 5.2820 #GCMRL# 523 dt 36.288000 rms 0.502 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1520 tsec 5.1440 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 524 dt 36.288000 rms 0.501 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1480 tsec 5.9490 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 525 dt 36.288000 rms 0.500 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1180 tsec 5.9650 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 526 dt 36.288000 rms 0.500 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1970 tsec 7.2660 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 527 dt 36.288000 rms 0.499 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1830 tsec 6.4130 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 528 dt 36.288000 rms 0.499 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1710 tsec 6.4240 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.498679) vs oldopt=(dt=25.92,rms=0.498685) #GCMRL# 529 dt 36.288000 rms 0.499 0.000% neg 0 invalid 762 tFOTS 14.5350 tGradient 4.1120 tsec 19.6220 #GCMRL# 530 dt 36.288000 rms 0.499 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1310 tsec 5.0820 #GCMRL# 531 dt 36.288000 rms 0.499 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1780 tsec 5.1340 #GCMRL# 532 dt 36.288000 rms 0.498 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1750 tsec 5.1270 #GCMRL# 533 dt 36.288000 rms 0.498 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1260 tsec 5.0820 #GCMRL# 534 dt 36.288000 rms 0.498 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1450 tsec 5.0960 #GCMRL# 535 dt 36.288000 rms 0.498 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1210 tsec 5.0790 #GCMRL# 536 dt 36.288000 rms 0.498 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1100 tsec 5.0750 #GCMRL# 537 dt 36.288000 rms 0.497 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2040 tsec 5.1630 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 538 dt 36.288000 rms 0.497 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1410 tsec 5.9460 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 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 0.498116 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.495147) vs oldopt=(dt=32,rms=0.495355) iter 0, gcam->neg = 22 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 540 dt 44.800000 rms 0.495 0.553% neg 0 invalid 762 tFOTS 14.6170 tGradient 3.3820 tsec 24.9200 #FOTS# QuadFit found better minimum quadopt=(dt=102.4,rms=0.490757) vs oldopt=(dt=128,rms=0.491037) iter 0, gcam->neg = 51 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 541 dt 102.400000 rms 0.491 0.872% neg 0 invalid 762 tFOTS 14.6450 tGradient 3.3610 tsec 25.3530 #FOTS# QuadFit found better minimum quadopt=(dt=21.7469,rms=0.489362) vs oldopt=(dt=32,rms=0.489821) iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 542 dt 21.746939 rms 0.489 0.339% neg 0 invalid 762 tFOTS 14.6130 tGradient 3.4310 tsec 20.6750 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.488405) vs oldopt=(dt=32,rms=0.488443) iter 0, gcam->neg = 17 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 543 dt 44.800000 rms 0.489 0.000% neg 0 invalid 762 tFOTS 14.6250 tGradient 3.4280 tsec 24.0630 iter 0, gcam->neg = 15 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 544 dt 44.800000 rms 0.488 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4230 tsec 9.8250 iter 0, gcam->neg = 19 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 545 dt 44.800000 rms 0.486 0.469% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4480 tsec 11.1290 iter 0, gcam->neg = 35 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 546 dt 44.800000 rms 0.485 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3710 tsec 9.8080 iter 0, gcam->neg = 50 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 547 dt 44.800000 rms 0.483 0.506% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3980 tsec 11.9560 iter 0, gcam->neg = 68 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 548 dt 44.800000 rms 0.483 -0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4220 tsec 12.8370 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.481959) vs oldopt=(dt=32,rms=0.482) iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 549 dt 25.600000 rms 0.482 0.156% neg 0 invalid 762 tFOTS 14.4920 tGradient 3.4170 tsec 20.5240 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 194.209 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 0.482132 #FOTS# QuadFit found better minimum quadopt=(dt=55.9456,rms=0.478571) vs oldopt=(dt=32,rms=0.478965) iter 0, gcam->neg = 7 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 551 dt 55.945578 rms 0.479 0.708% neg 0 invalid 762 tFOTS 14.5680 tGradient 3.3790 tsec 24.7980 #FOTS# QuadFit found better minimum quadopt=(dt=24.1848,rms=0.477342) vs oldopt=(dt=32,rms=0.477547) #GCMRL# 552 dt 24.184818 rms 0.477 0.287% neg 0 invalid 762 tFOTS 14.5510 tGradient 3.3680 tsec 18.8700 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.47647) vs oldopt=(dt=32,rms=0.476527) iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 553 dt 44.800000 rms 0.476 0.000% neg 0 invalid 762 tFOTS 14.5360 tGradient 3.3680 tsec 20.1190 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 0.483928 #FOTS# QuadFit found better minimum quadopt=(dt=6.26087,rms=0.482362) vs oldopt=(dt=2.88,rms=0.482584) #GCMRL# 555 dt 6.260870 rms 0.482 0.324% neg 0 invalid 762 tFOTS 14.6660 tGradient 3.0130 tsec 18.6360 #FOTS# QuadFit found better minimum quadopt=(dt=5.33333,rms=0.482072) vs oldopt=(dt=2.88,rms=0.482134) iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 556 dt 5.333333 rms 0.482 0.000% neg 0 invalid 762 tFOTS 14.6180 tGradient 2.9780 tsec 19.3940 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 557 dt 5.333333 rms 0.482 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9640 tsec 6.0000 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 558 dt 5.333333 rms 0.482 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9650 tsec 6.4390 iter 0, gcam->neg = 18 after 15 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 66.009 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 0.482302 #FOTS# QuadFit found better minimum quadopt=(dt=19.0303,rms=0.479009) vs oldopt=(dt=11.52,rms=0.479419) iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 560 dt 19.030303 rms 0.479 0.678% neg 0 invalid 762 tFOTS 14.6480 tGradient 2.9350 tsec 21.4750 #FOTS# QuadFit found better minimum quadopt=(dt=21.7436,rms=0.47689) vs oldopt=(dt=11.52,rms=0.477366) iter 0, gcam->neg = 35 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 561 dt 21.743590 rms 0.477 0.342% neg 0 invalid 762 tFOTS 14.6570 tGradient 3.0400 tsec 25.0030 #FOTS# QuadFit found better minimum quadopt=(dt=11.6471,rms=0.476409) vs oldopt=(dt=11.52,rms=0.47641) iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 562 dt 11.647059 rms 0.476 0.000% neg 0 invalid 762 tFOTS 14.5620 tGradient 3.0210 tsec 19.8100 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 563 dt 11.647059 rms 0.475 0.213% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9920 tsec 5.6050 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 564 dt 11.647059 rms 0.474 0.236% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9950 tsec 8.9810 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 565 dt 11.647059 rms 0.473 0.258% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0020 tsec 6.0470 iter 0, gcam->neg = 6 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 566 dt 11.647059 rms 0.472 0.258% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9830 tsec 6.8600 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 567 dt 11.647059 rms 0.470 0.297% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9280 tsec 8.5060 iter 0, gcam->neg = 16 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 568 dt 11.647059 rms 0.469 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0170 tsec 9.8560 iter 0, gcam->neg = 33 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 569 dt 11.647059 rms 0.469 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9260 tsec 9.3130 iter 0, gcam->neg = 42 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 570 dt 11.647059 rms 0.468 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9350 tsec 10.1950 iter 0, gcam->neg = 45 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 571 dt 11.647059 rms 0.467 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9370 tsec 10.1880 iter 0, gcam->neg = 41 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 572 dt 11.647059 rms 0.467 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0270 tsec 6.4900 iter 0, gcam->neg = 71 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 573 dt 11.647059 rms 0.467 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9970 tsec 10.6650 iter 0, gcam->neg = 47 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 574 dt 11.647059 rms 0.466 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9240 tsec 11.0280 #FOTS# QuadFit found better minimum quadopt=(dt=8.51064,rms=0.466133) vs oldopt=(dt=11.52,rms=0.466161) #GCMRL# 575 dt 8.510638 rms 0.466 0.052% neg 0 invalid 762 tFOTS 14.5790 tGradient 2.9670 tsec 18.4990 #FOTS# QuadFit found better minimum quadopt=(dt=5.33333,rms=0.466064) vs oldopt=(dt=2.88,rms=0.466077) #GCMRL# 576 dt 5.333333 rms 0.466 0.000% neg 0 invalid 762 tFOTS 14.6120 tGradient 2.9420 tsec 18.5330 #GCMRL# 577 dt 5.333333 rms 0.466 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9450 tsec 3.8990 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=0, neg = 0 #GCMRL# 578 dt 5.333333 rms 0.466 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9460 tsec 8.1120 iter 0, gcam->neg = 15 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 579 dt 5.333333 rms 0.466 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9320 tsec 6.4030 iter 0, gcam->neg = 11 after 2 iterations, nbhd size=0, neg = 0 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 0.473413 #GCMRL# 581 dt 0.000000 rms 0.473 0.132% neg 0 invalid 762 tFOTS 13.9230 tGradient 2.8030 tsec 17.6920 #GCAMreg# pass 0 level1 1 level2 1 tsec 39.878 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 0.473413 #GCMRL# 583 dt 0.000000 rms 0.473 0.132% neg 0 invalid 762 tFOTS 13.9050 tGradient 2.7940 tsec 17.6500 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 0.46199 #FOTS# QuadFit found better minimum quadopt=(dt=1.71214,rms=0.433436) vs oldopt=(dt=1.28,rms=0.435475) iter 0, gcam->neg = 1719 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 585 dt 1.712138 rms 0.440 4.754% neg 0 invalid 762 tFOTS 14.5930 tGradient 2.2320 tsec 25.4400 #GCMRL# 586 dt 0.000013 rms 0.440 0.000% neg 0 invalid 762 tFOTS 18.4280 tGradient 2.2660 tsec 21.6720 #GCAMreg# pass 0 level1 0 level2 1 tsec 54.832 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 0.440719 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.439948) vs oldopt=(dt=0.02,rms=0.439957) #GCMRL# 588 dt 0.028000 rms 0.440 0.175% neg 0 invalid 762 tFOTS 14.6660 tGradient 2.2850 tsec 17.9060 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.439938) vs oldopt=(dt=0.02,rms=0.439939) #GCMRL# 589 dt 0.016000 rms 0.440 0.000% neg 0 invalid 762 tFOTS 14.6910 tGradient 2.2770 tsec 17.9440 label assignment complete, 0 changed (0.00%) GCAMregister done in 18.8027 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 0.427054 #GCAMreg# pass 0 level1 5 level2 1 tsec 23.907 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 0.427054 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.427053) vs oldopt=(dt=5.78,rms=0.427053) #GCMRL# 592 dt 8.092000 rms 0.427 0.000% neg 0 invalid 762 tFOTS 14.2890 tGradient 5.1290 tsec 20.3630 #FOTS# QuadFit found better minimum quadopt=(dt=2.023,rms=0.427053) vs oldopt=(dt=1.445,rms=0.427053) #GCMRL# 593 dt 2.023000 rms 0.427 0.000% neg 0 invalid 762 tFOTS 14.2860 tGradient 5.1350 tsec 20.3790 #GCMRL# 594 dt 2.023000 rms 0.427 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1410 tsec 6.0740 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 0.427212 #FOTS# QuadFit found better minimum quadopt=(dt=7.776,rms=0.427188) vs oldopt=(dt=6.48,rms=0.427189) #GCMRL# 596 dt 7.776000 rms 0.427 0.006% neg 0 invalid 762 tFOTS 14.2830 tGradient 3.7820 tsec 19.0130 #FOTS# QuadFit found better minimum quadopt=(dt=1.944,rms=0.427187) vs oldopt=(dt=1.62,rms=0.427187) #GCMRL# 597 dt 1.944000 rms 0.427 0.000% neg 0 invalid 762 tFOTS 14.3400 tGradient 3.7720 tsec 19.0680 #GCAMreg# pass 0 level1 4 level2 1 tsec 47.114 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 0.427187 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.426971) vs oldopt=(dt=25.92,rms=0.427015) #GCMRL# 599 dt 36.288000 rms 0.427 0.051% neg 0 invalid 762 tFOTS 13.5140 tGradient 3.7470 tsec 18.1950 #GCMRL# 600 dt 103.680000 rms 0.427 0.053% neg 0 invalid 762 tFOTS 13.5010 tGradient 3.7590 tsec 18.1940 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.426462) vs oldopt=(dt=103.68,rms=0.426512) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 601 dt 145.152000 rms 0.426 0.066% neg 0 invalid 762 tFOTS 13.5210 tGradient 3.7470 tsec 19.0330 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.426444) vs oldopt=(dt=25.92,rms=0.426447) #GCMRL# 602 dt 36.288000 rms 0.426 0.000% neg 0 invalid 762 tFOTS 14.2440 tGradient 3.7810 tsec 18.9830 #GCMRL# 603 dt 36.288000 rms 0.426 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7510 tsec 4.6840 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 604 dt 36.288000 rms 0.426 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7270 tsec 5.4880 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 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 0.426988 #FOTS# QuadFit found better minimum quadopt=(dt=22.5251,rms=0.426352) vs oldopt=(dt=32,rms=0.42653) iter 0, gcam->neg = 18 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 606 dt 22.525140 rms 0.427 0.057% neg 0 invalid 762 tFOTS 14.2900 tGradient 3.1320 tsec 24.6450 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.426385) vs oldopt=(dt=32,rms=0.426397) iter 0, gcam->neg = 38 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 607 dt 25.600000 rms 0.427 0.000% neg 0 invalid 762 tFOTS 14.2910 tGradient 3.0570 tsec 24.5870 iter 0, gcam->neg = 38 after 17 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 65.696 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 0.426575 #FOTS# QuadFit found better minimum quadopt=(dt=71.0095,rms=0.423166) vs oldopt=(dt=32,rms=0.423966) iter 0, gcam->neg = 43 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 609 dt 71.009524 rms 0.423 0.739% neg 0 invalid 762 tFOTS 14.2410 tGradient 3.0670 tsec 24.1170 #FOTS# QuadFit found better minimum quadopt=(dt=29.7931,rms=0.422209) vs oldopt=(dt=32,rms=0.42223) iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 610 dt 29.793103 rms 0.422 0.274% neg 0 invalid 762 tFOTS 14.2390 tGradient 3.0830 tsec 23.2860 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.421623) vs oldopt=(dt=32,rms=0.421713) iter 0, gcam->neg = 15 after 16 iterations, nbhd size=2, neg = 0 #GCMRL# 611 dt 44.800000 rms 0.422 0.000% neg 0 invalid 762 tFOTS 14.2790 tGradient 3.0410 tsec 25.8840 iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 612 dt 44.800000 rms 0.422 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1080 tsec 6.1330 iter 0, gcam->neg = 20 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 613 dt 44.800000 rms 0.421 0.253% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0800 tsec 10.7520 iter 0, gcam->neg = 39 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 614 dt 44.800000 rms 0.420 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0640 tsec 9.0470 iter 0, gcam->neg = 49 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 615 dt 44.800000 rms 0.419 0.247% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0680 tsec 11.1700 iter 0, gcam->neg = 55 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 616 dt 44.800000 rms 0.418 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0740 tsec 10.3260 iter 0, gcam->neg = 41 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 617 dt 44.800000 rms 0.418 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1620 tsec 11.7220 iter 0, gcam->neg = 41 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 618 dt 44.800000 rms 0.417 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0740 tsec 10.7600 iter 0, gcam->neg = 34 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 619 dt 44.800000 rms 0.417 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0580 tsec 10.3070 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.41676) vs oldopt=(dt=32,rms=0.416766) iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 620 dt 25.600000 rms 0.417 0.000% neg 0 invalid 762 tFOTS 14.2750 tGradient 3.0600 tsec 19.9610 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 621 dt 25.600000 rms 0.417 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0740 tsec 4.8440 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 622 dt 25.600000 rms 0.417 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0780 tsec 4.8400 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 623 dt 25.600000 rms 0.416 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0670 tsec 5.2640 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 624 dt 25.600000 rms 0.416 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0660 tsec 5.6760 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 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 0.420996 #FOTS# QuadFit found better minimum quadopt=(dt=4,rms=0.420799) vs oldopt=(dt=2.88,rms=0.420813) iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 626 dt 4.000000 rms 0.421 0.043% neg 0 invalid 762 tFOTS 14.3120 tGradient 2.5190 tsec 19.0250 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.420801) vs oldopt=(dt=0.72,rms=0.420803) #GCMRL# 627 dt 1.008000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 14.3230 tGradient 2.5250 tsec 17.8030 #GCMRL# 628 dt 1.008000 rms 0.421 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5100 tsec 3.4490 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 52.693 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 0.420796 #FOTS# QuadFit found better minimum quadopt=(dt=9.11828,rms=0.420367) vs oldopt=(dt=11.52,rms=0.420404) iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 630 dt 9.118280 rms 0.420 0.101% neg 0 invalid 762 tFOTS 14.2880 tGradient 2.5210 tsec 19.8420 #FOTS# QuadFit found better minimum quadopt=(dt=16.128,rms=0.419893) vs oldopt=(dt=11.52,rms=0.419932) iter 0, gcam->neg = 12 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 631 dt 16.128000 rms 0.420 0.117% neg 0 invalid 762 tFOTS 14.3330 tGradient 2.5240 tsec 20.3130 #FOTS# QuadFit found better minimum quadopt=(dt=53.1282,rms=0.418292) vs oldopt=(dt=46.08,rms=0.418326) iter 0, gcam->neg = 88 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 632 dt 53.128205 rms 0.419 0.280% neg 0 invalid 762 tFOTS 14.2510 tGradient 2.5360 tsec 25.2880 #FOTS# QuadFit found better minimum quadopt=(dt=22.4444,rms=0.417707) vs oldopt=(dt=11.52,rms=0.417893) iter 0, gcam->neg = 69 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 633 dt 22.444444 rms 0.418 0.000% neg 0 invalid 762 tFOTS 14.2350 tGradient 2.5130 tsec 24.8660 iter 0, gcam->neg = 54 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 634 dt 22.444444 rms 0.418 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5140 tsec 11.4810 iter 0, gcam->neg = 101 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 635 dt 22.444444 rms 0.418 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5410 tsec 12.3220 iter 0, gcam->neg = 179 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 636 dt 22.444444 rms 0.418 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5140 tsec 11.8890 iter 0, gcam->neg = 307 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 637 dt 22.444444 rms 0.417 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5210 tsec 12.3220 iter 0, gcam->neg = 374 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 638 dt 22.444444 rms 0.417 -0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5360 tsec 13.6480 #FOTS# QuadFit found better minimum quadopt=(dt=13.6533,rms=0.41644) vs oldopt=(dt=11.52,rms=0.416454) iter 0, gcam->neg = 40 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 639 dt 13.653333 rms 0.417 0.168% neg 0 invalid 762 tFOTS 14.2750 tGradient 2.5170 tsec 23.6220 #FOTS# QuadFit found better minimum quadopt=(dt=13.1765,rms=0.416068) vs oldopt=(dt=11.52,rms=0.416079) iter 0, gcam->neg = 25 after 17 iterations, nbhd size=1, neg = 0 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 0.422901 #FOTS# QuadFit found better minimum quadopt=(dt=6e-05,rms=0.422901) vs oldopt=(dt=5e-05,rms=0.422901) #GCMRL# 641 dt 0.000060 rms 0.423 0.000% neg 0 invalid 762 tFOTS 18.0900 tGradient 2.4060 tsec 21.4300 #GCAMreg# pass 0 level1 1 level2 1 tsec 42.631 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 0.422901 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 0.412176 #FOTS# QuadFit found better minimum quadopt=(dt=1.1391,rms=0.400246) vs oldopt=(dt=1.28,rms=0.400396) iter 0, gcam->neg = 897 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 644 dt 1.139095 rms 0.406 1.535% neg 0 invalid 762 tFOTS 14.3020 tGradient 1.8570 tsec 25.9990 #FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.405849) vs oldopt=(dt=1.95313e-05,rms=0.405849) #GCMRL# 645 dt 0.000023 rms 0.406 0.000% neg 0 invalid 762 tFOTS 18.0510 tGradient 1.8460 tsec 20.8550 #GCAMreg# pass 0 level1 0 level2 1 tsec 53.978 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 0.405849 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.405579) vs oldopt=(dt=0.08,rms=0.405604) #GCMRL# 647 dt 0.112000 rms 0.406 0.067% neg 0 invalid 762 tFOTS 14.3290 tGradient 1.8450 tsec 17.1090 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.405455) vs oldopt=(dt=0.08,rms=0.405463) #GCMRL# 648 dt 0.112000 rms 0.405 0.000% neg 0 invalid 762 tFOTS 14.3720 tGradient 1.8520 tsec 17.2410 #GCMRL# 649 dt 0.112000 rms 0.405 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8410 tsec 2.7760 #GCMRL# 650 dt 0.112000 rms 0.405 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8430 tsec 2.7810 GCAMregister done in 15.2055 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4569 tmin = 16.7301 Calls to gcamLabelEnergy 3887 tmin = 1.11938 Calls to gcamJacobianEnergy 4569 tmin = 11.4002 Calls to gcamSmoothnessEnergy 4569 tmin = 10.5544 Calls to gcamLogLikelihoodTerm 652 tmin = 4.7276 Calls to gcamLabelTerm 591 tmin = 5.96662 Calls to gcamJacobianTerm 652 tmin = 9.95838 Calls to gcamSmoothnessTerm 652 tmin = 3.07708 Calls to gcamComputeGradient 652 tmin = 45.5164 Calls to gcamComputeMetricProperties 7161 tmin = 19.1917 mri_ca_register took 1 hours, 57 minutes and 17 seconds. #VMPC# mri_ca_register VmPeak 1993640 FSRUNTIME@ mri_ca_register 1.9548 hours 1 threads @#@FSTIME 2021:05:08:14:26:08 mri_ca_register N 9 e 7037.35 S 5.42 U 7030.21 P 99% M 1333076 F 0 R 1684861 W 0 c 67223 w 1 I 0 O 63200 L 1.69 1.71 1.68 @#@FSLOADPOST 2021:05:08:16:23:26 mri_ca_register N 9 1.49 1.51 1.57 #-------------------------------------- #@# SubCort Seg 2021��� 05��� 08��� ��������� 16:23:26 CST mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/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/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 6.68 Atlas used for the 3D morph was /usr/local/freesurfer/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 = 0.15118 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (2817 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2817 voxels, peak = 7), gca=8.0 gca peak = 0.20380 (13) mri peak = 0.18568 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (2425 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (2425 voxels, peak = 4), gca=5.2 gca peak = 0.26283 (96) mri peak = 0.20849 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (738 voxels, overlap=0.678) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (738 voxels, peak = 101), gca=101.3 gca peak = 0.15814 (97) mri peak = 0.19687 (101) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (659 voxels, overlap=0.489) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (659 voxels, peak = 102), gca=102.3 gca peak = 0.27624 (56) mri peak = 0.15996 (61) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (1007 voxels, overlap=0.968) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (1007 voxels, peak = 58), gca=58.0 gca peak = 0.28723 (59) mri peak = 0.10769 (62) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (979 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (979 voxels, peak = 63), gca=63.4 gca peak = 0.07623 (103) mri peak = 0.12300 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (46254 voxels, overlap=0.665) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (46254 voxels, peak = 105), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.12142 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (43128 voxels, overlap=0.620) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (43128 voxels, peak = 108), gca=107.6 gca peak = 0.10165 (58) mri peak = 0.04950 (55) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (27777 voxels, overlap=0.980) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (27777 voxels, peak = 59), gca=59.4 gca peak = 0.11113 (58) mri peak = 0.04016 (51) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24314 voxels, overlap=0.987) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24314 voxels, peak = 59), gca=59.4 gca peak = 0.27796 (67) mri peak = 0.22095 (75) Right_Caudate (50): linear fit = 1.08 x + 0.0 (761 voxels, overlap=0.627) Right_Caudate (50): linear fit = 1.08 x + 0.0 (761 voxels, peak = 72), gca=72.0 gca peak = 0.14473 (69) mri peak = 0.11205 (77) Left_Caudate (11): linear fit = 1.07 x + 0.0 (741 voxels, overlap=0.677) Left_Caudate (11): linear fit = 1.07 x + 0.0 (741 voxels, peak = 73), gca=73.5 gca peak = 0.14301 (56) mri peak = 0.05536 (60) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (20663 voxels, overlap=0.985) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (20663 voxels, peak = 59), gca=58.5 gca peak = 0.14610 (55) mri peak = 0.05551 (59) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (22834 voxels, overlap=0.929) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (22834 voxels, peak = 59), gca=58.6 gca peak = 0.16309 (85) mri peak = 0.15089 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7194 voxels, overlap=0.427) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7194 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.11442 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (6351 voxels, overlap=0.214) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (6351 voxels, peak = 93), gca=92.8 gca peak = 0.30461 (58) mri peak = 0.11553 (67) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (567 voxels, overlap=0.356) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (567 voxels, peak = 68), gca=67.6 gca peak = 0.32293 (57) mri peak = 0.13334 (66) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (699 voxels, overlap=0.279) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (699 voxels, peak = 66), gca=65.8 gca peak = 0.11083 (90) mri peak = 0.08323 (87) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (4517 voxels, overlap=0.944) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (4517 voxels, peak = 91), gca=91.3 gca peak = 0.11393 (83) mri peak = 0.08885 (90) Right_Thalamus (49): linear fit = 1.08 x + 0.0 (4405 voxels, overlap=0.893) Right_Thalamus (49): linear fit = 1.08 x + 0.0 (4405 voxels, peak = 89), gca=89.2 gca peak = 0.08575 (81) mri peak = 0.08013 (82) Left_Putamen (12): linear fit = 1.02 x + 0.0 (2184 voxels, overlap=0.779) Left_Putamen (12): linear fit = 1.02 x + 0.0 (2184 voxels, peak = 83), gca=83.0 gca peak = 0.08618 (78) mri peak = 0.08747 (81) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2260 voxels, overlap=0.892) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2260 voxels, peak = 82), gca=81.5 gca peak = 0.08005 (78) mri peak = 0.09137 (85) Brain_Stem (16): linear fit = 1.11 x + 0.0 (13179 voxels, overlap=0.492) Brain_Stem (16): linear fit = 1.11 x + 0.0 (13179 voxels, peak = 86), gca=86.2 gca peak = 0.12854 (88) mri peak = 0.10998 (97) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1361 voxels, overlap=0.336) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1361 voxels, peak = 96), gca=96.4 gca peak = 0.15703 (87) mri peak = 0.08087 (94) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1369 voxels, overlap=0.650) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1369 voxels, peak = 94), gca=94.4 gca peak = 0.17522 (25) mri peak = 0.18655 (10) Third_Ventricle (14): linear fit = 0.44 x + 0.0 (148 voxels, overlap=0.041) Third_Ventricle (14): linear fit = 0.44 x + 0.0 (148 voxels, peak = 11), gca=10.9 gca peak = 0.17113 (14) mri peak = 0.19669 (10) Fourth_Ventricle (15): linear fit = 0.65 x + 0.0 (221 voxels, overlap=0.505) Fourth_Ventricle (15): linear fit = 0.65 x + 0.0 (221 voxels, peak = 9), gca=9.2 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 1.08 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 Left_Pallidum too bright - rescaling by 1.006 (from 1.055) to 102.9 (was 102.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31706 ( 7) mri peak = 0.15118 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (2817 voxels, overlap=0.964) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (2817 voxels, peak = 6), gca=6.1 gca peak = 0.29334 ( 5) mri peak = 0.18568 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (2425 voxels, overlap=0.867) Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (2425 voxels, peak = 6), gca=5.5 gca peak = 0.20926 (101) mri peak = 0.20849 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (738 voxels, overlap=0.947) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (738 voxels, peak = 101), gca=101.0 gca peak = 0.14451 (103) mri peak = 0.19687 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (659 voxels, overlap=0.998) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (659 voxels, peak = 102), gca=102.5 gca peak = 0.23921 (57) mri peak = 0.15996 (61) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1007 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1007 voxels, peak = 58), gca=58.4 gca peak = 0.26942 (61) mri peak = 0.10769 (62) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (979 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (979 voxels, peak = 58), gca=58.3 gca peak = 0.07891 (105) mri peak = 0.12300 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46254 voxels, overlap=0.722) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46254 voxels, peak = 105), gca=105.0 gca peak = 0.07733 (107) mri peak = 0.12142 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43128 voxels, overlap=0.729) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43128 voxels, peak = 107), gca=107.0 gca peak = 0.09365 (59) mri peak = 0.04950 (55) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (27777 voxels, overlap=0.987) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (27777 voxels, peak = 58), gca=58.1 gca peak = 0.11145 (60) mri peak = 0.04016 (51) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (24314 voxels, overlap=0.966) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (24314 voxels, peak = 58), gca=57.9 gca peak = 0.26381 (72) mri peak = 0.22095 (75) Right_Caudate (50): linear fit = 1.00 x + 0.0 (761 voxels, overlap=0.757) Right_Caudate (50): linear fit = 1.00 x + 0.0 (761 voxels, peak = 72), gca=72.0 gca peak = 0.12644 (80) mri peak = 0.11205 (77) Left_Caudate (11): linear fit = 0.95 x + 0.0 (741 voxels, overlap=0.781) Left_Caudate (11): linear fit = 0.95 x + 0.0 (741 voxels, peak = 76), gca=76.4 gca peak = 0.13198 (58) mri peak = 0.05536 (60) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (20663 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (20663 voxels, peak = 56), gca=56.0 gca peak = 0.14392 (59) mri peak = 0.05551 (59) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22834 voxels, overlap=0.992) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22834 voxels, peak = 60), gca=60.5 gca peak = 0.15248 (90) mri peak = 0.15089 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7194 voxels, overlap=0.881) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7194 voxels, peak = 90), gca=89.6 gca peak = 0.14431 (93) mri peak = 0.11442 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6351 voxels, overlap=0.917) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6351 voxels, peak = 93), gca=92.5 gca peak = 0.22753 (67) mri peak = 0.11553 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (567 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (567 voxels, peak = 67), gca=67.0 gca peak = 0.24956 (66) mri peak = 0.13334 (66) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (699 voxels, overlap=0.842) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (699 voxels, peak = 67), gca=67.0 gca peak = 0.11322 (90) mri peak = 0.08323 (87) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4517 voxels, overlap=0.944) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4517 voxels, peak = 89), gca=88.7 gca peak = 0.10890 (87) mri peak = 0.08885 (90) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (4405 voxels, overlap=0.950) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (4405 voxels, peak = 86), gca=85.7 gca peak = 0.08550 (83) mri peak = 0.08013 (82) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2184 voxels, overlap=0.780) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2184 voxels, peak = 83), gca=83.0 gca peak = 0.11252 (79) mri peak = 0.08747 (81) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2260 voxels, overlap=0.901) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2260 voxels, peak = 78), gca=77.8 gca peak = 0.07920 (90) mri peak = 0.09137 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13179 voxels, overlap=0.767) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13179 voxels, peak = 90), gca=90.0 gca peak = 0.11002 (94) mri peak = 0.10998 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1361 voxels, overlap=0.786) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1361 voxels, peak = 94), gca=94.0 gca peak = 0.15666 (93) mri peak = 0.08087 (94) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1369 voxels, overlap=0.934) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1369 voxels, peak = 93), gca=93.0 gca peak = 0.32031 (10) mri peak = 0.18655 (10) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (148 voxels, overlap=0.996) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (148 voxels, peak = 10), gca=10.4 gca peak = 0.46125 ( 6) mri peak = 0.19669 (10) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (221 voxels, overlap=0.416) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (221 voxels, peak = 9), gca=9.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.15289 (30) gca peak Fourth_Ventricle = 0.46125 ( 6) gca peak CSF = 0.27810 (15) gca peak Left_Accumbens_area = 0.65402 (66) 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 = 0.30459 (24) gca peak Right_Accumbens_area = 0.30509 (70) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.92085 (13) gca peak WM_hypointensities = 0.10556 (78) gca peak non_WM_hypointensities = 0.08220 (42) gca peak Optic_Chiasm = 0.52441 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Left_Pallidum too bright - rescaling by 1.003 (from 0.995) to 102.8 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 67244 voxels changed in iteration 0 of unlikely voxel relabeling 333 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 35233 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 382 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 70952 changed. image ll: -2.142, PF=0.500 pass 2: 21396 changed. image ll: -2.142, PF=0.500 pass 3: 6608 changed. pass 4: 2445 changed. 44879 voxels changed in iteration 0 of unlikely voxel relabeling 210 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7749 voxels changed in iteration 0 of unlikely voxel relabeling 64 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7552 voxels changed in iteration 0 of unlikely voxel relabeling 92 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6077 voxels changed in iteration 0 of unlikely voxel relabeling 23 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 9345 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 8724 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 4 with volume 177 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1717.696627 mri_ca_label stimesec 3.503919 mri_ca_label ru_maxrss 2120436 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1129302 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 704 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 0 mri_ca_label ru_nivcsw 5259 auto-labeling took 28 minutes and 41 seconds. @#@FSTIME 2021:05:08:16:23:26 mri_ca_label N 10 e 1721.29 S 3.55 U 1717.69 P 99% M 2120436 F 0 R 1129303 W 0 c 5259 w 1 I 0 O 704 L 1.49 1.51 1.57 @#@FSLOADPOST 2021:05:08:16:52:07 mri_ca_label N 10 1.44 1.49 1.51 #-------------------------------------- #@# CC Seg 2021��� 05��� 08��� ��������� 16:52:07 CST mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/transforms/cc_up.lta pd_struc_recon will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/transforms/cc_up.lta reading aseg from /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/aseg.auto_noCCseg.mgz reading norm from /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/norm.mgz 26206 voxels in left wm, 22496 in right wm, xrange [124, 131] searching rotation angles z=[-3 11], y=[-8 6] 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 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.6 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.1 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.6 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.1 global minimum found at slice 127.0, rotations (-0.86, 4.38) final transformation (x=127.0, yr=-0.865, zr=4.382): 0.99696 -0.07641 -0.01505 11.93425; 0.07641 0.99708 -0.00115 3.76770; 0.01509 0.00000 0.99989 9.09635; 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 = 138 min_x_fornix = 142 min_x_fornix = 152 min_x_fornix = 134 min_x_fornix = 134 cc center is found at 128 115 117 eigenvectors: 0.00077 0.00240 1.00000; -0.04614 -0.99893 0.00243; 0.99893 -0.04615 -0.00066; writing aseg with callosum to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #VMPC# mri_cc VmPeak 454488 mri_cc done @#@FSTIME 2021:05:08:16:52:07 mri_cc N 7 e 23.17 S 0.21 U 22.96 P 99% M 343892 F 1 R 277785 W 0 c 53 w 2 I 256 O 688 L 1.44 1.49 1.51 @#@FSLOADPOST 2021:05:08:16:52:30 mri_cc N 7 1.60 1.53 1.52 #-------------------------------------- #@# Merge ASeg 2021��� 05��� 08��� ��������� 16:52:30 CST cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 2021��� 05��� 08��� ��������� 16:52:30 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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... 1597 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 110 gm peak at 65 (65), valley at 35 (35) csf peak at 18, setting threshold to 49 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 65 (65), valley at 35 (35) csf peak at 19, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 55 seconds. @#@FSTIME 2021:05:08:16:52:30 mri_normalize N 9 e 117.00 S 0.60 U 116.40 P 99% M 1204644 F 0 R 633557 W 0 c 282 w 1 I 0 O 2632 L 1.60 1.53 1.52 @#@FSLOADPOST 2021:05:08:16:54:27 mri_normalize N 9 1.38 1.45 1.49 #-------------------------------------------- #@# Mask BFS 2021��� 05��� 08��� ��������� 16:54:27 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1632101 voxels in mask (pct= 9.73) MRImask(): AllowDiffGeom = 1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2021:05:08:16:54:27 mri_mask N 5 e 1.15 S 0.02 U 1.12 P 99% M 74216 F 5 R 17267 W 0 c 3 w 6 I 1072 O 2592 L 1.38 1.45 1.49 @#@FSLOADPOST 2021:05:08:16:54:28 mri_mask N 5 1.38 1.45 1.49 #-------------------------------------------- #@# WM Segmentation 2021��� 05��� 08��� ��������� 16:54:28 CST AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2021:05:08:16:54:28 AntsDenoiseImageFs N 4 e 30.55 S 0.06 U 30.48 P 99% M 350816 F 17 R 86512 W 0 c 64 w 19 I 4192 O 2688 L 1.38 1.45 1.49 @#@FSLOADPOST 2021:05:08:16:54:59 AntsDenoiseImageFs N 4 1.31 1.42 1.48 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): 103.5 +- 5.1 [79.0 --> 125.0] CCS GM (72.0) : 70.3 +- 10.8 [30.0 --> 95.0] white_mean 103.499 white_sigma 5.09497 gray_mean 70.2554 gray_sigma 10.79 setting bottom of white matter range wm_low to 81.0 setting top of gray matter range gray_hi to 91.8 wm_low 81.0454 wm_hi 125 gray_low 30 gray_hi 91.8355 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 81.0454 wm_hi 125 gray_low 30 gray_hi 91.8355 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 91.8355, wm_low = 81.0454 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.8355, wmlow=81.0454 124027 voxels processed (0.74%) 58788 voxels white (0.35%) 65239 voxels non-white (0.39%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=76.0454, gray_hi=91.8355, wsize=13 207308 voxels tested (1.24%) 47044 voxels changed (0.28%) 47331 multi-scale searches (0.28%) Recovering bright white MRIrecoverBrightWhite() wm_low 81.0454 wm_hi 125 slack 5.09497 pct_thresh 0.33 intensity_thresh 130.095 nvox_thresh 8.58 137 voxels tested (0.00%) 103 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=76.0454, hithr=91.8355 smoothing input volume with sigma = 0.250 85122 voxels tested (0.51%) 15764 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 2496 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1331 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4538 filled MRIfindBrightNonWM(): 210 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 0.8 minutes writing output to wm.seg.mgz... @#@FSTIME 2021:05:08:16:54:59 mri_segment N 5 e 48.70 S 0.14 U 48.55 P 99% M 144432 F 4 R 299800 W 0 c 133 w 5 I 1008 O 840 L 1.31 1.42 1.48 @#@FSLOADPOST 2021:05:08:16:55:48 mri_segment N 5 1.31 1.40 1.47 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 0.38 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2421 additional wm voxels added 0 additional wm voxels added SEG EDIT: 48635 voxels turned on, 44473 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 2021:05:08:16:55:48 mri_edit_wm_with_aseg N 5 e 22.53 S 0.23 U 22.30 P 99% M 477172 F 4 R 318404 W 0 c 57 w 5 I 1336 O 776 L 1.31 1.40 1.47 @#@FSLOADPOST 2021:05:08:16:56:10 mri_edit_wm_with_aseg N 5 1.22 1.38 1.46 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 25 found - 25 modified | TOTAL: 25 pass 2 (xy+): 0 found - 25 modified | TOTAL: 25 pass 1 (xy-): 13 found - 13 modified | TOTAL: 38 pass 2 (xy-): 0 found - 13 modified | TOTAL: 38 pass 1 (yz+): 16 found - 16 modified | TOTAL: 54 pass 2 (yz+): 0 found - 16 modified | TOTAL: 54 pass 1 (yz-): 17 found - 17 modified | TOTAL: 71 pass 2 (yz-): 0 found - 17 modified | TOTAL: 71 pass 1 (xz+): 11 found - 11 modified | TOTAL: 82 pass 2 (xz+): 0 found - 11 modified | TOTAL: 82 pass 1 (xz-): 16 found - 16 modified | TOTAL: 98 pass 2 (xz-): 0 found - 16 modified | TOTAL: 98 Iteration Number : 1 pass 1 (+++): 11 found - 11 modified | TOTAL: 11 pass 2 (+++): 0 found - 11 modified | TOTAL: 11 pass 1 (+++): 4 found - 4 modified | TOTAL: 15 pass 2 (+++): 0 found - 4 modified | TOTAL: 15 pass 1 (+++): 8 found - 8 modified | TOTAL: 23 pass 2 (+++): 0 found - 8 modified | TOTAL: 23 pass 1 (+++): 6 found - 6 modified | TOTAL: 29 pass 2 (+++): 0 found - 6 modified | TOTAL: 29 Iteration Number : 1 pass 1 (++): 59 found - 59 modified | TOTAL: 59 pass 2 (++): 0 found - 59 modified | TOTAL: 59 pass 1 (+-): 43 found - 43 modified | TOTAL: 102 pass 2 (+-): 0 found - 43 modified | TOTAL: 102 pass 1 (--): 119 found - 119 modified | TOTAL: 221 pass 2 (--): 0 found - 119 modified | TOTAL: 221 pass 1 (-+): 56 found - 56 modified | TOTAL: 277 pass 2 (-+): 0 found - 56 modified | TOTAL: 277 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 3 found - 3 modified | TOTAL: 5 pass 2 (yz+): 0 found - 3 modified | TOTAL: 5 pass 1 (yz-): 3 found - 3 modified | TOTAL: 8 pass 2 (yz-): 0 found - 3 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 2 found - 2 modified | TOTAL: 13 pass 2 (xz-): 0 found - 2 modified | TOTAL: 13 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 3 found - 3 modified | TOTAL: 6 pass 2 (--): 0 found - 3 modified | TOTAL: 6 pass 1 (-+): 2 found - 2 modified | TOTAL: 8 pass 2 (-+): 0 found - 2 modified | TOTAL: 8 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 426 (out of 586892: 0.072586) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2021:05:08:16:56:10 mri_pretess N 4 e 2.74 S 0.01 U 2.73 P 99% M 56892 F 17 R 12977 W 0 c 6 w 19 I 4112 O 776 L 1.22 1.38 1.46 @#@FSLOADPOST 2021:05:08:16:56:13 mri_pretess N 4 1.20 1.37 1.46 #-------------------------------------------- #@# Fill 2021��� 05��� 08��� ��������� 16:56:13 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82954; -0.01059 -0.16632 1.05653 2.81153; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.95772 -0.09131 -0.00545 15.77490; 0.08186 1.14275 0.21385 -59.82954; -0.01059 -0.16632 1.05653 2.81153; 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] = 1409 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) need search nearby using seed (126, 110, 93), TAL = (2.0, -35.0, 18.0) talairach voxel to voxel transform 1.03708 0.08125 -0.01110 -11.46741; -0.07405 0.84424 -0.17126 52.15987; -0.00126 0.13372 0.91942 5.43512; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 110, 93) --> (2.0, -35.0, 18.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, -35.00, 18.00) Erasing brainstem...done. MRImask(): AllowDiffGeom = 1 seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -35.00, 18.00) SRC: (108.44, 121.10, 105.51) search lh wm seed point around talairach space (-16.00, -35.00, 18.00), SRC: (145.78, 118.44, 105.47) 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 2021:05:08:16:56:13 mri_fill N 8 e 56.51 S 0.53 U 55.98 P 99% M 980848 F 5 R 516923 W 0 c 135 w 6 I 1160 O 256 L 1.20 1.37 1.46 @#@FSLOADPOST 2021:05:08:16:57:10 mri_fill N 8 1.23 1.35 1.45 #-------------------------------------------- #@# Tessellate lh 2021��� 05��� 08��� ��������� 16:57:10 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 6 found - 6 modified | TOTAL: 9 pass 2 (yz+): 0 found - 6 modified | TOTAL: 9 pass 1 (yz-): 4 found - 4 modified | TOTAL: 13 pass 2 (yz-): 0 found - 4 modified | TOTAL: 13 pass 1 (xz+): 0 found - 0 modified | TOTAL: 13 pass 1 (xz-): 2 found - 2 modified | TOTAL: 15 pass 2 (xz-): 0 found - 2 modified | TOTAL: 15 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 16 (out of 281857: 0.005677) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2021:05:08:16:57:10 mri_pretess N 4 e 1.44 S 0.01 U 1.42 P 100% M 40464 F 0 R 8828 W 0 c 2 w 1 I 0 O 248 L 1.23 1.35 1.45 @#@FSLOADPOST 2021:05:08:16:57:11 mri_pretess N 4 1.23 1.35 1.45 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.1.1 7.1.1 slice 50: 313 vertices, 359 faces slice 60: 4889 vertices, 5085 faces slice 70: 13133 vertices, 13503 faces slice 80: 24764 vertices, 25174 faces slice 90: 35843 vertices, 36210 faces slice 100: 46505 vertices, 46889 faces slice 110: 57663 vertices, 58079 faces slice 120: 69113 vertices, 69497 faces slice 130: 80323 vertices, 80724 faces slice 140: 91068 vertices, 91453 faces slice 150: 101256 vertices, 101573 faces slice 160: 109758 vertices, 110080 faces slice 170: 117293 vertices, 117565 faces slice 180: 123309 vertices, 123536 faces slice 190: 128161 vertices, 128359 faces slice 200: 131691 vertices, 131770 faces slice 210: 131964 vertices, 131992 faces slice 220: 131964 vertices, 131992 faces slice 230: 131964 vertices, 131992 faces slice 240: 131964 vertices, 131992 faces slice 250: 131964 vertices, 131992 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 2021:05:08:16:57:11 mri_tessellate N 3 e 1.25 S 0.01 U 1.23 P 99% M 37404 F 3 R 8326 W 0 c 3 w 5 I 1168 O 6192 L 1.23 1.35 1.45 @#@FSLOADPOST 2021:05:08:16:57:12 mri_tessellate N 3 1.21 1.35 1.44 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 131964 voxel in cpt #1: X=-28 [v=131964,e=395976,f=263984] located at (-29.661119, -9.999894, 10.218802) For the whole surface: X=-28 [v=131964,e=395976,f=263984] One single component has been found nothing to do done @#@FSTIME 2021:05:08:16:57:12 mris_extract_main_component N 2 e 0.69 S 0.06 U 0.62 P 99% M 262464 F 14 R 69306 W 0 c 3 w 17 I 3560 O 9288 L 1.21 1.35 1.44 @#@FSLOADPOST 2021:05:08:16:57:13 mris_extract_main_component N 2 1.21 1.35 1.44 #-------------------------------------------- #@# Tessellate rh 2021��� 05��� 08��� ��������� 16:57:13 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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+): 8 found - 8 modified | TOTAL: 8 pass 2 (yz+): 0 found - 8 modified | TOTAL: 8 pass 1 (yz-): 6 found - 6 modified | TOTAL: 14 pass 2 (yz-): 0 found - 6 modified | TOTAL: 14 pass 1 (xz+): 1 found - 1 modified | TOTAL: 15 pass 2 (xz+): 0 found - 1 modified | TOTAL: 15 pass 1 (xz-): 0 found - 0 modified | TOTAL: 15 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 = 15 (out of 281566: 0.005327) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2021:05:08:16:57:13 mri_pretess N 4 e 1.38 S 0.01 U 1.36 P 99% M 40380 F 0 R 8829 W 0 c 6 w 1 I 0 O 248 L 1.21 1.35 1.44 @#@FSLOADPOST 2021:05:08:16:57:15 mri_pretess N 4 1.21 1.35 1.44 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.1.1 7.1.1 slice 50: 290 vertices, 333 faces slice 60: 4852 vertices, 5089 faces slice 70: 13282 vertices, 13653 faces slice 80: 24159 vertices, 24563 faces slice 90: 35704 vertices, 36093 faces slice 100: 46807 vertices, 47172 faces slice 110: 58365 vertices, 58759 faces slice 120: 70244 vertices, 70647 faces slice 130: 81022 vertices, 81411 faces slice 140: 91272 vertices, 91651 faces slice 150: 100914 vertices, 101247 faces slice 160: 109033 vertices, 109325 faces slice 170: 116816 vertices, 117053 faces slice 180: 122812 vertices, 123006 faces slice 190: 127564 vertices, 127742 faces slice 200: 130809 vertices, 130864 faces slice 210: 131198 vertices, 131202 faces slice 220: 131198 vertices, 131202 faces slice 230: 131198 vertices, 131202 faces slice 240: 131198 vertices, 131202 faces slice 250: 131198 vertices, 131202 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 2021:05:08:16:57:15 mri_tessellate N 3 e 1.25 S 0.01 U 1.24 P 100% M 37312 F 0 R 8305 W 0 c 5 w 1 I 0 O 6152 L 1.21 1.35 1.44 @#@FSLOADPOST 2021:05:08:16:57:16 mri_tessellate N 3 1.21 1.35 1.44 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 131198 voxel in cpt #1: X=-4 [v=131198,e=393606,f=262404] located at (31.372452, -10.406271, 6.210674) For the whole surface: X=-4 [v=131198,e=393606,f=262404] One single component has been found nothing to do done @#@FSTIME 2021:05:08:16:57:16 mris_extract_main_component N 2 e 0.75 S 0.08 U 0.66 P 99% M 261228 F 0 R 68912 W 0 c 5 w 1 I 0 O 9232 L 1.21 1.35 1.44 @#@FSLOADPOST 2021:05:08:16:57:17 mris_extract_main_component N 2 1.21 1.35 1.44 #-------------------------------------------- #@# Smooth1 lh 2021��� 05��� 08��� ��������� 16:57:17 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:16:57:17 mris_smooth N 5 e 2.13 S 0.08 U 2.05 P 99% M 209728 F 3 R 62703 W 0 c 5 w 4 I 600 O 9288 L 1.21 1.35 1.44 @#@FSLOADPOST 2021:05:08:16:57:19 mris_smooth N 5 1.20 1.34 1.44 #-------------------------------------------- #@# Smooth1 rh 2021��� 05��� 08��� ��������� 16:57:19 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:16:57:19 mris_smooth N 5 e 2.24 S 0.08 U 2.16 P 100% M 208336 F 0 R 62325 W 0 c 6 w 1 I 0 O 9232 L 1.20 1.34 1.44 @#@FSLOADPOST 2021:05:08:16:57:21 mris_smooth N 5 1.20 1.34 1.44 #-------------------------------------------- #@# Inflation1 lh 2021��� 05��� 08��� ��������� 16:57:21 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.3 mm, total surface area = 71463 mm^2 step 000: RMS=0.147 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 14.954097 mris_inflate stimesec 0.592083 mris_inflate ru_maxrss 209804 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 551913 mris_inflate ru_majflt 16 mris_inflate ru_nswap 0 mris_inflate ru_inblock 4008 mris_inflate ru_oublock 9288 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 18 mris_inflate ru_nivcsw 38 @#@FSTIME 2021:05:08:16:57:21 mris_inflate N 3 e 15.55 S 0.59 U 14.95 P 99% M 209804 F 16 R 551915 W 0 c 38 w 19 I 4008 O 9288 L 1.20 1.34 1.44 @#@FSLOADPOST 2021:05:08:16:57:37 mris_inflate N 3 1.15 1.32 1.43 #-------------------------------------------- #@# Inflation1 rh 2021��� 05��� 08��� ��������� 16:57:37 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.4 mm, total surface area = 71049 mm^2 step 000: RMS=0.145 (target=0.015) step 005: RMS=0.108 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.036 (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=0.030 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 14.921998 mris_inflate stimesec 0.631238 mris_inflate ru_maxrss 208504 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 548598 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9232 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1047 @#@FSTIME 2021:05:08:16:57:37 mris_inflate N 3 e 15.59 S 0.63 U 14.92 P 99% M 208504 F 0 R 548600 W 0 c 1047 w 1 I 0 O 9232 L 1.15 1.32 1.43 @#@FSLOADPOST 2021:05:08:16:57:52 mris_inflate N 3 1.18 1.32 1.43 #-------------------------------------------- #@# QSphere lh 2021��� 05��� 08��� ��������� 16:57:52 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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: 7.1.1 available threads: 1 scaling brain by 0.335... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.55 (0.00-->5.99) (max @ vno 98276 --> 99260) face area 0.03 +- 0.03 (-0.04-->0.60) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.702, avgs=0 005/300: dt: 0.9000, rms radial error=175.444, avgs=0 010/300: dt: 0.9000, rms radial error=174.891, avgs=0 015/300: dt: 0.9000, rms radial error=174.165, avgs=0 020/300: dt: 0.9000, rms radial error=173.338, avgs=0 025/300: dt: 0.9000, rms radial error=172.454, avgs=0 030/300: dt: 0.9000, rms radial error=171.537, avgs=0 035/300: dt: 0.9000, rms radial error=170.603, avgs=0 040/300: dt: 0.9000, rms radial error=169.662, avgs=0 045/300: dt: 0.9000, rms radial error=168.718, avgs=0 050/300: dt: 0.9000, rms radial error=167.774, avgs=0 055/300: dt: 0.9000, rms radial error=166.833, avgs=0 060/300: dt: 0.9000, rms radial error=165.896, avgs=0 065/300: dt: 0.9000, rms radial error=164.963, avgs=0 070/300: dt: 0.9000, rms radial error=164.034, avgs=0 075/300: dt: 0.9000, rms radial error=163.110, avgs=0 080/300: dt: 0.9000, rms radial error=162.190, avgs=0 085/300: dt: 0.9000, rms radial error=161.276, avgs=0 090/300: dt: 0.9000, rms radial error=160.366, avgs=0 095/300: dt: 0.9000, rms radial error=159.462, avgs=0 100/300: dt: 0.9000, rms radial error=158.562, avgs=0 105/300: dt: 0.9000, rms radial error=157.667, avgs=0 110/300: dt: 0.9000, rms radial error=156.777, avgs=0 115/300: dt: 0.9000, rms radial error=155.892, avgs=0 120/300: dt: 0.9000, rms radial error=155.012, avgs=0 125/300: dt: 0.9000, rms radial error=154.137, avgs=0 130/300: dt: 0.9000, rms radial error=153.266, avgs=0 135/300: dt: 0.9000, rms radial error=152.401, avgs=0 140/300: dt: 0.9000, rms radial error=151.540, avgs=0 145/300: dt: 0.9000, rms radial error=150.685, avgs=0 150/300: dt: 0.9000, rms radial error=149.834, avgs=0 155/300: dt: 0.9000, rms radial error=148.987, avgs=0 160/300: dt: 0.9000, rms radial error=148.146, avgs=0 165/300: dt: 0.9000, rms radial error=147.309, avgs=0 170/300: dt: 0.9000, rms radial error=146.477, avgs=0 175/300: dt: 0.9000, rms radial error=145.649, avgs=0 180/300: dt: 0.9000, rms radial error=144.826, avgs=0 185/300: dt: 0.9000, rms radial error=144.008, avgs=0 190/300: dt: 0.9000, rms radial error=143.194, avgs=0 195/300: dt: 0.9000, rms radial error=142.385, avgs=0 200/300: dt: 0.9000, rms radial error=141.580, avgs=0 205/300: dt: 0.9000, rms radial error=140.780, avgs=0 210/300: dt: 0.9000, rms radial error=139.984, avgs=0 215/300: dt: 0.9000, rms radial error=139.192, avgs=0 220/300: dt: 0.9000, rms radial error=138.406, avgs=0 225/300: dt: 0.9000, rms radial error=137.623, avgs=0 230/300: dt: 0.9000, rms radial error=136.845, avgs=0 235/300: dt: 0.9000, rms radial error=136.071, avgs=0 240/300: dt: 0.9000, rms radial error=135.302, avgs=0 245/300: dt: 0.9000, rms radial error=134.537, avgs=0 250/300: dt: 0.9000, rms radial error=133.776, avgs=0 255/300: dt: 0.9000, rms radial error=133.020, avgs=0 260/300: dt: 0.9000, rms radial error=132.268, avgs=0 265/300: dt: 0.9000, rms radial error=131.520, avgs=0 270/300: dt: 0.9000, rms radial error=130.776, avgs=0 275/300: dt: 0.9000, rms radial error=130.036, avgs=0 280/300: dt: 0.9000, rms radial error=129.301, avgs=0 285/300: dt: 0.9000, rms radial error=128.570, avgs=0 290/300: dt: 0.9000, rms radial error=127.843, avgs=0 295/300: dt: 0.9000, rms radial error=127.121, avgs=0 300/300: dt: 0.9000, rms radial error=126.402, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14928.77 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00030 epoch 2 (K=40.0), pass 1, starting sse = 2257.75 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00018 epoch 3 (K=160.0), pass 1, starting sse = 183.60 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/19 = 0.00926 epoch 4 (K=640.0), pass 1, starting sse = 6.63 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/25 = 0.00772 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0337 hours FSRUNTIME@ mris_sphere 0.0337 hours 1 threads #VMPC# mris_sphere VmPeak 497624 mris_sphere done @#@FSTIME 2021:05:08:16:57:52 mris_sphere N 9 e 121.40 S 3.59 U 117.80 P 99% M 214832 F 5 R 3691426 W 0 c 305 w 6 I 1616 O 9288 L 1.18 1.32 1.43 @#@FSLOADPOST 2021:05:08:16:59:54 mris_sphere N 9 1.61 1.43 1.46 #-------------------------------------------- #@# QSphere rh 2021��� 05��� 08��� ��������� 16:59:54 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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: 7.1.1 available threads: 1 scaling brain by 0.333... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.55 (0.00-->6.50) (max @ vno 97852 --> 97853) face area 0.03 +- 0.03 (-0.01-->0.75) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.919, avgs=0 005/300: dt: 0.9000, rms radial error=175.659, avgs=0 010/300: dt: 0.9000, rms radial error=175.103, avgs=0 015/300: dt: 0.9000, rms radial error=174.372, avgs=0 020/300: dt: 0.9000, rms radial error=173.539, avgs=0 025/300: dt: 0.9000, rms radial error=172.651, avgs=0 030/300: dt: 0.9000, rms radial error=171.732, avgs=0 035/300: dt: 0.9000, rms radial error=170.797, avgs=0 040/300: dt: 0.9000, rms radial error=169.854, avgs=0 045/300: dt: 0.9000, rms radial error=168.908, avgs=0 050/300: dt: 0.9000, rms radial error=167.963, avgs=0 055/300: dt: 0.9000, rms radial error=167.021, avgs=0 060/300: dt: 0.9000, rms radial error=166.082, avgs=0 065/300: dt: 0.9000, rms radial error=165.149, avgs=0 070/300: dt: 0.9000, rms radial error=164.223, avgs=0 075/300: dt: 0.9000, rms radial error=163.301, avgs=0 080/300: dt: 0.9000, rms radial error=162.384, avgs=0 085/300: dt: 0.9000, rms radial error=161.472, avgs=0 090/300: dt: 0.9000, rms radial error=160.564, avgs=0 095/300: dt: 0.9000, rms radial error=159.662, avgs=0 100/300: dt: 0.9000, rms radial error=158.764, avgs=0 105/300: dt: 0.9000, rms radial error=157.871, avgs=0 110/300: dt: 0.9000, rms radial error=156.984, avgs=0 115/300: dt: 0.9000, rms radial error=156.101, avgs=0 120/300: dt: 0.9000, rms radial error=155.222, avgs=0 125/300: dt: 0.9000, rms radial error=154.349, avgs=0 130/300: dt: 0.9000, rms radial error=153.480, avgs=0 135/300: dt: 0.9000, rms radial error=152.617, avgs=0 140/300: dt: 0.9000, rms radial error=151.757, avgs=0 145/300: dt: 0.9000, rms radial error=150.903, avgs=0 150/300: dt: 0.9000, rms radial error=150.053, avgs=0 155/300: dt: 0.9000, rms radial error=149.207, avgs=0 160/300: dt: 0.9000, rms radial error=148.367, avgs=0 165/300: dt: 0.9000, rms radial error=147.530, avgs=0 170/300: dt: 0.9000, rms radial error=146.699, avgs=0 175/300: dt: 0.9000, rms radial error=145.871, avgs=0 180/300: dt: 0.9000, rms radial error=145.049, avgs=0 185/300: dt: 0.9000, rms radial error=144.231, avgs=0 190/300: dt: 0.9000, rms radial error=143.417, avgs=0 195/300: dt: 0.9000, rms radial error=142.608, avgs=0 200/300: dt: 0.9000, rms radial error=141.803, avgs=0 205/300: dt: 0.9000, rms radial error=141.002, avgs=0 210/300: dt: 0.9000, rms radial error=140.206, avgs=0 215/300: dt: 0.9000, rms radial error=139.415, avgs=0 220/300: dt: 0.9000, rms radial error=138.628, avgs=0 225/300: dt: 0.9000, rms radial error=137.845, avgs=0 230/300: dt: 0.9000, rms radial error=137.067, avgs=0 235/300: dt: 0.9000, rms radial error=136.293, avgs=0 240/300: dt: 0.9000, rms radial error=135.523, avgs=0 245/300: dt: 0.9000, rms radial error=134.758, avgs=0 250/300: dt: 0.9000, rms radial error=133.997, avgs=0 255/300: dt: 0.9000, rms radial error=133.241, avgs=0 260/300: dt: 0.9000, rms radial error=132.489, avgs=0 265/300: dt: 0.9000, rms radial error=131.741, avgs=0 270/300: dt: 0.9000, rms radial error=130.998, avgs=0 275/300: dt: 0.9000, rms radial error=130.258, avgs=0 280/300: dt: 0.9000, rms radial error=129.523, avgs=0 285/300: dt: 0.9000, rms radial error=128.792, avgs=0 290/300: dt: 0.9000, rms radial error=128.065, avgs=0 295/300: dt: 0.9000, rms radial error=127.342, avgs=0 300/300: dt: 0.9000, rms radial error=126.623, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14867.86 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00032 epoch 2 (K=40.0), pass 1, starting sse = 2254.06 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 = 181.70 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.21/19 = 0.01096 epoch 4 (K=640.0), pass 1, starting sse = 5.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.28/29 = 0.00972 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0347 hours FSRUNTIME@ mris_sphere 0.0347 hours 1 threads #VMPC# mris_sphere VmPeak 496388 mris_sphere done @#@FSTIME 2021:05:08:16:59:54 mris_sphere N 9 e 124.95 S 3.84 U 121.10 P 99% M 213552 F 0 R 3808584 W 0 c 339 w 1 I 0 O 9232 L 1.61 1.43 1.46 @#@FSLOADPOST 2021:05:08:17:01:59 mris_sphere N 9 1.47 1.44 1.45 #@# Fix Topology lh 2021��� 05��� 08��� ��������� 17:01:59 CST mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 pd_struc_recon 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' 7.1.1 7.1.1 before topology correction, eno=-28 (nv=131964, nf=263984, ne=395976, g=15) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 1499 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 21 defects to be corrected 0 vertices coincident reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.3384 (-4.6692) -vertex loglikelihood: -6.4788 (-3.2394) -normal dot loglikelihood: -3.6446 (-3.6446) -quad curv loglikelihood: -6.1659 (-3.0830) Total Loglikelihood : -25.6277 CORRECTING DEFECT 0 (vertices=55, convex hull=106, v0=157) After retessellation of defect 0 (v0=157), euler #=-18 (131015,392578,261545) : difference with theory (-18) = 0 CORRECTING DEFECT 1 (vertices=21, convex hull=46, v0=2046) After retessellation of defect 1 (v0=2046), euler #=-17 (131023,392621,261581) : difference with theory (-17) = 0 CORRECTING DEFECT 2 (vertices=30, convex hull=62, v0=4475) After retessellation of defect 2 (v0=4475), euler #=-16 (131038,392691,261637) : difference with theory (-16) = 0 CORRECTING DEFECT 3 (vertices=96, convex hull=89, v0=14017) After retessellation of defect 3 (v0=14017), euler #=-15 (131066,392814,261733) : difference with theory (-15) = 0 CORRECTING DEFECT 4 (vertices=32, convex hull=76, v0=15352) After retessellation of defect 4 (v0=15352), euler #=-14 (131078,392876,261784) : difference with theory (-14) = 0 CORRECTING DEFECT 5 (vertices=36, convex hull=62, v0=28891) After retessellation of defect 5 (v0=28891), euler #=-13 (131098,392957,261846) : difference with theory (-13) = 0 CORRECTING DEFECT 6 (vertices=48, convex hull=91, v0=33109) After retessellation of defect 6 (v0=33109), euler #=-12 (131133,393102,261957) : difference with theory (-12) = 0 CORRECTING DEFECT 7 (vertices=50, convex hull=82, v0=38517) After retessellation of defect 7 (v0=38517), euler #=-11 (131159,393217,262047) : difference with theory (-11) = 0 CORRECTING DEFECT 8 (vertices=62, convex hull=80, v0=43194) After retessellation of defect 8 (v0=43194), euler #=-10 (131188,393337,262139) : difference with theory (-10) = 0 CORRECTING DEFECT 9 (vertices=43, convex hull=65, v0=47781) After retessellation of defect 9 (v0=47781), euler #=-9 (131203,393406,262194) : difference with theory (-9) = 0 CORRECTING DEFECT 10 (vertices=8, convex hull=24, v0=55908) After retessellation of defect 10 (v0=55908), euler #=-8 (131204,393415,262203) : difference with theory (-8) = 0 CORRECTING DEFECT 11 (vertices=26, convex hull=22, v0=66927) After retessellation of defect 11 (v0=66927), euler #=-7 (131207,393431,262217) : difference with theory (-7) = 0 CORRECTING DEFECT 12 (vertices=27, convex hull=35, v0=69897) After retessellation of defect 12 (v0=69897), euler #=-6 (131211,393453,262236) : difference with theory (-6) = 0 CORRECTING DEFECT 13 (vertices=28, convex hull=20, v0=72713) After retessellation of defect 13 (v0=72713), euler #=-5 (131213,393466,262248) : difference with theory (-5) = 0 CORRECTING DEFECT 14 (vertices=97, convex hull=31, v0=76533) After retessellation of defect 14 (v0=76533), euler #=-4 (131219,393494,262271) : difference with theory (-4) = 0 CORRECTING DEFECT 15 (vertices=51, convex hull=80, v0=81412) After retessellation of defect 15 (v0=81412), euler #=-3 (131254,393636,262379) : difference with theory (-3) = 0 CORRECTING DEFECT 16 (vertices=31, convex hull=79, v0=87536) After retessellation of defect 16 (v0=87536), euler #=-2 (131270,393715,262443) : difference with theory (-2) = 0 CORRECTING DEFECT 17 (vertices=47, convex hull=51, v0=92986) After retessellation of defect 17 (v0=92986), euler #=-1 (131275,393753,262477) : difference with theory (-1) = 0 CORRECTING DEFECT 18 (vertices=126, convex hull=60, v0=96113) After retessellation of defect 18 (v0=96113), euler #=0 (131299,393856,262557) : difference with theory (0) = 0 CORRECTING DEFECT 19 (vertices=28, convex hull=26, v0=98428) After retessellation of defect 19 (v0=98428), euler #=1 (131303,393878,262576) : difference with theory (1) = 0 CORRECTING DEFECT 20 (vertices=32, convex hull=61, v0=105573) After retessellation of defect 20 (v0=105573), euler #=2 (131323,393963,262642) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.10-->6.06) (max @ vno 12781 --> 19527) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.10-->6.06) (max @ vno 12781 --> 19527) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 77 mutations (35.8%), 138 crossovers (64.2%), 41 vertices were eliminated building final representation... 641 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=131323, nf=262642, ne=393963, g=0) writing corrected surface to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 127 intersecting 001: 3 intersecting terminating search with 0 intersecting topology fixing took 0.9 minutes FSRUNTIME@ mris_fix_topology lh 0.0146 hours 1 threads #VMPC# mris_fix_topology VmPeak 778348 @#@FSTIME 2021:05:08:17:01:59 mris_fix_topology N 14 e 52.56 S 0.22 U 52.34 P 99% M 730136 F 5 R 217184 W 0 c 150 w 6 I 1528 O 12336 L 1.47 1.44 1.45 @#@FSLOADPOST 2021:05:08:17:02:51 mris_fix_topology N 14 1.44 1.43 1.45 #@# Fix Topology rh 2021��� 05��� 08��� ��������� 17:02:51 CST mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 pd_struc_recon 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' 7.1.1 7.1.1 before topology correction, eno=-4 (nv=131198, nf=262404, ne=393606, g=3) 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 13 iterations marking ambiguous vertices... 833 ambiguous faces found in tessellation segmenting defects... 14 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 11 13 defects to be corrected 0 vertices coincident reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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: -9.4441 (-4.7220) -vertex loglikelihood: -6.5821 (-3.2911) -normal dot loglikelihood: -3.6457 (-3.6457) -quad curv loglikelihood: -6.2277 (-3.1138) Total Loglikelihood : -25.8996 CORRECTING DEFECT 0 (vertices=41, convex hull=69, v0=1199) After retessellation of defect 0 (v0=1199), euler #=-11 (130703,391949,261235) : difference with theory (-10) = 1 CORRECTING DEFECT 1 (vertices=28, convex hull=49, v0=10982) After retessellation of defect 1 (v0=10982), euler #=-10 (130713,391998,261275) : difference with theory (-9) = 1 CORRECTING DEFECT 2 (vertices=8, convex hull=24, v0=49820) After retessellation of defect 2 (v0=49820), euler #=-9 (130716,392014,261289) : difference with theory (-8) = 1 CORRECTING DEFECT 3 (vertices=50, convex hull=38, v0=55358) After retessellation of defect 3 (v0=55358), euler #=-8 (130725,392055,261322) : difference with theory (-7) = 1 CORRECTING DEFECT 4 (vertices=57, convex hull=33, v0=57350) After retessellation of defect 4 (v0=57350), euler #=-7 (130731,392084,261346) : difference with theory (-6) = 1 CORRECTING DEFECT 5 (vertices=14, convex hull=34, v0=61897) After retessellation of defect 5 (v0=61897), euler #=-6 (130731,392095,261358) : difference with theory (-5) = 1 CORRECTING DEFECT 6 (vertices=66, convex hull=24, v0=72664) After retessellation of defect 6 (v0=72664), euler #=-5 (130734,392114,261375) : difference with theory (-4) = 1 CORRECTING DEFECT 7 (vertices=13, convex hull=16, v0=74489) After retessellation of defect 7 (v0=74489), euler #=-4 (130736,392125,261385) : difference with theory (-3) = 1 CORRECTING DEFECT 8 (vertices=52, convex hull=24, v0=75287) After retessellation of defect 8 (v0=75287), euler #=-3 (130741,392148,261404) : difference with theory (-2) = 1 CORRECTING DEFECT 9 (vertices=24, convex hull=23, v0=85750) After retessellation of defect 9 (v0=85750), euler #=-2 (130746,392169,261421) : difference with theory (-1) = 1 CORRECTING DEFECT 10 (vertices=122, convex hull=61, v0=87991) After retessellation of defect 10 (v0=87991), euler #=-1 (130759,392232,261472) : difference with theory (0) = 1 CORRECTING DEFECT 11 (vertices=13, convex hull=40, v0=98791) After retessellation of defect 11 (v0=98791), euler #=1 (130759,392248,261490) : difference with theory (1) = 0 CORRECTING DEFECT 12 (vertices=27, convex hull=62, v0=120769) After retessellation of defect 12 (v0=120769), euler #=2 (130772,392310,261540) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.11-->5.62) (max @ vno 1205 --> 1613) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.11-->5.62) (max @ vno 1205 --> 1613) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 50 mutations (38.2%), 81 crossovers (61.8%), 8 vertices were eliminated building final representation... 426 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=130772, nf=261540, ne=392310, g=0) writing corrected surface to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 34 intersecting terminating search with 0 intersecting topology fixing took 0.4 minutes FSRUNTIME@ mris_fix_topology rh 0.0062 hours 1 threads #VMPC# mris_fix_topology VmPeak 777504 @#@FSTIME 2021:05:08:17:02:51 mris_fix_topology N 14 e 22.49 S 0.23 U 22.25 P 99% M 729288 F 0 R 216977 W 0 c 52 w 2 I 0 O 12296 L 1.44 1.43 1.45 @#@FSLOADPOST 2021:05:08:17:03:14 mris_fix_topology N 14 1.55 1.46 1.46 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 131323 - 393963 + 262642 = 2 --> 0 holes F =2V-4: 262642 = 262646-4 (0) 2E=3F: 787926 = 787926 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 130772 - 392310 + 261540 = 2 --> 0 holes F =2V-4: 261540 = 261544-4 (0) 2E=3F: 784620 = 784620 (0) total defect index = 0 2021��� 05��� 08��� ��������� 17:03:15 CST setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts /usr/local/freesurfer/bin/defect2seg --s pd_struc_recon freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 defect2seg 7.1.1 Linux yelab-Precision-5820-Tower 5.4.0-72-generic #80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux pid 13037 mri_label2vol --defects /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.orig.nofix /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.defect_labels /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz 1000 0 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/surface.defects.mgz mris_defects_pointset -s /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.orig.nofix -d /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.defect_labels -o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.defects.pointset Reading in surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.orig.nofix Reading in defect segmentation /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.defect_labels #VMPC# mris_defects_pointset 188072 mris_defects_pointset done mri_label2vol --defects /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.orig.nofix /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.defect_labels /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/surface.defects.mgz 2000 1 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 Writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/surface.defects.mgz mris_defects_pointset -s /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.orig.nofix -d /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.defect_labels -o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.defects.pointset Reading in surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.orig.nofix Reading in defect segmentation /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.defect_labels #VMPC# mris_defects_pointset 187176 mris_defects_pointset done Started at 2021��� 05��� 08��� ��������� 17:03:15 CST Ended at 2021��� 05��� 08��� ��������� 17:03:19 CST Defect2seg-Run-Time-Sec 4 Defect2seg-Run-Time-Min 0.08 Defect2seg-Run-Time-Hours 0.00 tkmeditfv pd_struc_recon brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2021:05:08:17:03:15 defect2seg N 2 e 4.00 S 0.25 U 3.76 P 100% M 240252 F 26 R 217434 W 0 c 19 w 212 I 5648 O 368 L 1.55 1.46 1.46 @#@FSLOADPOST 2021:05:08:17:03:19 defect2seg N 2 1.51 1.45 1.46 mris_remesh --remesh --iters 3 --input /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.orig.premesh --output /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.709663 remeshing to edge length 0.709663 with 3 iterations avg qual before : 0.890734 after: 0.971063 Removing intersections Remeshed surface quality stats nv0 = 131323 nv = 136905 1.04251 Area 273806 0.30194 0.03374 0.076903 0.4564 Corner 821418 60.00000 8.82287 16.518915 145.2904 Edge 410709 0.84303 0.08243 0.373277 1.2754 Hinge 410709 9.39876 9.96102 0.000004 124.8747 mris_remesh done @#@FSTIME 2021:05:08:17:03:19 mris_remesh N 7 e 27.11 S 0.28 U 26.80 P 99% M 723400 F 17 R 275923 W 0 c 679 w 19 I 3864 O 9632 L 1.51 1.45 1.46 @#@FSLOADPOST 2021:05:08:17:03:46 mris_remesh N 7 1.69 1.50 1.47 mris_remesh --remesh --iters 3 --input /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.orig.premesh --output /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.709284 remeshing to edge length 0.709284 with 3 iterations avg qual before : 0.891754 after: 0.97158 Removing intersections Remeshed surface quality stats nv0 = 130772 nv = 136622 1.04473 Area 273240 0.30166 0.03329 0.084436 0.4527 Corner 819720 60.00000 8.73466 18.107056 142.3130 Edge 409860 0.84251 0.08166 0.468812 1.2547 Hinge 409860 9.44716 9.90209 0.000004 123.7106 mris_remesh done @#@FSTIME 2021:05:08:17:03:46 mris_remesh N 7 e 27.31 S 0.21 U 27.09 P 99% M 721896 F 0 R 284235 W 0 c 88 w 1 I 0 O 9608 L 1.69 1.50 1.47 @#@FSLOADPOST 2021:05:08:17:04:13 mris_remesh N 7 1.56 1.48 1.47 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2021:05:08:17:04:13 mris_remove_intersection N 2 e 2.17 S 0.08 U 2.08 P 99% M 335696 F 17 R 88735 W 0 c 7 w 19 I 3608 O 9632 L 1.56 1.48 1.47 @#@FSLOADPOST 2021:05:08:17:04:16 mris_remove_intersection N 2 1.56 1.48 1.47 rm ../surf/lh.inflated rm: cannot remove '../surf/lh.inflated': No such file or directory /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2021:05:08:17:04:16 mris_remove_intersection N 2 e 2.16 S 0.10 U 2.06 P 100% M 334712 F 0 R 88556 W 0 c 6 w 1 I 0 O 9616 L 1.56 1.48 1.47 @#@FSLOADPOST 2021:05:08:17:04:18 mris_remove_intersection N 2 1.51 1.47 1.46 rm ../surf/rh.inflated rm: cannot remove '../surf/rh.inflated': No such file or directory #-------------------------------------------- #@# AutoDetGWStats lh 2021��� 05��� 08��� ��������� 17:04:18 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 247209 voxels (1.47%) border gray 280144 voxels (1.67%) 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=20407, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 98.7 +- 8.4 [70.0 --> 110.0] CCS GM (71.0) : 70.9 +- 11.4 [30.0 --> 110.0] white_mean = 98.7443 +/- 8.35536, gray_mean = 70.8835 +/- 11.3761 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=210 nbins=211 intensity peaks found at WM=103+-6.1, GM=65+-9.6 white_mode = 103, gray_mode = 65 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 53.6 (was 70.000000) setting MAX_BORDER_WHITE to 111.4 (was 105.000000) setting MIN_BORDER_WHITE to 65.0 (was 85.000000) setting MAX_CSF to 42.2 (was 40.000000) setting MAX_GRAY to 94.6 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 30.9 (was 40.000000) When placing the white surface white_border_hi = 111.355; white_border_low = 65; white_outside_low = 53.6239; white_inside_hi = 120; white_outside_hi = 111.355; When placing the pial surface pial_border_hi = 53.6239; pial_border_low = 30.8717; pial_outside_low = 10; pial_inside_hi = 94.6446; pial_outside_hi = 47.9359; #VMPC# mris_autodet_gwstats VmPeak 271988 mris_autodet_gwstats done @#@FSTIME 2021:05:08:17:04:18 mris_autodet_gwstats N 8 e 3.30 S 0.06 U 3.22 P 99% M 235916 F 17 R 66547 W 0 c 9 w 19 I 4152 O 8 L 1.51 1.47 1.46 @#@FSLOADPOST 2021:05:08:17:04:21 mris_autodet_gwstats N 8 1.51 1.47 1.46 #-------------------------------------------- #@# AutoDetGWStats rh 2021��� 05��� 08��� ��������� 17:04:21 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 247209 voxels (1.47%) border gray 280144 voxels (1.67%) 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=20407, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 98.7 +- 8.4 [70.0 --> 110.0] CCS GM (71.0) : 70.9 +- 11.4 [30.0 --> 110.0] white_mean = 98.7443 +/- 8.35536, gray_mean = 70.8835 +/- 11.3761 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=210 nbins=211 intensity peaks found at WM=103+-6.1, GM=66+-8.7 white_mode = 103, gray_mode = 66 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 54.6 (was 70.000000) setting MAX_BORDER_WHITE to 111.4 (was 105.000000) setting MIN_BORDER_WHITE to 66.0 (was 85.000000) setting MAX_CSF to 43.2 (was 40.000000) setting MAX_GRAY to 94.6 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 31.9 (was 40.000000) When placing the white surface white_border_hi = 111.355; white_border_low = 66; white_outside_low = 54.6239; white_inside_hi = 120; white_outside_hi = 111.355; When placing the pial surface pial_border_hi = 54.6239; pial_border_low = 31.8717; pial_outside_low = 10; pial_inside_hi = 94.6446; pial_outside_hi = 48.9359; #VMPC# mris_autodet_gwstats VmPeak 271504 mris_autodet_gwstats done @#@FSTIME 2021:05:08:17:04:21 mris_autodet_gwstats N 8 e 3.31 S 0.07 U 3.24 P 99% M 235656 F 0 R 66412 W 0 c 7 w 1 I 0 O 8 L 1.51 1.47 1.46 @#@FSLOADPOST 2021:05:08:17:04:24 mris_autodet_gwstats N 8 1.47 1.47 1.46 #-------------------------------------------- #@# WhitePreAparc lh 2021��� 05��� 08��� ��������� 17:04:25 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 7.1.1 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 273806 0.26797 0.06293 0.001690 0.5698 Corner 821418 60.00000 9.45039 5.346832 142.2741 Edge 410709 0.79034 0.11403 0.036935 1.3551 Hinge 410709 6.30859 6.40610 0.000016 146.6030 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=20407, wmmin=5, clip=110 MRIfindBrightNonWM(): 727 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 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6588, nmarked2=39, nripped=6588 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68453: xyz = (-5.11729,1.89373,55.875) oxyz = (-5.11729,1.89373,55.875) wxzy = (-5.11729,1.89373,55.875) pxyz = (0,0,0) CBVO Creating mask 136905 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=6588 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6588, nmarked2=39, nripped=6588 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=2 had to be increased for 97 vertices, nripped=6588 mean border=77.9, 93 (93) missing vertices, mean dist 0.4 [0.6 (%31.3)->0.9 (%68.7))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2017 min Finding expansion regions mean absolute distance = 0.81 +- 0.99 4567 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=yelab, 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=4024012.0, rms=12.196 001: dt: 0.5000, sse=2284283.5, rms=9.061 (25.708%) 002: dt: 0.5000, sse=1422212.0, rms=7.002 (22.717%) 003: dt: 0.5000, sse=953805.1, rms=5.570 (20.450%) 004: dt: 0.5000, sse=698839.2, rms=4.604 (17.340%) 005: dt: 0.5000, sse=566609.1, rms=4.011 (12.896%) 006: dt: 0.5000, sse=500037.6, rms=3.673 (8.414%) 007: dt: 0.5000, sse=471263.5, rms=3.511 (4.427%) 008: dt: 0.5000, sse=454793.2, rms=3.413 (2.783%) rms = 3.3782/3.4128, sse=449583.3/454793.2, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=449583.3, rms=3.378 (1.015%) 010: dt: 0.2500, sse=255446.3, rms=1.958 (42.038%) 011: dt: 0.2500, sse=223470.7, rms=1.607 (17.911%) 012: dt: 0.2500, sse=215991.0, rms=1.508 (6.189%) 013: dt: 0.2500, sse=211893.5, rms=1.450 (3.833%) rms = 1.4198/1.4501, sse=210948.8/211893.5, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=210948.8, rms=1.420 (2.089%) 015: dt: 0.1250, sse=207466.0, rms=1.366 (3.755%) rms = 1.3564/1.3665, sse=205565.4/207465.9, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=205565.4, rms=1.356 (0.739%) maximum number of reductions reached, breaking from loop positioning took 1.3 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=6588 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 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 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6741, nmarked2=43, nripped=6741 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=1 had to be increased for 92 vertices, nripped=6741 mean border=81.2, 144 (71) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.3 (%26.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1353 min Finding expansion regions mean absolute distance = 0.37 +- 0.62 3592 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=yelab, 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=873531.8, rms=5.046 017: dt: 0.5000, sse=507549.9, rms=3.377 (33.081%) rms = 3.2992/3.3768, sse=509640.1/507549.9, time step reduction 1 of 3 to 0.250 0 1 0 018: dt: 0.5000, sse=509640.1, rms=3.299 (2.297%) 019: dt: 0.2500, sse=298246.9, rms=1.846 (44.038%) 020: dt: 0.2500, sse=269483.8, rms=1.496 (18.953%) 021: dt: 0.2500, sse=257358.9, rms=1.343 (10.278%) 022: dt: 0.2500, sse=250811.2, rms=1.241 (7.579%) rms = 1.1995/1.2408, sse=248596.4/250811.2, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=248596.5, rms=1.200 (3.328%) 024: dt: 0.1250, sse=245426.5, rms=1.144 (4.628%) rms = 1.1335/1.1440, sse=244709.0/245426.5, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=244709.0, rms=1.134 (0.915%) maximum number of reductions reached, breaking from loop positioning took 0.7 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=6741 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6766, nmarked2=43, nripped=6766 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; 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=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 133 vertices, nripped=6766 mean border=83.6, 133 (63) missing vertices, mean dist -0.1 [0.3 (%71.5)->0.2 (%28.5))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0731 min Finding expansion regions mean absolute distance = 0.26 +- 0.40 2901 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=yelab, 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=500377.9, rms=3.366 026: dt: 0.5000, sse=397768.4, rms=2.707 (19.560%) rms = 2.9790/2.7074, sse=438381.4/397768.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=286638.7, rms=1.746 (35.493%) 028: dt: 0.2500, sse=247016.1, rms=1.253 (28.263%) 029: dt: 0.2500, sse=237811.0, rms=1.096 (12.498%) rms = 1.0679/1.0963, sse=236584.4/237811.0, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=236584.4, rms=1.068 (2.589%) 031: dt: 0.1250, sse=232683.6, rms=1.007 (5.744%) rms = 1.0030/1.0065, sse=231965.5/232683.6, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=231965.5, rms=1.003 (0.350%) 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=6766 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 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=6811, nmarked2=43, nripped=6811 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; 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=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 129 vertices, nripped=6811 mean border=84.4, 165 (54) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0452 min Finding expansion regions mean absolute distance = 0.22 +- 0.33 2678 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=yelab, 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=266044.1, rms=1.553 rms = 1.7243/1.5533, sse=280980.0/266044.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=231446.6, rms=1.042 (32.899%) 034: dt: 0.2500, sse=218664.5, rms=0.760 (27.037%) rms = 0.7603/0.7605, sse=218495.1/218664.5, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=218495.1, rms=0.760 (0.027%) rms = 0.7515/0.7603, sse=217905.3/218495.1, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=217905.3, rms=0.752 (1.148%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 3.47 minutes #VMPC# mris_place_surfaces VmPeak 2217516 mris_place_surface done @#@FSTIME 2021:05:08:17:04:25 mris_place_surface N 18 e 215.10 S 0.42 U 214.66 P 99% M 1942808 F 9 R 509735 W 0 c 567 w 10 I 2352 O 9632 L 1.47 1.47 1.46 @#@FSLOADPOST 2021:05:08:17:08:00 mris_place_surface N 18 1.95 1.80 1.60 #-------------------------------------------- #@# WhitePreAparc rh 2021��� 05��� 08��� ��������� 17:08:00 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 7.1.1 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 273240 0.26738 0.06223 0.001194 0.5599 Corner 819720 60.00000 9.38058 7.877788 154.3077 Edge 409860 0.78949 0.11311 0.044959 1.2786 Hinge 409860 6.31944 6.37697 0.000007 151.3075 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=20407, wmmin=5, clip=110 MRIfindBrightNonWM(): 727 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=7116, nmarked2=39, nripped=7116 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68311: xyz = (35.3648,-0.590589,-17.8888) oxyz = (35.3648,-0.590589,-17.8888) wxzy = (35.3648,-0.590589,-17.8888) pxyz = (0,0,0) CBVO Creating mask 136622 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=7116 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7116, nmarked2=39, nripped=7116 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=2 had to be increased for 40 vertices, nripped=7116 mean border=78.1, 42 (42) missing vertices, mean dist 0.3 [0.7 (%34.6)->0.9 (%65.4))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1939 min Finding expansion regions mean absolute distance = 0.81 +- 1.00 4092 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=yelab, 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=4110401.0, rms=12.365 001: dt: 0.5000, sse=2262128.5, rms=9.043 (26.873%) 002: dt: 0.5000, sse=1386988.5, rms=6.928 (23.384%) 003: dt: 0.5000, sse=930913.1, rms=5.510 (20.470%) 004: dt: 0.5000, sse=695297.2, rms=4.607 (16.382%) 005: dt: 0.5000, sse=578219.8, rms=4.083 (11.385%) 006: dt: 0.5000, sse=520630.2, rms=3.794 (7.081%) 007: dt: 0.5000, sse=497246.7, rms=3.664 (3.417%) 008: dt: 0.5000, sse=483401.7, rms=3.582 (2.225%) rms = 3.5616/3.5825, sse=481044.2/483401.7, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=481044.2, rms=3.562 (0.583%) 010: dt: 0.2500, sse=263918.4, rms=2.038 (42.773%) 011: dt: 0.2500, sse=228829.8, rms=1.638 (19.611%) 012: dt: 0.2500, sse=217532.2, rms=1.515 (7.555%) 013: dt: 0.2500, sse=211967.7, rms=1.445 (4.603%) rms = 1.4050/1.4450, sse=208394.0/211967.7, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=208394.0, rms=1.405 (2.763%) 015: dt: 0.1250, sse=202935.5, rms=1.325 (5.662%) rms = 1.3124/1.3255, sse=202311.4/202935.5, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=202311.4, rms=1.312 (0.989%) maximum number of reductions reached, breaking from loop positioning took 1.3 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=7116 removing 3 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 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7246, nmarked2=41, nripped=7246 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=1 had to be increased for 76 vertices, nripped=7246 mean border=81.2, 48 (8) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.3 (%28.4))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1268 min Finding expansion regions mean absolute distance = 0.36 +- 0.65 3412 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=yelab, 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=832114.0, rms=4.906 017: dt: 0.5000, sse=502335.3, rms=3.382 (31.068%) rms = 3.4463/3.3821, sse=512573.4/502335.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=371700.0, rms=2.533 (25.100%) 019: dt: 0.2500, sse=299308.4, rms=1.889 (25.447%) 020: dt: 0.2500, sse=270479.6, rms=1.564 (17.200%) 021: dt: 0.2500, sse=258105.7, rms=1.398 (10.592%) 022: dt: 0.2500, sse=250891.2, rms=1.285 (8.096%) 023: dt: 0.2500, sse=248156.5, rms=1.215 (5.452%) rms = 1.1724/1.2149, sse=247686.2/248156.5, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=247686.2, rms=1.172 (3.493%) rms = 1.1167/1.1724, sse=248396.8/247686.2, time step reduction 3 of 3 to 0.062 0 1 0 025: dt: 0.1250, sse=248396.8, rms=1.117 (4.750%) maximum number of reductions reached, breaking from loop positioning took 0.7 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=7246 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 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7271, nmarked2=42, nripped=7271 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; 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=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 141 vertices, nripped=7271 mean border=83.4, 74 (6) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.2 (%30.5))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0678 min Finding expansion regions mean absolute distance = 0.25 +- 0.43 2709 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=yelab, 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=471590.4, rms=3.168 026: dt: 0.5000, sse=406302.1, rms=2.778 (12.304%) rms = 3.1537/2.7784, sse=467616.8/406302.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=286234.9, rms=1.756 (36.793%) 028: dt: 0.2500, sse=249464.5, rms=1.246 (29.055%) 029: dt: 0.2500, sse=236186.3, rms=1.098 (11.871%) rms = 1.0651/1.0980, sse=233814.0/236186.3, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=233814.0, rms=1.065 (2.995%) 031: dt: 0.1250, sse=230311.0, rms=0.992 (6.820%) rms = 0.9899/0.9925, sse=230267.2/230311.0, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=230267.2, rms=0.990 (0.253%) 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=7271 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7298, nmarked2=42, nripped=7298 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; 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=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 139 vertices, nripped=7298 mean border=84.2, 101 (6) missing vertices, mean dist -0.0 [0.2 (%55.5)->0.2 (%44.5))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0426 min Finding expansion regions mean absolute distance = 0.21 +- 0.34 2448 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=yelab, 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=260995.4, rms=1.503 rms = 1.7826/1.5030, sse=288216.6/260995.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=227834.1, rms=0.988 (34.293%) 034: dt: 0.2500, sse=217379.4, rms=0.743 (24.806%) rms = 0.7556/0.7426, sse=217319.4/217379.4, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.7390/0.7426, sse=217093.7/217379.4, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=217093.7, rms=0.739 (0.491%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 3.45 minutes #VMPC# mris_place_surfaces VmPeak 2188616 mris_place_surface done @#@FSTIME 2021:05:08:17:08:00 mris_place_surface N 18 e 213.72 S 0.43 U 213.28 P 99% M 1913788 F 0 R 502426 W 0 c 396 w 1 I 0 O 9616 L 1.95 1.80 1.60 @#@FSLOADPOST 2021:05:08:17:11:33 mris_place_surface N 18 1.68 1.67 1.58 #-------------------------------------------- #@# CortexLabel lh 2021��� 05��� 08��� ��������� 17:11:33 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 3 non-cortical segments detected only using segment with 8857 vertices erasing segment 1 (vno[0] = 80798) erasing segment 2 (vno[0] = 123341) @#@FSTIME 2021:05:08:17:11:33 mri_label2label N 5 e 12.78 S 0.08 U 12.69 P 99% M 311424 F 7 R 93614 W 0 c 19 w 8 I 1280 O 11128 L 1.68 1.67 1.58 @#@FSLOADPOST 2021:05:08:17:11:46 mri_label2label N 5 1.65 1.67 1.58 #-------------------------------------------- #@# CortexLabel+HipAmyg lh 2021��� 05��� 08��� ��������� 17:11:46 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 4 non-cortical segments detected only using segment with 6591 vertices erasing segment 1 (vno[0] = 73566) erasing segment 2 (vno[0] = 80798) erasing segment 3 (vno[0] = 123341) @#@FSTIME 2021:05:08:17:11:46 mri_label2label N 5 e 13.22 S 0.09 U 13.12 P 99% M 316112 F 0 R 94842 W 0 c 17 w 1 I 0 O 11320 L 1.65 1.67 1.58 @#@FSLOADPOST 2021:05:08:17:12:00 mri_label2label N 5 1.57 1.65 1.58 #-------------------------------------------- #@# CortexLabel rh 2021��� 05��� 08��� ��������� 17:12:00 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 3 non-cortical segments detected only using segment with 8845 vertices erasing segment 1 (vno[0] = 79725) erasing segment 2 (vno[0] = 118655) @#@FSTIME 2021:05:08:17:12:00 mri_label2label N 5 e 12.25 S 0.19 U 12.06 P 99% M 311020 F 0 R 95759 W 0 c 61 w 0 I 0 O 10864 L 1.57 1.65 1.58 @#@FSLOADPOST 2021:05:08:17:12:12 mri_label2label N 5 1.48 1.63 1.57 #-------------------------------------------- #@# CortexLabel+HipAmyg rh 2021��� 05��� 08��� ��������� 17:12:12 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 8 non-cortical segments detected only using segment with 6323 vertices erasing segment 1 (vno[0] = 48806) erasing segment 2 (vno[0] = 54777) erasing segment 3 (vno[0] = 68337) erasing segment 4 (vno[0] = 78846) erasing segment 5 (vno[0] = 79725) erasing segment 6 (vno[0] = 81396) erasing segment 7 (vno[0] = 118655) @#@FSTIME 2021:05:08:17:12:12 mri_label2label N 5 e 12.22 S 0.11 U 12.10 P 99% M 334892 F 0 R 101822 W 0 c 48 w 1 I 0 O 11080 L 1.48 1.63 1.57 @#@FSLOADPOST 2021:05:08:17:12:24 mri_label2label N 5 1.46 1.61 1.57 #-------------------------------------------- #@# Smooth2 lh 2021��� 05��� 08��� ��������� 17:12:24 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:17:12:24 mris_smooth N 7 e 2.56 S 0.07 U 2.49 P 100% M 210676 F 0 R 63441 W 0 c 10 w 1 I 0 O 9632 L 1.46 1.61 1.57 @#@FSLOADPOST 2021:05:08:17:12:27 mris_smooth N 7 1.46 1.61 1.57 #-------------------------------------------- #@# Smooth2 rh 2021��� 05��� 08��� ��������� 17:12:27 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:17:12:27 mris_smooth N 7 e 2.55 S 0.05 U 2.49 P 99% M 210164 F 0 R 63281 W 0 c 9 w 2 I 0 O 9616 L 1.46 1.61 1.57 @#@FSLOADPOST 2021:05:08:17:12:29 mris_smooth N 7 1.42 1.60 1.56 #-------------------------------------------- #@# Inflation2 lh 2021��� 05��� 08��� ��������� 17:12:29 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.3 mm, total surface area = 85613 mm^2 step 000: RMS=0.170 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.020 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 19.866001 mris_inflate stimesec 0.551944 mris_inflate ru_maxrss 210816 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 544217 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 47 @#@FSTIME 2021:05:08:17:12:29 mris_inflate N 2 e 20.42 S 0.55 U 19.86 P 100% M 210816 F 0 R 544219 W 0 c 47 w 1 I 0 O 10704 L 1.42 1.60 1.56 @#@FSLOADPOST 2021:05:08:17:12:50 mris_inflate N 2 1.58 1.63 1.57 #-------------------------------------------- #@# Inflation2 rh 2021��� 05��� 08��� ��������� 17:12:50 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.4 mm, total surface area = 85249 mm^2 step 000: RMS=0.171 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 19.784311 mris_inflate stimesec 0.331938 mris_inflate ru_maxrss 211360 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 56514 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10688 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 126 @#@FSTIME 2021:05:08:17:12:50 mris_inflate N 2 e 20.12 S 0.33 U 19.78 P 99% M 211524 F 0 R 56516 W 0 c 126 w 1 I 0 O 10688 L 1.58 1.63 1.57 @#@FSLOADPOST 2021:05:08:17:13:10 mris_inflate N 2 1.56 1.62 1.57 #-------------------------------------------- #@# Curv .H and .K lh 2021��� 05��� 08��� ��������� 17:13:10 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 16.578*4pi (208.322) --> -16 handles ICI = 155.6, FI = 1427.9, variation=22946.828 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2021:05:08:17:13:10 mris_curvature N 4 e 1.38 S 0.06 U 1.31 P 99% M 156888 F 4 R 42836 W 0 c 5 w 5 I 696 O 2144 L 1.56 1.62 1.57 @#@FSLOADPOST 2021:05:08:17:13:11 mris_curvature N 4 1.56 1.62 1.57 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 166 vertices thresholded to be in k1 ~ [-0.57 1.08], k2 ~ [-0.11 0.29] total integrated curvature = 0.624*4pi (7.845) --> 0 handles ICI = 1.7, FI = 10.2, variation=176.364 136 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 119 vertices thresholded to be in [-0.16 0.42] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.025 done. @#@FSTIME 2021:05:08:17:13:11 mris_curvature N 12 e 37.70 S 0.12 U 37.57 P 99% M 371088 F 0 R 96463 W 0 c 83 w 1 I 0 O 2144 L 1.56 1.62 1.57 @#@FSLOADPOST 2021:05:08:17:13:49 mris_curvature N 12 1.51 1.60 1.57 #-------------------------------------------- #@# Curv .H and .K rh 2021��� 05��� 08��� ��������� 17:13:49 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 14.210*4pi (178.568) --> -13 handles ICI = 150.9, FI = 1440.6, variation=22983.270 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2021:05:08:17:13:49 mris_curvature N 4 e 1.37 S 0.05 U 1.31 P 99% M 156264 F 0 R 42748 W 0 c 6 w 1 I 0 O 2144 L 1.51 1.60 1.57 @#@FSLOADPOST 2021:05:08:17:13:51 mris_curvature N 4 1.51 1.60 1.57 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 178 vertices thresholded to be in k1 ~ [-0.30 3.60], k2 ~ [-0.19 0.26] total integrated curvature = 0.599*4pi (7.524) --> 0 handles ICI = 1.7, FI = 10.7, variation=182.860 127 vertices thresholded to be in [-0.12 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 104 vertices thresholded to be in [-0.15 0.72] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.026 done. @#@FSTIME 2021:05:08:17:13:51 mris_curvature N 12 e 37.66 S 0.09 U 37.56 P 99% M 370032 F 0 R 96239 W 0 c 74 w 1 I 0 O 2144 L 1.51 1.60 1.57 @#@FSLOADPOST 2021:05:08:17:14:28 mris_curvature N 12 1.44 1.58 1.56 #-------------------------------------------- #@# Sphere lh 2021��� 05��� 08��� ��������� 17:14:28 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.1.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.305... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=yelab, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.91 pass 1: epoch 2 of 3 starting distance error %19.88 unfolding complete - removing small folds... starting distance error %19.82 removing remaining folds... final distance error %19.85 MRISunfold() return, current seed 1234 -01: dt=0.0000, 13 negative triangles VmPeak 564928 200: dt=0.9900, 13 negative triangles 201: dt=0.9900, 8 negative triangles 202: dt=0.9900, 5 negative triangles 203: dt=0.9900, 3 negative triangles 204: dt=0.9900, 3 negative triangles 205: dt=0.9900, 3 negative triangles 206: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1728 hours FSRUNTIME@ mris_sphere 0.1728 hours 1 threads #VMPC# mris_sphere VmPeak 564928 mris_sphere done @#@FSTIME 2021:05:08:17:14:28 mris_sphere N 4 e 622.17 S 14.23 U 607.92 P 99% M 281900 F 0 R 15115028 W 0 c 1475 w 1 I 0 O 9632 L 1.44 1.58 1.56 @#@FSLOADPOST 2021:05:08:17:24:50 mris_sphere N 4 1.79 1.52 1.51 #-------------------------------------------- #@# Sphere rh 2021��� 05��� 08��� ��������� 17:24:50 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.1.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=yelab, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.16 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %20.00 removing remaining folds... final distance error %20.03 MRISunfold() return, current seed 1234 -01: dt=0.0000, 52 negative triangles VmPeak 564308 189: dt=0.9900, 52 negative triangles 190: dt=0.9900, 40 negative triangles 191: dt=0.9900, 40 negative triangles 192: dt=0.9900, 35 negative triangles 193: dt=0.9900, 32 negative triangles 194: dt=0.9900, 27 negative triangles 195: dt=0.9900, 24 negative triangles 196: dt=0.9900, 22 negative triangles 197: dt=0.9900, 22 negative triangles 198: dt=0.9900, 19 negative triangles 199: dt=0.9900, 23 negative triangles 200: dt=0.9900, 21 negative triangles 201: dt=0.9900, 23 negative triangles 202: dt=0.9900, 22 negative triangles 203: dt=0.9900, 23 negative triangles 204: dt=0.9900, 22 negative triangles 205: dt=0.9900, 22 negative triangles 206: dt=0.9900, 23 negative triangles 207: dt=0.9900, 25 negative triangles 208: dt=0.9405, 23 negative triangles 209: dt=0.9405, 23 negative triangles 210: dt=0.9405, 25 negative triangles 211: dt=0.9405, 25 negative triangles 212: dt=0.9405, 26 negative triangles 213: dt=0.9405, 24 negative triangles 214: dt=0.9405, 24 negative triangles 215: dt=0.9405, 25 negative triangles 216: dt=0.9405, 23 negative triangles 217: dt=0.9405, 23 negative triangles 218: dt=0.8935, 21 negative triangles 219: dt=0.8935, 24 negative triangles 220: dt=0.8935, 21 negative triangles 221: dt=0.8935, 22 negative triangles 222: dt=0.8935, 21 negative triangles 223: dt=0.8935, 20 negative triangles 224: dt=0.8935, 22 negative triangles 225: dt=0.8935, 23 negative triangles 226: dt=0.8935, 21 negative triangles 227: dt=0.8935, 23 negative triangles 228: dt=0.8488, 24 negative triangles 229: dt=0.8488, 22 negative triangles 230: dt=0.8488, 20 negative triangles 231: dt=0.8488, 22 negative triangles 232: dt=0.8488, 23 negative triangles 233: dt=0.8488, 19 negative triangles 234: dt=0.8488, 18 negative triangles 235: dt=0.8488, 22 negative triangles 236: dt=0.8488, 20 negative triangles 237: dt=0.8488, 21 negative triangles 238: dt=0.8488, 20 negative triangles 239: dt=0.8488, 20 negative triangles 240: dt=0.8488, 19 negative triangles 241: dt=0.8488, 21 negative triangles 242: dt=0.8488, 20 negative triangles 243: dt=0.8488, 20 negative triangles 244: dt=0.8064, 20 negative triangles 245: dt=0.8064, 18 negative triangles 246: dt=0.8064, 17 negative triangles 247: dt=0.8064, 18 negative triangles 248: dt=0.8064, 20 negative triangles 249: dt=0.8064, 15 negative triangles 250: dt=0.8064, 20 negative triangles 251: dt=0.8064, 18 negative triangles 252: dt=0.8064, 19 negative triangles 253: dt=0.8064, 22 negative triangles 254: dt=0.8064, 18 negative triangles 255: dt=0.8064, 17 negative triangles 256: dt=0.8064, 22 negative triangles 257: dt=0.8064, 17 negative triangles 258: dt=0.8064, 21 negative triangles 259: dt=0.7660, 17 negative triangles 260: dt=0.7660, 21 negative triangles 261: dt=0.7660, 21 negative triangles 262: dt=0.7660, 17 negative triangles 263: dt=0.7660, 16 negative triangles 264: dt=0.7660, 16 negative triangles 265: dt=0.7660, 19 negative triangles 266: dt=0.7660, 15 negative triangles 267: dt=0.7660, 12 negative triangles 268: dt=0.7660, 11 negative triangles 269: dt=0.7660, 11 negative triangles 270: dt=0.7660, 18 negative triangles 271: dt=0.7660, 11 negative triangles 272: dt=0.7660, 12 negative triangles 273: dt=0.7660, 13 negative triangles 274: dt=0.7660, 14 negative triangles 275: dt=0.7660, 11 negative triangles 276: dt=0.7660, 14 negative triangles 277: dt=0.7660, 12 negative triangles 278: dt=0.7660, 10 negative triangles 279: dt=0.7660, 12 negative triangles 280: dt=0.7660, 14 negative triangles 281: dt=0.7660, 15 negative triangles 282: dt=0.7660, 12 negative triangles 283: dt=0.7660, 10 negative triangles 284: dt=0.7660, 16 negative triangles 285: dt=0.7660, 8 negative triangles 286: dt=0.7660, 18 negative triangles 287: dt=0.7660, 11 negative triangles 288: dt=0.7660, 8 negative triangles 289: dt=0.7660, 12 negative triangles 290: dt=0.7660, 9 negative triangles 291: dt=0.7660, 7 negative triangles 292: dt=0.7660, 13 negative triangles 293: dt=0.7660, 10 negative triangles 294: dt=0.7660, 6 negative triangles 295: dt=0.7660, 8 negative triangles 296: dt=0.7660, 8 negative triangles 297: dt=0.7660, 10 negative triangles 298: dt=0.7660, 7 negative triangles 299: dt=0.7660, 7 negative triangles 300: dt=0.7660, 7 negative triangles 301: dt=0.7660, 6 negative triangles 302: dt=0.7660, 8 negative triangles 303: dt=0.7660, 4 negative triangles 304: dt=0.7660, 5 negative triangles 305: dt=0.7660, 5 negative triangles 306: dt=0.7660, 4 negative triangles 307: dt=0.7660, 7 negative triangles 308: dt=0.7660, 3 negative triangles 309: dt=0.7660, 4 negative triangles 310: dt=0.7660, 2 negative triangles 311: dt=0.7660, 4 negative triangles 312: dt=0.7660, 2 negative triangles 313: dt=0.7660, 4 negative triangles 314: dt=0.7660, 5 negative triangles 315: dt=0.7660, 2 negative triangles 316: dt=0.7660, 5 negative triangles 317: dt=0.7660, 2 negative triangles 318: dt=0.7660, 4 negative triangles 319: dt=0.7660, 3 negative triangles 320: dt=0.7277, 2 negative triangles 321: dt=0.7277, 4 negative triangles 322: dt=0.7277, 3 negative triangles 323: dt=0.7277, 3 negative triangles 324: dt=0.7277, 2 negative triangles 325: dt=0.7277, 2 negative triangles 326: dt=0.7277, 4 negative triangles 327: dt=0.7277, 2 negative triangles 328: dt=0.7277, 3 negative triangles 329: dt=0.7277, 2 negative triangles 330: dt=0.6914, 2 negative triangles 331: dt=0.6914, 2 negative triangles 332: dt=0.6914, 2 negative triangles 333: dt=0.6914, 4 negative triangles 334: dt=0.6914, 2 negative triangles 335: dt=0.6914, 1 negative triangles 336: dt=0.6914, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1851 hours FSRUNTIME@ mris_sphere 0.1851 hours 1 threads #VMPC# mris_sphere VmPeak 564308 mris_sphere done @#@FSTIME 2021:05:08:17:24:51 mris_sphere N 4 e 666.52 S 15.31 U 651.14 P 99% M 281336 F 0 R 16498175 W 0 c 3138 w 1 I 0 O 9616 L 1.79 1.52 1.51 @#@FSLOADPOST 2021:05:08:17:35:57 mris_sphere N 4 1.50 1.52 1.50 #-------------------------------------------- #@# Surf Reg lh 2021��� 05��� 08��� ��������� 17:35:57 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.1 7.1.1 reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/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=yelab, 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=yelab, 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=yelab, 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 = 5.670 curvature mean = 0.041, std = 0.819 curvature mean = 0.006, std = 0.868 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (2.00, -4.00, -0.50) sse = 190137.3, elapsed since starting=0.3078 min MRISrigidBodyAlignGlobal() done 0.31 min curvature mean = 0.030, std = 0.838 curvature mean = 0.003, std = 0.952 curvature mean = 0.030, std = 0.850 curvature mean = 0.002, std = 0.982 curvature mean = 0.029, std = 0.852 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.015, std = 0.251 curvature mean = 0.046, std = 0.249 curvature mean = 0.046, std = 0.389 curvature mean = 0.042, std = 0.307 curvature mean = 0.029, std = 0.590 curvature mean = 0.042, std = 0.333 curvature mean = 0.016, std = 0.732 curvature mean = 0.041, std = 0.345 curvature mean = 0.005, std = 0.836 MRISregister() return, current seed 0 -01: dt=0.0000, 4 negative triangles VmPeak 547076 108: dt=0.9900, 4 negative triangles expanding nbhd size to 1 109: dt=0.9900, 5 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.11 hours #VMPC# mris_register VmPeak 547076 FSRUNTIME@ mris_register 0.1081 hours 1 threads @#@FSTIME 2021:05:08:17:35:57 mris_register N 4 e 389.13 S 7.16 U 381.94 P 99% M 264160 F 8 R 7590841 W 0 c 1231 w 21 I 7248 O 9632 L 1.50 1.52 1.50 @#@FSLOADPOST 2021:05:08:17:42:26 mris_register N 4 1.66 1.49 1.49 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh 2021��� 05��� 08��� ��������� 17:42:26 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.1.1 7.1.1 reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/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=yelab, 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=yelab, 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=yelab, 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 = 5.611 curvature mean = 0.034, std = 0.812 curvature mean = 0.006, std = 0.868 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.00, -2.50, 3.00) sse = 203102.5, elapsed since starting=0.3345 min MRISrigidBodyAlignGlobal() done 0.33 min curvature mean = 0.018, std = 0.832 curvature mean = 0.003, std = 0.952 curvature mean = 0.016, std = 0.844 curvature mean = 0.001, std = 0.982 curvature mean = 0.016, std = 0.846 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.016, std = 0.265 curvature mean = 0.039, std = 0.246 curvature mean = 0.049, std = 0.370 curvature mean = 0.036, std = 0.303 curvature mean = 0.031, std = 0.564 curvature mean = 0.035, std = 0.331 curvature mean = 0.017, std = 0.704 curvature mean = 0.034, std = 0.342 curvature mean = 0.005, std = 0.808 MRISregister() return, current seed 0 -01: dt=0.0000, 83 negative triangles VmPeak 546228 109: dt=0.9900, 83 negative triangles 110: dt=0.9900, 71 negative triangles 111: dt=0.9900, 56 negative triangles 112: dt=0.9900, 63 negative triangles 113: dt=0.9900, 52 negative triangles 114: dt=0.9900, 58 negative triangles 115: dt=0.9900, 55 negative triangles 116: dt=0.9900, 57 negative triangles 117: dt=0.9900, 48 negative triangles 118: dt=0.9900, 48 negative triangles 119: dt=0.9900, 49 negative triangles 120: dt=0.9900, 46 negative triangles 121: dt=0.9900, 49 negative triangles 122: dt=0.9900, 47 negative triangles 123: dt=0.9900, 45 negative triangles 124: dt=0.9900, 45 negative triangles 125: dt=0.9900, 46 negative triangles 126: dt=0.9900, 53 negative triangles 127: dt=0.9900, 50 negative triangles 128: dt=0.9900, 42 negative triangles 129: dt=0.9900, 50 negative triangles 130: dt=0.9900, 46 negative triangles 131: dt=0.9900, 47 negative triangles 132: dt=0.9900, 40 negative triangles 133: dt=0.9900, 42 negative triangles 134: dt=0.9900, 46 negative triangles 135: dt=0.9900, 42 negative triangles 136: dt=0.9900, 39 negative triangles 137: dt=0.9900, 36 negative triangles 138: dt=0.9900, 33 negative triangles 139: dt=0.9900, 35 negative triangles 140: dt=0.9900, 36 negative triangles 141: dt=0.9900, 41 negative triangles 142: dt=0.9900, 39 negative triangles 143: dt=0.9900, 37 negative triangles 144: dt=0.9900, 31 negative triangles 145: dt=0.9900, 34 negative triangles 146: dt=0.9900, 37 negative triangles 147: dt=0.9900, 30 negative triangles 148: dt=0.9900, 29 negative triangles 149: dt=0.9900, 28 negative triangles 150: dt=0.9900, 28 negative triangles 151: dt=0.9900, 31 negative triangles 152: dt=0.9900, 26 negative triangles 153: dt=0.9900, 27 negative triangles 154: dt=0.9900, 24 negative triangles 155: dt=0.9900, 25 negative triangles 156: dt=0.9900, 18 negative triangles 157: dt=0.9900, 20 negative triangles 158: dt=0.9900, 17 negative triangles 159: dt=0.9900, 18 negative triangles 160: dt=0.9900, 20 negative triangles 161: dt=0.9900, 21 negative triangles 162: dt=0.9900, 14 negative triangles 163: dt=0.9900, 10 negative triangles 164: dt=0.9900, 17 negative triangles 165: dt=0.9900, 14 negative triangles 166: dt=0.9900, 13 negative triangles 167: dt=0.9900, 14 negative triangles 168: dt=0.9900, 15 negative triangles 169: dt=0.9900, 14 negative triangles 170: dt=0.9900, 10 negative triangles 171: dt=0.9900, 17 negative triangles 172: dt=0.9900, 10 negative triangles 173: dt=0.9405, 13 negative triangles 174: dt=0.9405, 12 negative triangles 175: dt=0.9405, 13 negative triangles 176: dt=0.9405, 13 negative triangles 177: dt=0.9405, 6 negative triangles 178: dt=0.9405, 9 negative triangles 179: dt=0.9405, 4 negative triangles 180: dt=0.9405, 10 negative triangles 181: dt=0.9405, 6 negative triangles 182: dt=0.9405, 11 negative triangles 183: dt=0.9405, 9 negative triangles 184: dt=0.9405, 3 negative triangles 185: dt=0.9405, 6 negative triangles 186: dt=0.9405, 3 negative triangles 187: dt=0.9405, 4 negative triangles 188: dt=0.9405, 2 negative triangles 189: dt=0.9405, 3 negative triangles 190: dt=0.9405, 4 negative triangles 191: dt=0.9405, 2 negative triangles 192: dt=0.9405, 3 negative triangles 193: dt=0.9405, 2 negative triangles 194: dt=0.9405, 2 negative triangles 195: dt=0.9405, 2 negative triangles 196: dt=0.9405, 1 negative triangles 197: dt=0.9405, 1 negative triangles 198: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.12 hours #VMPC# mris_register VmPeak 546228 FSRUNTIME@ mris_register 0.1188 hours 1 threads @#@FSTIME 2021:05:08:17:42:26 mris_register N 4 e 427.74 S 8.67 U 419.05 P 99% M 263648 F 0 R 9007429 W 0 c 1129 w 13 I 5584 O 9616 L 1.66 1.49 1.49 @#@FSLOADPOST 2021:05:08:17:49:34 mris_register N 4 1.64 1.56 1.52 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh 2021��� 05��� 08��� ��������� 17:49:34 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:17:49:34 mris_jacobian N 3 e 0.96 S 0.06 U 0.89 P 99% M 210120 F 3 R 63375 W 0 c 6 w 4 I 704 O 1072 L 1.64 1.56 1.52 @#@FSLOADPOST 2021:05:08:17:49:35 mris_jacobian N 3 1.59 1.55 1.52 #-------------------------------------------- #@# Jacobian white rh 2021��� 05��� 08��� ��������� 17:49:35 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:17:49:35 mris_jacobian N 3 e 0.95 S 0.06 U 0.89 P 100% M 209640 F 0 R 63229 W 0 c 2 w 1 I 0 O 1072 L 1.59 1.55 1.52 @#@FSLOADPOST 2021:05:08:17:49:36 mris_jacobian N 3 1.59 1.55 1.52 #-------------------------------------------- #@# AvgCurv lh 2021��� 05��� 08��� ��������� 17:49:36 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mrisp_paint -a 5 /usr/local/freesurfer/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/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2021:05:08:17:49:36 mrisp_paint N 5 e 0.76 S 0.06 U 0.69 P 99% M 161768 F 5 R 44105 W 0 c 3 w 6 I 1072 O 1072 L 1.59 1.55 1.52 @#@FSLOADPOST 2021:05:08:17:49:37 mrisp_paint N 5 1.59 1.55 1.52 #-------------------------------------------- #@# AvgCurv rh 2021��� 05��� 08��� ��������� 17:49:37 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mrisp_paint -a 5 /usr/local/freesurfer/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/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2021:05:08:17:49:37 mrisp_paint N 5 e 0.77 S 0.06 U 0.71 P 100% M 161484 F 0 R 44005 W 0 c 2 w 1 I 0 O 1072 L 1.59 1.55 1.52 @#@FSLOADPOST 2021:05:08:17:49:38 mrisp_paint N 5 1.59 1.55 1.52 #----------------------------------------- #@# Cortical Parc lh 2021��� 05��� 08��� ��������� 17:49:38 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 pd_struc_recon lh ../surf/lh.sphere.reg /usr/local/freesurfer/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 7.1.1 7.1.1 reading atlas from /usr/local/freesurfer/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... 1233 labels changed using aseg relabeling using gibbs priors... 000: 3120 changed, 136905 examined... 001: 700 changed, 13165 examined... 002: 142 changed, 3923 examined... 003: 59 changed, 911 examined... 004: 19 changed, 358 examined... 005: 4 changed, 108 examined... 006: 0 changed, 26 examined... 217 labels changed using aseg 000: 87 total segments, 45 labels (193 vertices) changed 001: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2192 vertices marked for relabeling... 2192 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 8 seconds. @#@FSTIME 2021:05:08:17:49:38 mris_ca_label N 11 e 8.46 S 0.27 U 8.18 P 99% M 1087628 F 3 R 351810 W 0 c 17 w 7 I 64192 O 2144 L 1.59 1.55 1.52 @#@FSLOADPOST 2021:05:08:17:49:46 mris_ca_label N 11 1.50 1.53 1.51 #----------------------------------------- #@# Cortical Parc rh 2021��� 05��� 08��� ��������� 17:49:46 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 pd_struc_recon rh ../surf/rh.sphere.reg /usr/local/freesurfer/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 7.1.1 7.1.1 reading atlas from /usr/local/freesurfer/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... 1409 labels changed using aseg relabeling using gibbs priors... 000: 2893 changed, 136622 examined... 001: 620 changed, 12384 examined... 002: 129 changed, 3599 examined... 003: 55 changed, 828 examined... 004: 19 changed, 334 examined... 005: 6 changed, 125 examined... 006: 4 changed, 37 examined... 007: 0 changed, 24 examined... 144 labels changed using aseg 000: 91 total segments, 52 labels (180 vertices) changed 001: 41 total segments, 2 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1818 vertices marked for relabeling... 1818 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2021:05:08:17:49:46 mris_ca_label N 11 e 8.56 S 0.34 U 8.21 P 99% M 1104452 F 0 R 402392 W 0 c 16 w 2 I 36352 O 2144 L 1.50 1.53 1.51 @#@FSLOADPOST 2021:05:08:17:49:55 mris_ca_label N 11 1.42 1.51 1.50 #-------------------------------------------- #@# WhiteSurfs lh 2021��� 05��� 08��� ��������� 17:49:55 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 7.1.1 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 273806 0.34451 0.12506 0.000540 1.7942 Corner 821418 60.00000 14.06154 0.182660 179.4715 Edge 410709 0.90379 0.20773 0.029341 3.5742 Hinge 410709 10.52797 11.33043 0.000023 179.9153 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=20407, wmmin=5, clip=110 MRIfindBrightNonWM(): 727 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 414 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68453: xyz = (-5.07651,1.70222,55.6251) oxyz = (-5.07651,1.70222,55.6251) wxzy = (-5.07651,1.70222,55.6251) pxyz = (0,0,0) CBVO Creating mask 136905 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=2 had to be increased for 95 vertices, nripped=9548 mean border=77.4, 101 (101) missing vertices, mean dist 0.4 [1.3 (%11.8)->0.6 (%88.2))] %59 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1831 min Finding expansion regions mean absolute distance = 0.67 +- 0.95 2984 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=yelab, 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=2027625.1, rms=8.480 001: dt: 0.5000, sse=817524.2, rms=4.942 (41.717%) 002: dt: 0.5000, sse=520364.2, rms=3.573 (27.711%) 003: dt: 0.5000, sse=473090.5, rms=3.300 (7.647%) 004: dt: 0.5000, sse=436096.7, rms=3.062 (7.184%) rms = 3.1833/3.0625, sse=457297.5/436096.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=308169.8, rms=2.067 (32.513%) 006: dt: 0.2500, sse=262838.5, rms=1.562 (24.418%) 007: dt: 0.2500, sse=249181.9, rms=1.389 (11.084%) rms = 1.3422/1.3890, sse=246760.9/249181.9, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=246760.9, rms=1.342 (3.365%) 009: dt: 0.1250, sse=243948.7, rms=1.292 (3.727%) rms = 1.2827/1.2922, sse=243684.3/243948.7, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=243684.3, rms=1.283 (0.737%) 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=1 had to be increased for 75 vertices, nripped=9548 mean border=80.8, 101 (67) missing vertices, mean dist -0.2 [0.4 (%73.2)->0.2 (%26.8))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1308 min Finding expansion regions mean absolute distance = 0.37 +- 0.62 3193 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=yelab, 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=832498.6, rms=4.923 011: dt: 0.5000, sse=482860.1, rms=3.240 (34.184%) 012: dt: 0.5000, sse=465060.4, rms=3.142 (3.021%) 013: dt: 0.5000, sse=453882.7, rms=3.082 (1.906%) rms = 3.2300/3.0823, sse=478918.4/453882.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 014: dt: 0.2500, sse=312297.1, rms=1.957 (36.503%) 015: dt: 0.2500, sse=262284.3, rms=1.355 (30.788%) 016: dt: 0.2500, sse=250629.8, rms=1.151 (15.016%) rms = 1.1044/1.1512, sse=247843.6/250629.8, time step reduction 2 of 3 to 0.125 0 0 1 017: dt: 0.2500, sse=247843.6, rms=1.104 (4.070%) 018: dt: 0.1250, sse=244860.2, rms=1.045 (5.351%) rms = 1.0424/1.0453, sse=244647.7/244860.2, time step reduction 3 of 3 to 0.062 0 0 1 019: dt: 0.1250, sse=244647.7, rms=1.042 (0.278%) 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; 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=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 102 vertices, nripped=9548 mean border=83.4, 95 (54) missing vertices, mean dist -0.1 [0.3 (%72.2)->0.2 (%27.8))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0717 min Finding expansion regions mean absolute distance = 0.26 +- 0.39 3306 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=yelab, 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=500416.8, rms=3.383 020: dt: 0.5000, sse=397870.5, rms=2.684 (20.668%) rms = 2.9360/2.6838, sse=427630.3/397870.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 021: dt: 0.2500, sse=288014.4, rms=1.712 (36.190%) 022: dt: 0.2500, sse=248162.2, rms=1.197 (30.080%) 023: dt: 0.2500, sse=239136.6, rms=1.041 (13.063%) rms = 1.0123/1.0410, sse=237866.0/239136.6, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=237866.0, rms=1.012 (2.750%) 025: dt: 0.1250, sse=234682.8, rms=0.957 (5.495%) rms = 0.9578/0.9567, sse=235065.6/234682.8, time step reduction 3 of 3 to 0.062 0 1 1 RMS increased, rejecting step 026: dt: 0.1250, sse=235065.6, rms=0.958 (-0.118%) 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 = 111.3553620; border_low = 65.0000000; outside_low = 53.6239170; outside_hi = 111.3553620; 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=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 108 vertices, nripped=9548 mean border=84.2, 113 (44) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))] %87 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0439 min Finding expansion regions mean absolute distance = 0.22 +- 0.32 2459 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=yelab, 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=267961.0, rms=1.529 rms = 1.7077/1.5287, sse=284421.1/267961.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=233731.2, rms=1.012 (33.808%) 028: dt: 0.2500, sse=221740.2, rms=0.726 (28.261%) rms = 0.7240/0.7259, sse=222099.9/221740.2, time step reduction 2 of 3 to 0.125 0 1 1 029: dt: 0.2500, sse=222099.9, rms=0.724 (0.256%) rms = 0.7166/0.7240, sse=221796.0/222099.9, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=221796.0, rms=0.717 (1.030%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 3.01 minutes #VMPC# mris_place_surfaces VmPeak 2120444 mris_place_surface done @#@FSTIME 2021:05:08:17:49:55 mris_place_surface N 25 e 188.12 S 0.45 U 187.66 P 99% M 1845800 F 2 R 500978 W 0 c 351 w 3 I 352 O 9632 L 1.42 1.51 1.50 @#@FSLOADPOST 2021:05:08:17:53:03 mris_place_surface N 25 1.50 1.49 1.49 #-------------------------------------------- #@# WhiteSurfs rh 2021��� 05��� 08��� ��������� 17:53:03 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 7.1.1 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 273240 0.34372 0.12483 0.000842 2.8120 Corner 819720 60.00000 14.17636 0.286399 179.2915 Edge 409860 0.90274 0.20761 0.009038 2.9986 Hinge 409860 10.40370 11.15028 0.000054 179.9602 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=20407, wmmin=5, clip=110 MRIfindBrightNonWM(): 727 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 374 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68311: xyz = (35.6139,-0.484854,-17.5568) oxyz = (35.6139,-0.484854,-17.5568) wxzy = (35.6139,-0.484854,-17.5568) pxyz = (0,0,0) CBVO Creating mask 136622 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=2 had to be increased for 86 vertices, nripped=9761 mean border=77.8, 116 (116) missing vertices, mean dist 0.3 [1.4 (%13.9)->0.5 (%86.1))] %52 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1758 min Finding expansion regions mean absolute distance = 0.65 +- 1.00 3013 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=yelab, 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=1792510.6, rms=7.929 001: dt: 0.5000, sse=752584.8, rms=4.676 (41.034%) 002: dt: 0.5000, sse=516532.6, rms=3.545 (24.183%) 003: dt: 0.5000, sse=498767.7, rms=3.442 (2.896%) 004: dt: 0.5000, sse=461645.0, rms=3.211 (6.726%) rms = 3.3759/3.2108, sse=489294.6/461645.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=313196.2, rms=2.096 (34.720%) 006: dt: 0.2500, sse=259175.4, rms=1.543 (26.375%) 007: dt: 0.2500, sse=245171.3, rms=1.346 (12.804%) 008: dt: 0.2500, sse=242557.2, rms=1.295 (3.796%) rms = 1.2574/1.2945, sse=240518.6/242557.2, time step reduction 2 of 3 to 0.125 0 0 1 009: dt: 0.2500, sse=240518.6, rms=1.257 (2.868%) rms = 1.2104/1.2574, sse=238003.4/240518.6, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=238003.4, rms=1.210 (3.735%) 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=1 had to be increased for 101 vertices, nripped=9761 mean border=80.9, 107 (71) missing vertices, mean dist -0.2 [0.4 (%69.9)->0.2 (%30.1))] %68 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1241 min Finding expansion regions mean absolute distance = 0.36 +- 0.66 3036 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=yelab, 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=767707.6, rms=4.679 011: dt: 0.5000, sse=468446.3, rms=3.179 (32.072%) rms = 3.2840/3.1786, sse=484123.0/468446.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=354767.6, rms=2.372 (25.379%) 013: dt: 0.2500, sse=287030.4, rms=1.715 (27.695%) 014: dt: 0.2500, sse=259607.8, rms=1.375 (19.804%) 015: dt: 0.2500, sse=248231.9, rms=1.201 (12.671%) 016: dt: 0.2500, sse=243138.9, rms=1.113 (7.366%) rms = 1.0779/1.1126, sse=241493.3/243138.9, time step reduction 2 of 3 to 0.125 0 0 1 017: dt: 0.2500, sse=241493.2, rms=1.078 (3.123%) rms = 1.0332/1.0779, sse=239078.1/241493.3, time step reduction 3 of 3 to 0.062 0 0 1 018: dt: 0.1250, sse=239078.1, rms=1.033 (4.140%) 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; 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=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 160 vertices, nripped=9761 mean border=83.2, 122 (61) missing vertices, mean dist -0.1 [0.3 (%69.9)->0.2 (%30.1))] %80 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0668 min Finding expansion regions mean absolute distance = 0.25 +- 0.43 2555 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=yelab, 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=460865.4, rms=3.173 019: dt: 0.5000, sse=403025.1, rms=2.757 (13.095%) rms = 3.1009/2.7574, sse=451645.5/403025.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=285219.0, rms=1.727 (37.361%) 021: dt: 0.2500, sse=244559.9, rms=1.194 (30.870%) 022: dt: 0.2500, sse=235506.8, rms=1.038 (13.106%) rms = 1.0066/1.0376, sse=234189.4/235506.8, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=234189.4, rms=1.007 (2.981%) 024: dt: 0.1250, sse=230161.0, rms=0.941 (6.483%) rms = 0.9403/0.9414, sse=229768.1/230161.0, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=229768.1, rms=0.940 (0.109%) 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 = 111.3553620; border_low = 66.0000000; outside_low = 54.6239170; outside_hi = 111.3553620; 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=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 160 vertices, nripped=9761 mean border=84.0, 171 (60) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %83 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0412 min Finding expansion regions mean absolute distance = 0.21 +- 0.34 2333 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=yelab, 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=258913.8, rms=1.462 rms = 1.7696/1.4625, sse=292183.2/258913.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=227811.8, rms=0.940 (35.744%) 027: dt: 0.2500, sse=219766.6, rms=0.703 (25.187%) rms = 0.7100/0.7030, sse=220852.7/219766.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6994/0.7030, sse=219522.3/219766.6, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=219522.3, rms=0.699 (0.513%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.88 minutes #VMPC# mris_place_surfaces VmPeak 2077216 mris_place_surface done @#@FSTIME 2021:05:08:17:53:03 mris_place_surface N 25 e 180.35 S 0.45 U 179.89 P 99% M 1802896 F 0 R 490182 W 0 c 341 w 1 I 0 O 9616 L 1.50 1.49 1.49 @#@FSLOADPOST 2021:05:08:17:56:03 mris_place_surface N 25 1.40 1.46 1.48 #-------------------------------------------- #@# T1PialSurf lh 2021��� 05��� 08��� ��������� 17:56:03 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 7.1.1 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 273806 0.34738 0.13829 0.000369 2.2164 Corner 821418 60.00000 15.43220 0.081786 179.8161 Edge 410709 0.90916 0.22606 0.036232 3.4775 Hinge 410709 10.63914 11.56434 0.000016 179.9759 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=20407, wmmin=5, clip=110 MRIfindBrightNonWM(): 727 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 62.7582 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 68453: xyz = (-5.02575,1.69253,55.6354) oxyz = (-5.02575,1.69253,55.6354) wxzy = (-5.02575,1.69253,55.6354) pxyz = (-5.02575,1.69253,55.6354) CBVO Creating mask 136905 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.6446380; border_hi = 53.6239170; border_low = 30.8717460; outside_low = 10.0000000; outside_hi = 47.9358750; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=2 had to be increased for 140 vertices, nripped=6986 mean border=51.4, 130 (130) missing vertices, mean dist 1.8 [0.3 (%0.0)->2.6 (%100.0))] %15 local maxima, %51 large gradients and %29 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1382 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=yelab, 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=29270948.0, rms=33.464 001: dt: 0.5000, sse=20604756.0, rms=28.035 (16.224%) 002: dt: 0.5000, sse=14406251.0, rms=23.390 (16.568%) 003: dt: 0.5000, sse=10343859.0, rms=19.761 (15.516%) 004: dt: 0.5000, sse=7795646.5, rms=17.094 (13.495%) 005: dt: 0.5000, sse=6146428.5, rms=15.118 (11.561%) 006: dt: 0.5000, sse=4946865.0, rms=13.499 (10.709%) 007: dt: 0.5000, sse=3992359.0, rms=12.055 (10.695%) 008: dt: 0.5000, sse=3206575.2, rms=10.721 (11.069%) 009: dt: 0.5000, sse=2562505.0, rms=9.487 (11.505%) 010: dt: 0.5000, sse=2040565.8, rms=8.354 (11.942%) 011: dt: 0.5000, sse=1634728.1, rms=7.353 (11.984%) 012: dt: 0.5000, sse=1332830.9, rms=6.508 (11.489%) 013: dt: 0.5000, sse=1123058.5, rms=5.849 (10.125%) 014: dt: 0.5000, sse=992557.3, rms=5.397 (7.726%) 015: dt: 0.5000, sse=916890.1, rms=5.116 (5.210%) 016: dt: 0.5000, sse=879516.8, rms=4.969 (2.869%) 017: dt: 0.5000, sse=853411.6, rms=4.864 (2.127%) rms = 4.8191/4.8637, sse=843038.9/853411.7, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=843038.9, rms=4.819 (0.918%) 019: dt: 0.2500, sse=631731.1, rms=3.859 (19.920%) 020: dt: 0.2500, sse=585498.9, rms=3.618 (6.251%) rms = 3.5866/3.6178, sse=580083.5/585498.9, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=580083.5, rms=3.587 (0.864%) 022: dt: 0.1250, sse=537284.7, rms=3.344 (6.755%) rms = 3.3041/3.3443, sse=530476.8/537284.7, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=530476.8, rms=3.304 (1.201%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.6446380; border_hi = 53.6239170; border_low = 30.8717460; outside_low = 10.0000000; outside_hi = 47.9358750; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7265 vertices, nripped=6986 mean border=49.7, 1040 (9) missing vertices, mean dist 0.1 [0.1 (%49.7)->0.5 (%50.3))] %27 local maxima, %42 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0409 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=yelab, 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=799615.3, rms=4.370 rms = 4.5592/4.3700, sse=844224.8/799615.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=691926.4, rms=3.863 (11.600%) 025: dt: 0.2500, sse=628197.7, rms=3.528 (8.677%) 026: dt: 0.2500, sse=610235.2, rms=3.430 (2.776%) rms = 3.4151/3.4300, sse=607573.2/610235.2, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=607573.2, rms=3.415 (0.433%) 028: dt: 0.1250, sse=574074.9, rms=3.217 (5.804%) rms = 3.1746/3.2169, sse=567085.3/574074.9, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=567085.3, rms=3.175 (1.315%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.6446380; border_hi = 53.6239170; border_low = 30.8717460; outside_low = 10.0000000; outside_hi = 47.9358750; 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=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 8087 vertices, nripped=6986 mean border=48.4, 1229 (5) missing vertices, mean dist 0.1 [0.1 (%45.1)->0.4 (%54.9))] %41 local maxima, %28 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0230 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=yelab, 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=679647.6, rms=3.779 rms = 4.4392/3.7787, sse=820742.3/679647.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=610347.3, rms=3.404 (9.908%) 031: dt: 0.2500, sse=588112.4, rms=3.276 (3.772%) rms = 3.2701/3.2759, sse=586505.9/588112.4, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=586505.9, rms=3.270 (0.175%) 033: dt: 0.1250, sse=565736.8, rms=3.143 (3.885%) rms = 3.1194/3.1431, sse=561822.5/565736.7, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=561822.5, rms=3.119 (0.754%) 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 = 94.6446380; border_hi = 53.6239170; border_low = 30.8717460; outside_low = 10.0000000; outside_hi = 47.9358750; 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=136905 Gdiag_no=-1 vno start=0, stop=136905 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7025 vertices, nripped=6986 mean border=47.5, 2950 (4) missing vertices, mean dist 0.1 [0.2 (%47.7)->0.3 (%52.3))] %45 local maxima, %23 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0146 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=yelab, 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=601476.8, rms=3.352 rms = 4.0072/3.3520, sse=725659.8/601476.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=572074.7, rms=3.177 (5.226%) 036: dt: 0.2500, sse=562858.8, rms=3.124 (1.652%) rms = 3.1323/3.1244, sse=563483.9/562858.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 3.0923/3.1244, sse=557759.1/562858.8, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=557759.1, rms=3.092 (1.027%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 35 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 3.11 minutes #VMPC# mris_place_surfaces VmPeak 1393496 mris_place_surface done @#@FSTIME 2021:05:08:17:56:03 mris_place_surface N 28 e 193.70 S 0.29 U 193.41 P 99% M 1119104 F 0 R 301393 W 0 c 386 w 2 I 0 O 9632 L 1.40 1.46 1.48 @#@FSLOADPOST 2021:05:08:17:59:17 mris_place_surface N 28 1.29 1.41 1.45 #-------------------------------------------- #@# T1PialSurf rh 2021��� 05��� 08��� ��������� 17:59:17 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 7.1.1 7.1.1 cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 273240 0.34651 0.13852 0.001371 2.8120 Corner 819720 60.00000 15.58147 0.090913 178.4031 Edge 409860 0.90792 0.22617 0.032008 3.0396 Hinge 409860 10.54143 11.56618 0.000023 179.9898 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=20407, wmmin=5, clip=110 MRIfindBrightNonWM(): 727 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 63.2582 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 68311: xyz = (35.6139,-0.484854,-17.5568) oxyz = (35.6139,-0.484854,-17.5568) wxzy = (35.6139,-0.484854,-17.5568) pxyz = (35.6139,-0.484854,-17.5568) CBVO Creating mask 136622 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.6446380; border_hi = 54.6239170; border_low = 31.8717460; outside_low = 10.0000000; outside_hi = 48.9358750; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=2 had to be increased for 162 vertices, nripped=6888 mean border=51.9, 170 (170) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.4 (%100.0))] %16 local maxima, %56 large gradients and %23 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1363 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=yelab, 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=27886318.0, rms=32.686 001: dt: 0.5000, sse=19147314.0, rms=27.039 (17.277%) 002: dt: 0.5000, sse=12960066.0, rms=22.187 (17.944%) 003: dt: 0.5000, sse=9021080.0, rms=18.443 (16.874%) 004: dt: 0.5000, sse=6657397.0, rms=15.774 (14.472%) 005: dt: 0.5000, sse=5196764.0, rms=13.869 (12.079%) 006: dt: 0.5000, sse=4151039.8, rms=12.324 (11.139%) 007: dt: 0.5000, sse=3324195.0, rms=10.948 (11.166%) 008: dt: 0.5000, sse=2648472.8, rms=9.677 (11.602%) 009: dt: 0.5000, sse=2108295.5, rms=8.526 (11.899%) 010: dt: 0.5000, sse=1684184.4, rms=7.498 (12.056%) 011: dt: 0.5000, sse=1372525.4, rms=6.641 (11.426%) 012: dt: 0.5000, sse=1151448.0, rms=5.958 (10.287%) 013: dt: 0.5000, sse=1006465.2, rms=5.463 (8.309%) 014: dt: 0.5000, sse=912980.8, rms=5.117 (6.335%) 015: dt: 0.5000, sse=855928.3, rms=4.893 (4.380%) 016: dt: 0.5000, sse=815925.1, rms=4.729 (3.358%) 017: dt: 0.5000, sse=796039.8, rms=4.643 (1.802%) 018: dt: 0.5000, sse=780585.9, rms=4.575 (1.469%) rms = 4.5279/4.5751, sse=770107.8/780585.9, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=770107.9, rms=4.528 (1.032%) 020: dt: 0.2500, sse=565213.5, rms=3.524 (22.170%) 021: dt: 0.2500, sse=520027.8, rms=3.265 (7.362%) rms = 3.2234/3.2646, sse=513421.0/520027.7, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=513421.0, rms=3.223 (1.261%) 023: dt: 0.1250, sse=473637.7, rms=2.972 (7.809%) rms = 2.9277/2.9717, sse=467008.8/473637.7, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=467008.8, rms=2.928 (1.482%) 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 = 94.6446380; border_hi = 54.6239170; border_low = 31.8717460; outside_low = 10.0000000; outside_hi = 48.9358750; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=1 had to be increased for 5857 vertices, nripped=6888 mean border=49.8, 949 (34) missing vertices, mean dist 0.1 [0.1 (%49.1)->0.5 (%50.9))] %28 local maxima, %46 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0438 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=yelab, 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=805105.4, rms=4.402 rms = 4.4348/4.4024, sse=813536.6/805105.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=683925.4, rms=3.831 (12.970%) 026: dt: 0.2500, sse=595795.8, rms=3.355 (12.447%) 027: dt: 0.2500, sse=569752.0, rms=3.203 (4.532%) rms = 3.1592/3.2025, sse=562528.7/569752.0, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=562528.8, rms=3.159 (1.352%) 029: dt: 0.1250, sse=526925.2, rms=2.930 (7.262%) 030: dt: 0.1250, sse=518995.9, rms=2.877 (1.799%) rms = 2.8573/2.8771, sse=516013.7/518995.9, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=516013.8, rms=2.857 (0.689%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.6446380; border_hi = 54.6239170; border_low = 31.8717460; outside_low = 10.0000000; outside_hi = 48.9358750; 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=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 6445 vertices, nripped=6888 mean border=48.2, 1160 (19) missing vertices, mean dist 0.1 [0.1 (%43.8)->0.4 (%56.2))] %41 local maxima, %33 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0249 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=yelab, 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=672999.9, rms=3.754 rms = 4.2950/3.7539, sse=786946.6/672999.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=585891.4, rms=3.272 (12.840%) 033: dt: 0.2500, sse=544542.0, rms=3.015 (7.837%) rms = 2.9756/3.0155, sse=537739.6/544542.0, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=537739.6, rms=2.976 (1.324%) 035: dt: 0.1250, sse=514741.7, rms=2.820 (5.232%) rms = 2.7892/2.8199, sse=510237.1/514741.7, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=510237.1, rms=2.789 (1.088%) 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 = 94.6446380; border_hi = 54.6239170; border_low = 31.8717460; outside_low = 10.0000000; outside_hi = 48.9358750; 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=136622 Gdiag_no=-1 vno start=0, stop=136622 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 5537 vertices, nripped=6888 mean border=47.2, 2637 (16) missing vertices, mean dist 0.1 [0.2 (%47.0)->0.3 (%53.0))] %46 local maxima, %27 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0157 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=yelab, 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=552308.4, rms=3.067 rms = 3.8086/3.0673, sse=683855.8/552308.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=519426.1, rms=2.850 (7.070%) 038: dt: 0.2500, sse=508450.6, rms=2.779 (2.513%) rms = 2.7922/2.7788, sse=509662.2/508450.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 2.7404/2.7788, sse=503030.4/508450.6, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=503030.4, rms=2.740 (1.384%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 9 intersecting 001: 3 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 3.26 minutes #VMPC# mris_place_surfaces VmPeak 1396812 mris_place_surface done @#@FSTIME 2021:05:08:17:59:17 mris_place_surface N 28 e 202.46 S 0.26 U 202.19 P 99% M 1122012 F 0 R 301977 W 0 c 473 w 1 I 0 O 9616 L 1.29 1.41 1.45 @#@FSLOADPOST 2021:05:08:18:02:40 mris_place_surface N 28 1.45 1.46 1.46 #@# white curv lh 2021��� 05��� 08��� ��������� 18:02:40 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:18:02:40 mris_place_surface N 5 e 1.60 S 0.07 U 1.53 P 99% M 188160 F 0 R 50777 W 0 c 6 w 1 I 0 O 1072 L 1.45 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:02:41 mris_place_surface N 5 1.49 1.47 1.46 #@# white area lh 2021��� 05��� 08��� ��������� 18:02:41 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2021:05:08:18:02:41 mris_place_surface N 3 e 0.79 S 0.07 U 0.71 P 99% M 188052 F 0 R 50775 W 0 c 57 w 1 I 0 O 1072 L 1.49 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:02:42 mris_place_surface N 3 1.49 1.47 1.46 #@# pial curv lh 2021��� 05��� 08��� ��������� 18:02:42 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:18:02:42 mris_place_surface N 5 e 1.68 S 0.04 U 1.64 P 100% M 188136 F 0 R 50777 W 0 c 4 w 1 I 0 O 1072 L 1.49 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:02:44 mris_place_surface N 5 1.49 1.47 1.46 #@# pial area lh 2021��� 05��� 08��� ��������� 18:02:44 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2021:05:08:18:02:44 mris_place_surface N 3 e 0.79 S 0.05 U 0.73 P 99% M 188280 F 0 R 50781 W 0 c 4 w 2 I 0 O 1072 L 1.49 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:02:45 mris_place_surface N 3 1.49 1.47 1.46 #@# thickness lh 2021��� 05��� 08��� ��������� 18:02:45 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 136905 vertices processed 25000 of 136905 vertices processed 50000 of 136905 vertices processed 75000 of 136905 vertices processed 100000 of 136905 vertices processed 125000 of 136905 vertices processed 0 of 136905 vertices processed 25000 of 136905 vertices processed 50000 of 136905 vertices processed 75000 of 136905 vertices processed 100000 of 136905 vertices processed 125000 of 136905 vertices processed thickness calculation complete, 115:855 truncations. 61205 vertices at 0 distance 118957 vertices at 1 distance 62965 vertices at 2 distance 20373 vertices at 3 distance 6443 vertices at 4 distance 2301 vertices at 5 distance 934 vertices at 6 distance 348 vertices at 7 distance 128 vertices at 8 distance 41 vertices at 9 distance 34 vertices at 10 distance 20 vertices at 11 distance 8 vertices at 12 distance 19 vertices at 13 distance 10 vertices at 14 distance 7 vertices at 15 distance 1 vertices at 16 distance 2 vertices at 17 distance 5 vertices at 18 distance 1 vertices at 19 distance 8 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2021:05:08:18:02:45 mris_place_surface N 6 e 27.16 S 0.05 U 27.10 P 100% M 188052 F 0 R 57905 W 0 c 41 w 1 I 0 O 1072 L 1.49 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:03:12 mris_place_surface N 6 1.63 1.50 1.47 #@# area and vertex vol lh 2021��� 05��� 08��� ��������� 18:03:12 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon lh /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.volume masking with /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Total face volume 254591 Total vertex volume 254335 (mask=0) #@# pd_struc_recon lh 254335 vertexvol Done @#@FSTIME 2021:05:08:18:03:12 vertexvol N 4 e 1.55 S 0.10 U 1.45 P 99% M 313188 F 5 R 88683 W 0 c 115 w 28 I 1224 O 3216 L 1.63 1.50 1.47 @#@FSLOADPOST 2021:05:08:18:03:13 vertexvol N 4 1.63 1.50 1.47 #@# white curv rh 2021��� 05��� 08��� ��������� 18:03:13 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:18:03:14 mris_place_surface N 5 e 1.61 S 0.08 U 1.52 P 99% M 187932 F 0 R 50663 W 0 c 106 w 1 I 0 O 1072 L 1.63 1.50 1.47 @#@FSLOADPOST 2021:05:08:18:03:15 mris_place_surface N 5 1.66 1.51 1.48 #@# white area rh 2021��� 05��� 08��� ��������� 18:03:15 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2021:05:08:18:03:15 mris_place_surface N 3 e 0.79 S 0.05 U 0.73 P 99% M 187968 F 0 R 50663 W 0 c 1 w 1 I 0 O 1072 L 1.66 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:03:16 mris_place_surface N 3 1.66 1.51 1.48 #@# pial curv rh 2021��� 05��� 08��� ��������� 18:03:16 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 2021:05:08:18:03:16 mris_place_surface N 5 e 1.59 S 0.05 U 1.53 P 99% M 187968 F 0 R 50663 W 0 c 6 w 1 I 0 O 1072 L 1.66 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:03:18 mris_place_surface N 5 1.66 1.51 1.48 #@# pial area rh 2021��� 05��� 08��� ��������� 18:03:18 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2021:05:08:18:03:18 mris_place_surface N 3 e 0.79 S 0.04 U 0.74 P 100% M 188044 F 0 R 50665 W 0 c 1 w 1 I 0 O 1072 L 1.66 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:03:18 mris_place_surface N 3 1.66 1.51 1.48 #@# thickness rh 2021��� 05��� 08��� ��������� 18:03:18 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 136622 vertices processed 25000 of 136622 vertices processed 50000 of 136622 vertices processed 75000 of 136622 vertices processed 100000 of 136622 vertices processed 125000 of 136622 vertices processed 0 of 136622 vertices processed 25000 of 136622 vertices processed 50000 of 136622 vertices processed 75000 of 136622 vertices processed 100000 of 136622 vertices processed 125000 of 136622 vertices processed thickness calculation complete, 121:818 truncations. 66312 vertices at 0 distance 121347 vertices at 1 distance 59238 vertices at 2 distance 18073 vertices at 3 distance 5312 vertices at 4 distance 1779 vertices at 5 distance 635 vertices at 6 distance 248 vertices at 7 distance 85 vertices at 8 distance 65 vertices at 9 distance 40 vertices at 10 distance 22 vertices at 11 distance 17 vertices at 12 distance 7 vertices at 13 distance 7 vertices at 14 distance 9 vertices at 15 distance 8 vertices at 16 distance 6 vertices at 17 distance 17 vertices at 18 distance 9 vertices at 19 distance 8 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2021:05:08:18:03:19 mris_place_surface N 6 e 26.84 S 0.05 U 26.78 P 99% M 187772 F 0 R 57776 W 0 c 71 w 1 I 0 O 1072 L 1.66 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:03:45 mris_place_surface N 6 1.53 1.49 1.47 #@# area and vertex vol rh 2021��� 05��� 08��� ��������� 18:03:45 CST cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon rh /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.volume masking with /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Total face volume 247033 Total vertex volume 246785 (mask=0) #@# pd_struc_recon rh 246785 vertexvol Done @#@FSTIME 2021:05:08:18:03:45 vertexvol N 4 e 1.54 S 0.11 U 1.42 P 99% M 312372 F 0 R 88462 W 0 c 7 w 22 I 0 O 3216 L 1.53 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:03:47 vertexvol N 4 1.53 1.49 1.47 #----------------------------------------- #@# Curvature Stats lh 2021��� 05��� 08��� ��������� 18:03:47 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm pd_struc_recon 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 [ pd_struc_recon/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 [ 215 ] Gb_filter = 0 WARN: S lookup min: -0.078778 WARN: S explicit min: 0.000000 vertex = 2660 @#@FSTIME 2021:05:08:18:03:47 mris_curvature_stats N 11 e 2.19 S 0.08 U 2.10 P 99% M 188232 F 5 R 50899 W 0 c 8 w 6 I 872 O 8616 L 1.53 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:03:49 mris_curvature_stats N 11 1.53 1.49 1.47 #----------------------------------------- #@# Curvature Stats rh 2021��� 05��� 08��� ��������� 18:03:49 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm pd_struc_recon 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 [ pd_struc_recon/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 [ 213 ] Gb_filter = 0 @#@FSTIME 2021:05:08:18:03:49 mris_curvature_stats N 11 e 2.19 S 0.06 U 2.12 P 99% M 187852 F 0 R 50783 W 0 c 9 w 1 I 0 O 8616 L 1.53 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:03:51 mris_curvature_stats N 11 1.48 1.48 1.47 #-------------------------------------------- #@# Cortical ribbon mask 2021��� 05��� 08��� ��������� 18:03:51 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon SUBJECTS_DIR is /media/yelab/data/PD/PD_Nii/sub1/STRUC 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 = 33 writing volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/ribbon.mgz mris_volmask took 5.07 minutes writing ribbon files @#@FSTIME 2021:05:08:18:03:51 mris_volmask N 12 e 304.51 S 0.43 U 304.06 P 99% M 990996 F 4 R 523613 W 0 c 571 w 5 I 1224 O 888 L 1.48 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:08:56 mris_volmask N 12 1.86 1.51 1.47 #----------------------------------------- #@# Cortical Parc 2 lh 2021��� 05��� 08��� ��������� 18:08:56 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 pd_struc_recon lh ../surf/lh.sphere.reg /usr/local/freesurfer/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 7.1.1 7.1.1 reading atlas from /usr/local/freesurfer/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... 89 labels changed using aseg relabeling using gibbs priors... 000: 8962 changed, 136905 examined... 001: 2111 changed, 34709 examined... 002: 627 changed, 11177 examined... 003: 253 changed, 3676 examined... 004: 116 changed, 1509 examined... 005: 68 changed, 654 examined... 006: 30 changed, 372 examined... 007: 16 changed, 172 examined... 008: 14 changed, 96 examined... 009: 4 changed, 76 examined... 010: 0 changed, 25 examined... 56 labels changed using aseg 000: 242 total segments, 153 labels (1875 vertices) changed 001: 97 total segments, 11 labels (497 vertices) changed 002: 86 total segments, 1 labels (141 vertices) changed 003: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1455 vertices marked for relabeling... 1455 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. @#@FSTIME 2021:05:08:18:08:56 mris_ca_label N 11 e 11.81 S 0.73 U 11.08 P 99% M 1852164 F 0 R 816797 W 0 c 20 w 2 I 42432 O 2152 L 1.86 1.51 1.47 @#@FSLOADPOST 2021:05:08:18:09:08 mris_ca_label N 11 1.88 1.52 1.47 #----------------------------------------- #@# Cortical Parc 2 rh 2021��� 05��� 08��� ��������� 18:09:08 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 pd_struc_recon rh ../surf/rh.sphere.reg /usr/local/freesurfer/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 7.1.1 7.1.1 reading atlas from /usr/local/freesurfer/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... 1 labels changed using aseg relabeling using gibbs priors... 000: 9206 changed, 136622 examined... 001: 2039 changed, 35781 examined... 002: 584 changed, 10809 examined... 003: 264 changed, 3425 examined... 004: 130 changed, 1505 examined... 005: 56 changed, 755 examined... 006: 26 changed, 358 examined... 007: 17 changed, 154 examined... 008: 13 changed, 103 examined... 009: 10 changed, 76 examined... 010: 4 changed, 63 examined... 011: 1 changed, 23 examined... 012: 0 changed, 7 examined... 1 labels changed using aseg 000: 251 total segments, 163 labels (2142 vertices) changed 001: 97 total segments, 11 labels (62 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1280 vertices marked for relabeling... 1280 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 11 seconds. @#@FSTIME 2021:05:08:18:09:08 mris_ca_label N 11 e 11.48 S 0.62 U 10.85 P 99% M 1894444 F 0 R 723536 W 0 c 46 w 2 I 42776 O 2144 L 1.88 1.52 1.47 @#@FSLOADPOST 2021:05:08:18:09:19 mris_ca_label N 11 2.06 1.57 1.49 #----------------------------------------- #@# Cortical Parc 3 lh 2021��� 05��� 08��� ��������� 18:09:19 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 pd_struc_recon lh ../surf/lh.sphere.reg /usr/local/freesurfer/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 7.1.1 7.1.1 reading atlas from /usr/local/freesurfer/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... 1901 labels changed using aseg relabeling using gibbs priors... 000: 2087 changed, 136905 examined... 001: 465 changed, 9624 examined... 002: 134 changed, 2659 examined... 003: 58 changed, 796 examined... 004: 29 changed, 352 examined... 005: 23 changed, 175 examined... 006: 14 changed, 141 examined... 007: 11 changed, 84 examined... 008: 10 changed, 60 examined... 009: 7 changed, 70 examined... 010: 9 changed, 48 examined... 011: 5 changed, 37 examined... 012: 5 changed, 27 examined... 013: 6 changed, 28 examined... 014: 4 changed, 35 examined... 015: 3 changed, 27 examined... 016: 4 changed, 20 examined... 017: 4 changed, 26 examined... 018: 4 changed, 24 examined... 019: 5 changed, 31 examined... 020: 3 changed, 31 examined... 021: 3 changed, 16 examined... 022: 3 changed, 18 examined... 023: 4 changed, 23 examined... 024: 1 changed, 28 examined... 025: 0 changed, 7 examined... 344 labels changed using aseg 000: 46 total segments, 13 labels (205 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1092 vertices marked for relabeling... 1092 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2021:05:08:18:09:19 mris_ca_label N 11 e 8.91 S 0.31 U 8.60 P 99% M 902768 F 0 R 294724 W 0 c 19 w 2 I 42976 O 2144 L 2.06 1.57 1.49 @#@FSLOADPOST 2021:05:08:18:09:28 mris_ca_label N 11 2.05 1.59 1.49 #----------------------------------------- #@# Cortical Parc 3 rh 2021��� 05��� 08��� ��������� 18:09:28 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 pd_struc_recon rh ../surf/rh.sphere.reg /usr/local/freesurfer/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 7.1.1 7.1.1 reading atlas from /usr/local/freesurfer/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... 2012 labels changed using aseg relabeling using gibbs priors... 000: 2145 changed, 136622 examined... 001: 484 changed, 9709 examined... 002: 129 changed, 2755 examined... 003: 53 changed, 801 examined... 004: 22 changed, 311 examined... 005: 12 changed, 121 examined... 006: 10 changed, 74 examined... 007: 7 changed, 53 examined... 008: 8 changed, 35 examined... 009: 5 changed, 35 examined... 010: 7 changed, 34 examined... 011: 6 changed, 38 examined... 012: 3 changed, 31 examined... 013: 2 changed, 18 examined... 014: 1 changed, 13 examined... 015: 1 changed, 6 examined... 016: 0 changed, 7 examined... 259 labels changed using aseg 000: 49 total segments, 16 labels (153 vertices) changed 001: 33 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... 1091 vertices marked for relabeling... 1091 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2021:05:08:18:09:28 mris_ca_label N 11 e 8.83 S 0.30 U 8.53 P 99% M 916316 F 0 R 298130 W 0 c 18 w 2 I 42952 O 2144 L 2.05 1.59 1.49 @#@FSLOADPOST 2021:05:08:18:09:37 mris_ca_label N 11 1.89 1.57 1.49 #----------------------------------------- #@# WM/GM Contrast lh 2021��� 05��� 08��� ��������� 18:09:37 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts pctsurfcon --s pd_struc_recon --lh-only Log file is /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts/pctsurfcon.log 2021��� 05��� 08��� ��������� 18:09:37 CST setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts /usr/local/freesurfer/bin/pctsurfcon pctsurfcon 7.1.1 Linux yelab-Precision-5820-Tower 5.4.0-72-generic #80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15584/lh.wm.mgh --regheader pd_struc_recon --cortex srcvol = /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00784 0.99848 0.05447 -0.00002; 0.99494 0.01324 -0.09958 0.00002; -0.10015 0.05341 -0.99354 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Reading surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 = 82125 Masking with /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15584/lh.wm.mgh Dim: 136905 1 1 mri_vol2surf --mov /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15584/lh.gm.mgh --projfrac 0.3 --regheader pd_struc_recon --cortex srcvol = /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00784 0.99848 0.05447 -0.00002; 0.99494 0.01324 -0.09958 0.00002; -0.10015 0.05341 -0.99354 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Reading surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Done reading source surface Reading thickness /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 = 93658 Masking with /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15584/lh.gm.mgh Dim: 136905 1 1 mri_concat /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15584/lh.wm.mgh /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15584/lh.gm.mgh --paired-diff-norm --mul 100 --o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.w-g.pct.mgh mri_segstats --in /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.w-g.pct.mgh --annot pd_struc_recon lh aparc --sum /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/stats/lh.w-g.pct.stats --snr 7.1.1 cwd cmdline mri_segstats --in /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.w-g.pct.mgh --annot pd_struc_recon lh aparc --sum /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/stats/lh.w-g.pct.stats --snr sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.w-g.pct.mgh Vertex Area is 0.694755 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 2021:05:08:18:09:37 pctsurfcon N 3 e 3.26 S 0.23 U 3.02 P 99% M 285284 F 10 R 205242 W 0 c 116 w 79 I 2368 O 3344 L 1.89 1.57 1.49 @#@FSLOADPOST 2021:05:08:18:09:41 pctsurfcon N 3 1.90 1.58 1.49 #----------------------------------------- #@# WM/GM Contrast rh 2021��� 05��� 08��� ��������� 18:09:41 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts pctsurfcon --s pd_struc_recon --rh-only Log file is /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts/pctsurfcon.log 2021��� 05��� 08��� ��������� 18:09:41 CST setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC cd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/scripts /usr/local/freesurfer/bin/pctsurfcon pctsurfcon 7.1.1 Linux yelab-Precision-5820-Tower 5.4.0-72-generic #80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15652/rh.wm.mgh --regheader pd_struc_recon --cortex srcvol = /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00784 0.99848 0.05447 -0.00002; 0.99494 0.01324 -0.09958 0.00002; -0.10015 0.05341 -0.99354 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Reading surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 = 82077 Masking with /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15652/rh.wm.mgh Dim: 136622 1 1 mri_vol2surf --mov /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15652/rh.gm.mgh --projfrac 0.3 --regheader pd_struc_recon --cortex srcvol = /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00784 0.99848 0.05447 -0.00002; 0.99494 0.01324 -0.09958 0.00002; -0.10015 0.05341 -0.99354 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Reading surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Done reading source surface Reading thickness /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 = 93362 Masking with /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Writing to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15652/rh.gm.mgh Dim: 136622 1 1 mri_concat /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15652/rh.wm.mgh /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/tmp.pctsurfcon.15652/rh.gm.mgh --paired-diff-norm --mul 100 --o /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.w-g.pct.mgh mri_segstats --in /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.w-g.pct.mgh --annot pd_struc_recon rh aparc --sum /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/stats/rh.w-g.pct.stats --snr 7.1.1 cwd cmdline mri_segstats --in /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.w-g.pct.mgh --annot pd_struc_recon rh aparc --sum /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/stats/rh.w-g.pct.stats --snr sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.w-g.pct.mgh Vertex Area is 0.693019 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 2021:05:08:18:09:41 pctsurfcon N 3 e 3.25 S 0.26 U 2.99 P 100% M 284500 F 0 R 205028 W 0 c 14 w 68 I 0 O 3320 L 1.90 1.58 1.49 @#@FSLOADPOST 2021:05:08:18:09:44 pctsurfcon N 3 1.90 1.58 1.49 #----------------------------------------- #@# Relabel Hypointensities 2021��� 05��� 08��� ��������� 18:09:44 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3338 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2657 voxels changed to hypointensity... 6027 hypointense voxels neighboring cortex changed @#@FSTIME 2021:05:08:18:09:44 mri_relabel_hypointensities N 3 e 13.12 S 0.29 U 12.83 P 99% M 475236 F 5 R 340070 W 0 c 29 w 6 I 1280 O 680 L 1.90 1.58 1.49 @#@FSLOADPOST 2021:05:08:18:09:57 mri_relabel_hypointensities N 3 1.85 1.58 1.49 #----------------------------------------- #@# APas-to-ASeg 2021��� 05��� 08��� ��������� 18:09:57 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/ribbon.mgz --threads 1 --lh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label --lh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white --lh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial --rh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label --rh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white --rh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC outvol aseg.mgz 12 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/ribbon.mgz Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 = 142133 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 950180 mri_surf2volseg done @#@FSTIME 2021:05:08:18:09:57 mri_surf2volseg N 20 e 11.48 S 0.29 U 11.18 P 99% M 905652 F 4 R 255999 W 0 c 45 w 5 I 1424 O 720 L 1.85 1.58 1.49 @#@FSLOADPOST 2021:05:08:18:10:09 mri_surf2volseg N 20 1.80 1.58 1.49 mri_brainvol_stats pd_struc_recon ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1663981.0 #CBVS2 BrainSegVol 1233542.0 #CBVS2 BrainSegVolNotVent 1208799.0 #CBVS2 SupraTentVol 1095879.0 #CBVS2 SupraTentVolNotVent 1071136.0 #CBVS2 lhCtxGM 254612.8 #CBVS2 rhCtxGM 247331.5 #CBVS2 lhCerebralWM 255855.5 #CBVS2 rhCerebralWM 254783.5 #CBVS2 SubCortGMVol 58774.0 #CBVS2 CerebellumVol 137663.0 #CBVS2 CerebellumGMVol 108275.0 #CBVS2 VentChorVol 20562.0 #CBVS2 3rd4th5thCSF 4181.0 #CBVS2 AllCSF 24743.0 #CBVS2 CCVol 4561.0 @#@FSTIME 2021:05:08:18:10:09 mri_brainvol_stats N 1 e 4.20 S 0.14 U 4.05 P 99% M 223856 F 15 R 125754 W 0 c 7 w 21 I 4264 O 8 L 1.80 1.58 1.49 @#@FSLOADPOST 2021:05:08:18:10:13 mri_brainvol_stats N 1 1.81 1.59 1.50 #----------------------------------------- #@# AParc-to-ASeg aparc 2021��� 05��� 08��� ��������� 18:10:13 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.aparc.annot 1000 --lh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label --lh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white --lh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial --rh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.aparc.annot 2000 --rh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label --rh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white --rh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC outvol aparc+aseg.mgz 12 avail.processors, using 1 Loading aseg.mgz Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9134 vertices from lh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9387 vertices from rh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 = 501702 ndotcheck = 20009 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 934388 mri_surf2volseg done @#@FSTIME 2021:05:08:18:10:13 mri_surf2volseg N 25 e 114.96 S 0.21 U 114.51 P 99% M 890148 F 2 R 248558 W 0 c 6313 w 3 I 344 O 832 L 1.81 1.59 1.50 @#@FSLOADPOST 2021:05:08:18:12:08 mri_surf2volseg N 25 1.38 1.53 1.49 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s 2021��� 05��� 08��� ��������� 18:12:08 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label --lh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white --lh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial --rh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label --rh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white --rh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC outvol aparc.a2009s+aseg.mgz 12 avail.processors, using 1 Loading aseg.mgz Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9134 vertices from lh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9387 vertices from rh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 501702 ndotcheck = 20009 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 934484 mri_surf2volseg done @#@FSTIME 2021:05:08:18:12:08 mri_surf2volseg N 25 e 117.43 S 0.23 U 117.19 P 99% M 890144 F 0 R 248677 W 0 c 369 w 1 I 0 O 896 L 1.38 1.53 1.49 @#@FSLOADPOST 2021:05:08:18:14:05 mri_surf2volseg N 25 1.33 1.45 1.46 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas 2021��� 05��� 08��� ��������� 18:14:05 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label --lh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white --lh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial --rh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label --rh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white --rh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC outvol aparc.DKTatlas+aseg.mgz 12 avail.processors, using 1 Loading aseg.mgz Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9134 vertices from lh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9387 vertices from rh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 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/media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.aparc.annot 3000 --lh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label --lh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white --lh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial --rh-annot /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.aparc.annot 4000 --rh-cortex-mask /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label --rh-white /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white --rh-pial /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC outvol wmparc.mgz 12 avail.processors, using 1 Loading aparc+aseg.mgz Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9134 vertices from lh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9387 vertices from rh hemi Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 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--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 pd_struc_recon --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1622534 mm^3 (det: 1.200656 ) 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 2021:05:08:18:16:47 mri_segstats N 24 e 257.53 S 0.47 U 256.98 P 99% M 240040 F 0 R 1232537 W 0 c 2846 w 3 I 56 O 24 L 1.55 1.45 1.46 @#@FSLOADPOST 2021:05:08:18:21:04 mri_segstats N 24 1.58 1.48 1.46 #----------------------------------------- #@# Parcellation Stats lh 2021��� 05��� 08��� ��������� 18:21:04 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 254591 Total vertex volume 254335 (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) = 1622534 mm^3 (det: 1.200656 ) 1596 1113 2984 2.620 0.398 0.096 0.016 10 1.2 bankssts 755 489 1277 2.390 0.482 0.105 0.015 7 0.4 caudalanteriorcingulate 3570 2466 7129 2.578 0.517 0.113 0.024 29 3.7 caudalmiddlefrontal 2226 1528 3324 1.979 0.425 0.132 0.030 27 2.8 cuneus 781 557 2203 3.010 0.749 0.140 0.041 10 1.1 entorhinal 4382 2997 10177 2.882 0.590 0.125 0.028 47 5.0 fusiform 6406 4491 12020 2.289 0.602 0.117 0.025 71 6.5 inferiorparietal 4239 3047 10100 2.834 0.719 0.125 0.027 47 4.6 inferiortemporal 1837 1287 3241 2.231 0.795 0.113 0.024 21 1.8 isthmuscingulate 6837 4634 12131 2.241 0.655 0.130 0.028 79 7.8 lateraloccipital 3537 2592 7883 2.853 0.573 0.130 0.030 40 4.2 lateralorbitofrontal 4622 3299 7402 2.073 0.535 0.135 0.032 53 6.3 lingual 2368 1784 5081 2.643 0.557 0.132 0.029 33 2.8 medialorbitofrontal 5284 3712 13301 2.857 0.662 0.122 0.027 64 5.4 middletemporal 1100 705 2423 2.871 0.729 0.098 0.027 10 1.0 parahippocampal 1935 1237 3482 2.596 0.578 0.102 0.022 12 1.8 paracentral 2279 1560 4196 2.406 0.459 0.111 0.024 21 2.0 parsopercularis 820 675 2159 2.540 0.663 0.171 0.046 16 1.6 parsorbitalis 2268 1599 4347 2.398 0.497 0.120 0.025 24 2.2 parstriangularis 2008 1408 2136 1.622 0.395 0.114 0.025 20 2.2 pericalcarine 6604 4455 11173 2.142 0.637 0.108 0.023 57 6.2 postcentral 1645 1204 3089 2.440 0.668 0.131 0.027 23 2.1 posteriorcingulate 8788 5733 17122 2.678 0.609 0.103 0.024 60 8.3 precentral 5926 4290 10758 2.314 0.475 0.130 0.027 68 6.5 precuneus 1133 745 2055 2.667 0.694 0.107 0.020 12 0.9 rostralanteriorcingulate 8280 6239 16743 2.317 0.536 0.132 0.029 102 10.8 rostralmiddlefrontal 11141 8010 24366 2.634 0.523 0.123 0.027 106 12.6 superiorfrontal 7755 5396 13793 2.225 0.547 0.123 0.024 86 7.7 superiorparietal 6542 4439 14427 2.808 0.676 0.112 0.027 61 6.7 superiortemporal 5287 3744 10781 2.532 0.531 0.126 0.026 60 5.6 supramarginal 329 277 1099 2.788 0.548 0.174 0.040 7 0.5 frontalpole 790 588 2882 3.546 0.639 0.135 0.042 9 1.1 temporalpole 823 499 1340 2.329 0.300 0.093 0.026 5 0.7 transversetemporal 3878 2616 7708 2.980 0.791 0.118 0.034 40 5.2 insula @#@FSTIME 2021:05:08:18:21:04 mris_anatomical_stats N 14 e 14.62 S 0.09 U 14.50 P 99% M 482972 F 6 R 136402 W 0 c 535 w 7 I 1416 O 24 L 1.58 1.48 1.46 @#@FSLOADPOST 2021:05:08:18:21:19 mris_anatomical_stats N 14 1.45 1.45 1.46 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 pd_struc_recon lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 254591 Total vertex volume 254335 (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) = 1622534 mm^3 (det: 1.200656 ) 1596 1214 2984 2.620 0.398 0.126 0.033 34 2.1 bankssts 755 603 1277 2.390 0.482 0.129 0.037 13 0.9 caudalanteriorcingulate 3570 2994 7129 2.578 0.517 0.139 0.032 54 4.9 caudalmiddlefrontal 2226 1974 3324 1.979 0.425 0.161 0.041 44 3.7 cuneus 781 902 2203 3.010 0.749 0.260 0.070 29 3.0 entorhinal 4382 3944 10177 2.882 0.590 0.158 0.047 122 7.9 fusiform 6406 5780 12020 2.289 0.602 0.151 0.032 100 9.3 inferiorparietal 4239 3892 10100 2.834 0.719 0.159 0.042 156 7.7 inferiortemporal 1837 1677 3241 2.231 0.795 0.173 0.050 76 3.8 isthmuscingulate 6837 5984 12131 2.241 0.655 0.148 0.035 108 10.0 lateraloccipital 3537 3057 7883 2.853 0.573 0.154 0.043 258 5.9 lateralorbitofrontal 4622 4128 7402 2.073 0.535 0.157 0.043 100 7.5 lingual 2368 2162 5081 2.643 0.557 0.155 0.037 38 3.6 medialorbitofrontal 5284 5354 13301 2.857 0.662 0.165 0.038 199 7.9 middletemporal 1100 1035 2423 2.871 0.729 0.180 0.048 17 2.6 parahippocampal 1935 1420 3482 2.596 0.578 0.117 0.028 26 2.1 paracentral 2279 1831 4196 2.406 0.459 0.135 0.028 27 2.7 parsopercularis 820 1021 2159 2.540 0.663 0.215 0.049 14 1.8 parsorbitalis 2268 2030 4347 2.398 0.497 0.152 0.033 1643 2.8 parstriangularis 2008 1289 2136 1.622 0.395 0.121 0.041 44 2.4 pericalcarine 6604 5834 11173 2.142 0.637 0.131 0.026 54 7.0 postcentral 1645 1373 3089 2.440 0.668 0.158 0.045 41 3.1 posteriorcingulate 8788 6688 17122 2.678 0.609 0.110 0.024 103 8.6 precentral 5926 4973 10758 2.314 0.475 0.152 0.037 188 8.7 precuneus 1133 837 2055 2.667 0.694 0.139 0.035 21 1.6 rostralanteriorcingulate 8280 8069 16743 2.317 0.536 0.173 0.038 199 13.2 rostralmiddlefrontal 11141 10060 24366 2.634 0.523 0.148 0.036 183 15.1 superiorfrontal 7755 6819 13793 2.225 0.547 0.147 0.033 117 10.2 superiorparietal 6542 5537 14427 2.808 0.676 0.138 0.032 148 8.6 superiortemporal 5287 4585 10781 2.532 0.531 0.154 0.037 145 7.9 supramarginal 329 538 1099 2.788 0.548 0.277 0.045 5 0.7 frontalpole 790 996 2882 3.546 0.639 0.178 0.042 10 1.4 temporalpole 823 682 1340 2.329 0.300 0.109 0.040 9 0.8 transversetemporal 3878 2540 7708 2.980 0.791 0.141 0.045 81 7.7 insula @#@FSTIME 2021:05:08:18:21:19 mris_anatomical_stats N 14 e 14.84 S 0.12 U 14.72 P 100% M 483080 F 0 R 136402 W 0 c 49 w 1 I 0 O 24 L 1.45 1.45 1.46 @#@FSLOADPOST 2021:05:08:18:21:34 mris_anatomical_stats N 14 1.50 1.46 1.46 #----------------------------------------- #@# Parcellation Stats rh 2021��� 05��� 08��� ��������� 18:21:34 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 247033 Total vertex volume 246785 (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) = 1622534 mm^3 (det: 1.200656 ) 1169 776 1896 2.566 0.408 0.105 0.022 7 1.2 bankssts 1217 844 2170 2.361 0.618 0.126 0.019 15 1.0 caudalanteriorcingulate 3648 2578 6675 2.302 0.505 0.114 0.021 31 3.4 caudalmiddlefrontal 2355 1570 4112 2.315 0.480 0.137 0.034 30 3.2 cuneus 594 398 1570 3.209 0.626 0.106 0.041 8 0.9 entorhinal 4773 3258 10565 2.750 0.665 0.119 0.026 47 4.9 fusiform 6448 4583 13259 2.371 0.693 0.125 0.023 72 6.4 inferiorparietal 5191 3594 12223 2.712 0.749 0.121 0.031 77 6.5 inferiortemporal 1823 1329 3275 2.186 0.793 0.124 0.029 26 2.2 isthmuscingulate 7045 5001 13382 2.241 0.662 0.132 0.028 88 8.0 lateraloccipital 3709 2691 7569 2.660 0.562 0.136 0.034 45 5.2 lateralorbitofrontal 4829 3449 7641 2.114 0.497 0.138 0.034 58 6.6 lingual 2962 2140 5965 2.519 0.580 0.122 0.027 37 3.3 medialorbitofrontal 5046 3543 12093 2.669 0.789 0.115 0.025 56 5.0 middletemporal 1098 676 2347 2.819 0.764 0.084 0.020 13 0.7 parahippocampal 2479 1629 4170 2.398 0.539 0.111 0.023 20 2.2 paracentral 2707 1912 4926 2.385 0.424 0.114 0.022 25 2.4 parsopercularis 1142 840 2946 2.561 0.665 0.126 0.026 12 1.3 parsorbitalis 2867 2114 5596 2.290 0.513 0.129 0.027 33 3.1 parstriangularis 2313 1602 2838 1.851 0.527 0.134 0.028 27 2.6 pericalcarine 6877 4508 11387 2.157 0.617 0.109 0.024 68 6.3 postcentral 1938 1414 3511 2.283 0.603 0.124 0.025 21 2.1 posteriorcingulate 7804 5138 14388 2.520 0.615 0.107 0.023 55 7.1 precentral 5559 3986 9917 2.335 0.531 0.124 0.026 58 5.8 precuneus 923 696 2173 2.704 0.574 0.126 0.023 13 0.9 rostralanteriorcingulate 7804 5926 14702 2.155 0.562 0.137 0.030 110 10.3 rostralmiddlefrontal 9537 6924 19838 2.489 0.484 0.125 0.028 103 11.0 superiorfrontal 6895 4706 11437 2.126 0.534 0.116 0.021 67 6.0 superiorparietal 6007 3944 11682 2.661 0.569 0.105 0.023 52 5.7 superiortemporal 5467 3737 10361 2.443 0.615 0.108 0.020 45 4.5 supramarginal 425 333 1218 2.630 0.673 0.162 0.039 8 0.6 frontalpole 826 624 3306 3.490 0.757 0.144 0.044 11 1.4 temporalpole 605 378 925 2.438 0.469 0.123 0.022 6 0.5 transversetemporal 3153 2138 6724 3.145 0.777 0.106 0.025 23 3.0 insula @#@FSTIME 2021:05:08:18:21:34 mris_anatomical_stats N 14 e 14.75 S 0.14 U 14.60 P 99% M 481728 F 0 R 139594 W 0 c 33 w 1 I 0 O 24 L 1.50 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:21:49 mris_anatomical_stats N 14 1.47 1.46 1.46 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 pd_struc_recon rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 247033 Total vertex volume 246785 (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) = 1622534 mm^3 (det: 1.200656 ) 1169 695 1896 2.566 0.408 0.127 0.041 38 1.5 bankssts 1217 965 2170 2.361 0.618 0.157 0.058 130 1.8 caudalanteriorcingulate 3648 3098 6675 2.302 0.505 0.136 0.025 45 4.1 caudalmiddlefrontal 2355 2093 4112 2.315 0.480 0.145 0.036 47 3.4 cuneus 594 618 1570 3.209 0.626 0.232 0.062 36 1.7 entorhinal 4773 4223 10565 2.750 0.665 0.154 0.041 123 7.9 fusiform 6448 6147 13259 2.371 0.693 0.158 0.035 90 9.9 inferiorparietal 5191 5105 12223 2.712 0.749 0.167 0.040 108 8.9 inferiortemporal 1823 1693 3275 2.186 0.793 0.154 0.040 35 2.8 isthmuscingulate 7045 6812 13382 2.241 0.662 0.162 0.038 350 11.3 lateraloccipital 3709 3195 7569 2.660 0.562 0.154 0.040 85 5.7 lateralorbitofrontal 4829 4017 7641 2.114 0.497 0.151 0.042 84 8.0 lingual 2962 2665 5965 2.519 0.580 0.159 0.039 109 5.2 medialorbitofrontal 5046 5044 12093 2.669 0.789 0.161 0.037 76 7.9 middletemporal 1098 950 2347 2.819 0.764 0.145 0.036 13 1.8 parahippocampal 2479 1804 4170 2.398 0.539 0.121 0.023 32 2.4 paracentral 2707 2221 4926 2.385 0.424 0.133 0.027 35 3.1 parsopercularis 1142 1385 2946 2.561 0.665 0.194 0.038 14 2.0 parsorbitalis 2867 2805 5596 2.290 0.513 0.164 0.032 39 3.8 parstriangularis 2313 1584 2838 1.851 0.527 0.139 0.035 35 3.2 pericalcarine 6877 5918 11387 2.157 0.617 0.128 0.025 62 7.0 postcentral 1938 1656 3511 2.283 0.603 0.169 0.046 122 3.6 posteriorcingulate 7804 5938 14388 2.520 0.615 0.114 0.025 92 7.9 precentral 5559 4554 9917 2.335 0.531 0.144 0.033 100 7.4 precuneus 923 908 2173 2.704 0.574 0.160 0.030 19 1.3 rostralanteriorcingulate 7804 7547 14702 2.155 0.562 0.176 0.037 128 12.8 rostralmiddlefrontal 9537 8755 19838 2.489 0.484 0.154 0.034 152 12.6 superiorfrontal 6895 5839 11437 2.126 0.534 0.135 0.028 83 7.7 superiorparietal 6007 4719 11682 2.661 0.569 0.122 0.029 84 6.5 superiortemporal 5467 4438 10361 2.443 0.615 0.133 0.029 76 6.4 supramarginal 425 601 1218 2.630 0.673 0.230 0.042 9 0.9 frontalpole 826 1268 3306 3.490 0.757 0.241 0.052 12 2.1 temporalpole 605 402 925 2.438 0.469 0.095 0.028 8 0.5 transversetemporal 3153 1952 6724 3.145 0.777 0.127 0.039 57 4.9 insula @#@FSTIME 2021:05:08:18:21:49 mris_anatomical_stats N 14 e 14.60 S 0.12 U 14.48 P 99% M 481696 F 0 R 139594 W 0 c 62 w 1 I 0 O 24 L 1.47 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:22:03 mris_anatomical_stats N 14 1.44 1.45 1.45 #----------------------------------------- #@# Parcellation Stats 2 lh 2021��� 05��� 08��� ��������� 18:22:03 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 254591 Total vertex volume 254335 (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) = 1622534 mm^3 (det: 1.200656 ) 1076 846 2210 2.318 0.533 0.151 0.039 14 2.0 G_and_S_frontomargin 1504 1074 3571 2.743 0.599 0.133 0.029 17 1.9 G_and_S_occipital_inf 1342 894 2854 2.590 0.640 0.120 0.029 12 1.5 G_and_S_paracentral 1791 1247 4047 2.715 0.525 0.120 0.031 18 1.9 G_and_S_subcentral 657 557 1789 2.454 0.554 0.150 0.034 13 0.9 G_and_S_transv_frontopol 2218 1586 4360 2.671 0.521 0.119 0.024 23 2.2 G_and_S_cingul-Ant 1199 794 1971 2.552 0.336 0.097 0.015 7 0.8 G_and_S_cingul-Mid-Ant 1266 910 2393 2.630 0.446 0.120 0.026 13 1.4 G_and_S_cingul-Mid-Post 596 465 1585 2.803 0.627 0.153 0.037 10 1.0 G_cingul-Post-dorsal 379 274 1028 2.864 0.859 0.137 0.035 5 0.5 G_cingul-Post-ventral 2056 1408 3190 1.941 0.523 0.138 0.033 30 2.8 G_cuneus 1250 885 3058 2.684 0.377 0.116 0.028 15 1.2 G_front_inf-Opercular 361 270 1066 2.810 0.525 0.127 0.029 4 0.4 G_front_inf-Orbital 1283 958 3136 2.589 0.487 0.147 0.036 21 1.8 G_front_inf-Triangul 3990 3052 10610 2.601 0.586 0.140 0.034 58 5.7 G_front_middle 7862 5689 19187 2.728 0.554 0.129 0.030 84 9.7 G_front_sup 655 470 1438 3.277 0.654 0.133 0.044 7 1.2 G_Ins_lg_and_S_cent_ins 717 479 2289 3.465 0.698 0.139 0.041 11 1.2 G_insular_short 2214 1617 5401 2.520 0.653 0.128 0.029 27 2.6 G_occipital_middle 1398 944 2704 2.338 0.603 0.133 0.028 18 1.5 G_occipital_sup 1724 1179 4696 2.991 0.564 0.132 0.032 24 2.1 G_oc-temp_lat-fusifor 3069 2279 5803 2.138 0.563 0.156 0.040 45 5.2 G_oc-temp_med-Lingual 1350 905 3687 3.053 0.791 0.124 0.039 17 1.7 G_oc-temp_med-Parahip 2165 1729 6052 2.798 0.627 0.156 0.040 38 3.5 G_orbital 2301 1663 5607 2.508 0.696 0.129 0.030 36 2.5 G_pariet_inf-Angular 2465 1839 6442 2.695 0.560 0.140 0.032 36 3.0 G_pariet_inf-Supramar 3090 2222 6784 2.353 0.613 0.136 0.029 46 3.6 G_parietal_sup 2539 1717 5157 2.335 0.560 0.120 0.028 30 2.7 G_postcentral 3149 1955 7982 3.035 0.602 0.105 0.026 24 3.3 G_precentral 2598 2062 6197 2.431 0.509 0.154 0.034 45 3.6 G_precuneus 1001 790 2796 2.832 0.442 0.151 0.035 22 1.4 G_rectus 878 558 1407 2.461 0.844 0.119 0.046 15 1.3 G_subcallosal 647 383 1178 2.422 0.309 0.098 0.027 5 0.6 G_temp_sup-G_T_transv 2170 1515 6900 3.197 0.664 0.135 0.038 28 3.1 G_temp_sup-Lateral 869 581 2069 3.360 0.705 0.082 0.018 3 0.6 G_temp_sup-Plan_polar 1096 743 2064 2.486 0.439 0.095 0.017 7 0.7 G_temp_sup-Plan_tempo 2292 1731 6967 2.955 0.785 0.145 0.037 38 3.3 G_temporal_inf 2885 2075 8887 3.017 0.699 0.135 0.034 46 3.3 G_temporal_middle 331 219 374 1.863 0.303 0.091 0.013 1 0.2 Lat_Fis-ant-Horizont 418 274 485 2.011 0.363 0.077 0.008 1 0.1 Lat_Fis-ant-Vertical 1348 872 1710 2.340 0.441 0.114 0.024 9 1.4 Lat_Fis-post 1774 1180 2649 1.946 0.600 0.145 0.036 28 2.4 Pole_occipital 1696 1256 5983 3.389 0.717 0.145 0.040 23 2.4 Pole_temporal 2702 1867 3003 1.797 0.471 0.106 0.021 21 2.4 S_calcarine 3431 2282 3963 1.980 0.595 0.097 0.020 16 2.9 S_central 991 651 1300 2.133 0.402 0.090 0.013 5 0.6 S_cingul-Marginalis 437 294 690 2.726 0.370 0.083 0.014 1 0.2 S_circular_insula_ant 1658 1092 2543 2.787 0.819 0.087 0.017 7 1.4 S_circular_insula_inf 1842 1205 2597 2.537 0.436 0.097 0.018 7 1.6 S_circular_insula_sup 1083 716 1763 2.764 0.498 0.110 0.021 7 1.0 S_collat_transv_ant 403 262 561 2.372 0.408 0.112 0.015 3 0.3 S_collat_transv_post 2640 1804 3837 2.167 0.400 0.108 0.019 18 2.2 S_front_inf 1688 1245 2905 2.288 0.484 0.128 0.026 17 2.1 S_front_middle 3061 2134 4892 2.334 0.432 0.104 0.020 22 2.6 S_front_sup 178 134 410 3.017 0.614 0.133 0.024 1 0.2 S_interm_prim-Jensen 2434 1600 2871 2.066 0.353 0.102 0.017 17 1.8 S_intrapariet_and_P_trans 989 644 1067 1.843 0.353 0.118 0.023 7 1.0 S_oc_middle_and_Lunatus 1246 854 1719 1.995 0.441 0.124 0.022 10 1.3 S_oc_sup_and_transversal 748 471 1016 2.128 0.571 0.094 0.015 4 0.6 S_occipital_ant 602 423 1009 2.632 0.435 0.113 0.020 4 0.6 S_oc-temp_lat 2324 1532 3192 2.353 0.489 0.094 0.016 11 1.6 S_oc-temp_med_and_Lingual 475 331 569 1.991 0.302 0.105 0.017 3 0.3 S_orbital_lateral 679 472 902 2.533 0.636 0.109 0.017 4 0.5 S_orbital_med-olfact 1205 900 2712 2.995 0.618 0.146 0.038 15 1.8 S_orbital-H_Shaped 2537 1724 3758 2.236 0.425 0.112 0.020 19 2.2 S_parieto_occipital 1235 784 1136 1.684 0.575 0.104 0.018 16 0.9 S_pericallosal 2852 1935 3689 2.061 0.443 0.109 0.021 21 2.7 S_postcentral 1979 1335 3069 2.410 0.390 0.096 0.017 13 1.3 S_precentral-inf-part 1966 1268 2709 2.439 0.451 0.094 0.017 9 1.6 S_precentral-sup-part 641 468 989 2.460 0.561 0.130 0.021 6 0.6 S_suborbital 1306 897 1708 2.135 0.361 0.116 0.021 9 1.3 S_subparietal 1577 1050 2419 2.614 0.519 0.102 0.018 9 1.3 S_temporal_inf 6676 4558 10998 2.451 0.478 0.105 0.021 57 5.6 S_temporal_sup 517 340 574 2.126 0.253 0.103 0.018 3 0.4 S_temporal_transverse @#@FSTIME 2021:05:08:18:22:03 mris_anatomical_stats N 14 e 15.34 S 0.15 U 15.19 P 100% M 483092 F 0 R 139914 W 0 c 32 w 1 I 0 O 40 L 1.44 1.45 1.45 @#@FSLOADPOST 2021:05:08:18:22:19 mris_anatomical_stats N 14 1.57 1.48 1.46 #----------------------------------------- #@# Parcellation Stats 2 rh 2021��� 05��� 08��� ��������� 18:22:19 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 247033 Total vertex volume 246785 (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) = 1622534 mm^3 (det: 1.200656 ) 850 662 1430 1.911 0.581 0.149 0.035 19 1.3 G_and_S_frontomargin 1326 967 2630 2.194 0.775 0.124 0.023 13 1.3 G_and_S_occipital_inf 1404 905 2800 2.518 0.590 0.115 0.026 12 1.4 G_and_S_paracentral 1862 1266 3839 2.502 0.590 0.130 0.033 31 2.2 G_and_S_subcentral 986 822 2470 2.364 0.613 0.150 0.037 16 1.5 G_and_S_transv_frontopol 2660 1930 5086 2.445 0.510 0.116 0.022 31 2.5 G_and_S_cingul-Ant 1509 1088 2939 2.487 0.404 0.125 0.022 19 1.4 G_and_S_cingul-Mid-Ant 1630 1180 2892 2.403 0.471 0.113 0.022 11 1.6 G_and_S_cingul-Mid-Post 490 386 1416 2.843 0.603 0.162 0.042 8 0.8 G_cingul-Post-dorsal 453 326 1054 2.727 0.460 0.136 0.027 7 0.4 G_cingul-Post-ventral 2144 1423 3775 2.250 0.526 0.147 0.039 33 3.2 G_cuneus 1765 1302 4066 2.556 0.425 0.127 0.029 22 1.9 G_front_inf-Opercular 456 332 1295 2.745 0.630 0.132 0.030 6 0.5 G_front_inf-Orbital 1412 1092 3353 2.404 0.471 0.153 0.034 23 2.0 G_front_inf-Triangul 3671 2908 9571 2.483 0.571 0.144 0.031 59 4.8 G_front_middle 6133 4581 15386 2.669 0.496 0.137 0.034 83 8.4 G_front_sup 566 398 1518 3.596 0.705 0.106 0.030 5 0.4 G_Ins_lg_and_S_cent_ins 687 513 2267 3.535 0.915 0.129 0.035 9 1.0 G_insular_short 2330 1667 5974 2.711 0.627 0.137 0.027 33 2.7 G_occipital_middle 1687 1156 3149 2.265 0.551 0.135 0.028 23 1.8 G_occipital_sup 2326 1599 5862 2.809 0.676 0.123 0.029 29 2.7 G_oc-temp_lat-fusifor 2958 2150 5026 2.108 0.497 0.149 0.041 42 4.6 G_oc-temp_med-Lingual 1350 872 3841 3.188 0.757 0.112 0.039 24 1.7 G_oc-temp_med-Parahip 2509 1918 6905 2.758 0.579 0.147 0.039 41 3.8 G_orbital 2323 1670 5738 2.590 0.673 0.138 0.027 35 2.8 G_pariet_inf-Angular 2978 2088 7095 2.671 0.635 0.120 0.026 34 3.0 G_pariet_inf-Supramar 2285 1584 4688 2.298 0.584 0.124 0.023 27 2.1 G_parietal_sup 2419 1524 4685 2.350 0.613 0.113 0.025 24 2.2 G_postcentral 2763 1789 6817 2.859 0.549 0.109 0.027 24 2.8 G_precentral 2236 1724 5308 2.489 0.585 0.145 0.032 32 3.0 G_precuneus 799 598 2209 2.725 0.432 0.131 0.033 12 1.1 G_rectus 627 439 1093 2.570 0.836 0.133 0.041 7 1.1 G_subcallosal 451 278 791 2.440 0.425 0.093 0.018 3 0.3 G_temp_sup-G_T_transv 1826 1198 4634 2.836 0.657 0.118 0.031 22 2.1 G_temp_sup-Lateral 1098 711 2310 3.112 0.647 0.086 0.017 4 0.9 G_temp_sup-Plan_polar 1091 726 1873 2.432 0.423 0.091 0.014 7 0.6 G_temp_sup-Plan_tempo 2844 2029 8321 2.930 0.754 0.135 0.040 61 4.5 G_temporal_inf 2759 2002 8627 2.984 0.767 0.128 0.030 42 3.2 G_temporal_middle 405 273 481 2.071 0.424 0.091 0.013 1 0.2 Lat_Fis-ant-Horizont 420 285 525 2.169 0.408 0.105 0.017 2 0.3 Lat_Fis-ant-Vertical 1698 1103 2170 2.450 0.600 0.106 0.018 11 1.3 Lat_Fis-post 2963 2123 5239 2.059 0.607 0.142 0.034 46 3.6 Pole_occipital 1766 1353 6709 3.309 0.776 0.148 0.039 26 2.8 Pole_temporal 2893 2019 3527 1.931 0.497 0.121 0.024 26 3.0 S_calcarine 3352 2250 3890 1.941 0.557 0.100 0.020 16 3.0 S_central 1472 1009 2007 2.090 0.413 0.106 0.017 10 1.1 S_cingul-Marginalis 520 339 881 3.045 0.631 0.093 0.019 2 0.4 S_circular_insula_ant 1212 781 1689 2.622 0.574 0.079 0.012 4 0.7 S_circular_insula_inf 1481 964 2079 2.585 0.441 0.103 0.019 7 1.3 S_circular_insula_sup 1213 807 1914 2.515 0.534 0.105 0.018 7 1.0 S_collat_transv_ant 328 214 350 1.993 0.385 0.112 0.017 2 0.2 S_collat_transv_post 2497 1695 3372 2.086 0.402 0.115 0.020 19 2.2 S_front_inf 2043 1487 2994 1.961 0.461 0.125 0.028 19 2.6 S_front_middle 2677 1790 3682 2.214 0.365 0.101 0.018 15 2.2 S_front_sup 324 230 463 2.121 0.431 0.127 0.020 3 0.3 S_interm_prim-Jensen 2398 1668 3244 1.984 0.401 0.111 0.019 18 2.1 S_intrapariet_and_P_trans 854 591 991 1.827 0.361 0.121 0.026 6 0.9 S_oc_middle_and_Lunatus 1106 751 1467 2.016 0.439 0.110 0.019 7 1.0 S_oc_sup_and_transversal 943 652 1499 2.253 0.427 0.111 0.020 7 0.8 S_occipital_ant 811 569 1470 2.550 0.518 0.103 0.018 4 0.6 S_oc-temp_lat 2108 1394 3041 2.472 0.465 0.097 0.016 12 1.4 S_oc-temp_med_and_Lingual 550 408 859 1.947 0.489 0.132 0.029 6 0.7 S_orbital_lateral 748 528 1058 2.439 0.618 0.120 0.021 7 0.7 S_orbital_med-olfact 1315 945 2413 2.534 0.618 0.129 0.028 12 1.6 S_orbital-H_Shaped 2683 1769 3785 2.266 0.463 0.106 0.019 18 2.2 S_parieto_occipital 1975 1293 1877 1.793 0.647 0.111 0.019 26 1.5 S_pericallosal 2382 1544 2981 2.053 0.381 0.093 0.015 11 1.6 S_postcentral 2136 1416 2706 2.089 0.447 0.097 0.016 13 1.4 S_precentral-inf-part 1349 910 1787 2.156 0.395 0.100 0.016 7 1.0 S_precentral-sup-part 443 314 637 2.380 0.430 0.122 0.022 3 0.4 S_suborbital 851 641 1569 2.544 0.475 0.138 0.036 11 1.2 S_subparietal 1666 1043 1764 2.015 0.452 0.092 0.014 7 1.2 S_temporal_inf 5720 3833 8594 2.291 0.536 0.103 0.020 40 4.7 S_temporal_sup 270 183 336 2.313 0.479 0.128 0.020 3 0.3 S_temporal_transverse @#@FSTIME 2021:05:08:18:22:19 mris_anatomical_stats N 14 e 15.24 S 0.13 U 15.10 P 99% M 481852 F 0 R 136092 W 0 c 26 w 3 I 0 O 40 L 1.57 1.48 1.46 @#@FSLOADPOST 2021:05:08:18:22:34 mris_anatomical_stats N 14 1.58 1.49 1.47 #----------------------------------------- #@# Parcellation Stats 3 lh 2021��� 05��� 08��� ��������� 18:22:34 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 254591 Total vertex volume 254335 (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) = 1622534 mm^3 (det: 1.200656 ) 1700 1116 3042 2.533 0.484 0.107 0.018 14 1.2 caudalanteriorcingulate 3746 2610 7531 2.567 0.517 0.111 0.024 31 3.7 caudalmiddlefrontal 3175 2137 4622 2.006 0.457 0.125 0.027 37 3.5 cuneus 651 454 1827 3.024 0.785 0.136 0.043 8 0.9 entorhinal 4071 2770 8832 2.819 0.550 0.122 0.026 42 4.4 fusiform 6379 4462 12193 2.315 0.595 0.118 0.025 71 6.5 inferiorparietal 4317 3103 11120 2.920 0.740 0.127 0.029 50 4.9 inferiortemporal 1810 1270 3208 2.243 0.791 0.114 0.024 21 1.8 isthmuscingulate 6783 4606 12048 2.233 0.655 0.131 0.028 80 7.9 lateraloccipital 3986 2998 9171 2.838 0.633 0.141 0.037 56 6.1 lateralorbitofrontal 4686 3358 7488 2.069 0.538 0.135 0.032 53 6.4 lingual 2230 1655 4714 2.589 0.614 0.135 0.033 37 2.6 medialorbitofrontal 6713 4737 15918 2.767 0.660 0.119 0.026 76 6.7 middletemporal 1134 733 2516 2.877 0.730 0.100 0.027 11 1.0 parahippocampal 2383 1549 4632 2.645 0.574 0.101 0.022 15 2.2 paracentral 2169 1472 3945 2.429 0.448 0.111 0.024 19 1.8 parsopercularis 920 688 1952 2.412 0.582 0.134 0.027 11 1.1 parsorbitalis 2760 1935 5229 2.388 0.488 0.116 0.025 28 2.7 parstriangularis 2005 1402 2170 1.647 0.420 0.114 0.025 20 2.2 pericalcarine 7336 4948 12158 2.141 0.624 0.108 0.023 62 6.7 postcentral 1790 1291 3229 2.442 0.654 0.129 0.027 24 2.2 posteriorcingulate 8670 5639 16926 2.689 0.606 0.104 0.024 59 8.2 precentral 5793 4260 10818 2.309 0.485 0.133 0.027 71 6.6 precuneus 1718 1188 3423 2.691 0.640 0.118 0.027 20 1.9 rostralanteriorcingulate 6118 4562 12483 2.335 0.551 0.133 0.029 73 8.0 rostralmiddlefrontal 11389 8396 24880 2.565 0.538 0.127 0.028 121 13.4 superiorfrontal 6208 4321 11330 2.260 0.547 0.122 0.024 68 6.2 superiorparietal 8621 5890 19646 2.867 0.693 0.112 0.027 77 8.9 superiortemporal 4839 3444 9905 2.536 0.541 0.128 0.028 56 5.4 supramarginal 826 500 1343 2.329 0.300 0.094 0.026 5 0.8 transversetemporal 2845 1927 6035 3.114 0.706 0.111 0.028 23 3.3 insula @#@FSTIME 2021:05:08:18:22:34 mris_anatomical_stats N 14 e 14.51 S 0.11 U 14.38 P 99% M 483048 F 0 R 136402 W 0 c 541 w 1 I 0 O 24 L 1.58 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:22:49 mris_anatomical_stats N 14 1.74 1.53 1.48 #----------------------------------------- #@# Parcellation Stats 3 rh 2021��� 05��� 08��� ��������� 18:22:49 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 pd_struc_recon rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 247033 Total vertex volume 246785 (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) = 1622534 mm^3 (det: 1.200656 ) 1326 918 2307 2.339 0.596 0.127 0.019 18 1.0 caudalanteriorcingulate 3811 2682 6956 2.304 0.503 0.116 0.021 35 3.6 caudalmiddlefrontal 2878 1917 4818 2.255 0.503 0.128 0.030 34 3.4 cuneus 527 345 1331 3.159 0.629 0.108 0.046 9 0.8 entorhinal 4387 2986 9403 2.729 0.630 0.118 0.026 43 4.4 fusiform 6396 4529 12859 2.352 0.690 0.125 0.023 71 6.5 inferiorparietal 5642 3916 13874 2.751 0.771 0.122 0.030 82 6.9 inferiortemporal 1807 1308 3204 2.186 0.786 0.123 0.029 26 2.1 isthmuscingulate 7061 5012 13365 2.235 0.648 0.133 0.028 88 8.0 lateraloccipital 4037 2980 8351 2.575 0.628 0.142 0.036 55 5.9 lateralorbitofrontal 4741 3386 7376 2.098 0.489 0.138 0.034 57 6.4 lingual 2109 1562 4560 2.580 0.575 0.130 0.031 27 2.6 medialorbitofrontal 6045 4227 13864 2.651 0.759 0.114 0.024 64 5.8 middletemporal 1189 743 2543 2.817 0.759 0.085 0.019 12 0.8 parahippocampal 2619 1729 4620 2.425 0.539 0.113 0.023 22 2.4 paracentral 3279 2301 5971 2.365 0.420 0.115 0.023 32 3.1 parsopercularis 974 683 2260 2.615 0.544 0.113 0.022 9 0.9 parsorbitalis 2664 1972 5082 2.257 0.540 0.133 0.027 31 3.0 parstriangularis 2271 1559 2819 1.870 0.526 0.131 0.028 26 2.5 pericalcarine 7511 4941 12215 2.142 0.610 0.108 0.023 71 6.7 postcentral 2125 1547 3915 2.317 0.602 0.126 0.026 23 2.4 posteriorcingulate 7547 4985 14018 2.519 0.613 0.107 0.023 54 7.0 precentral 5770 4145 10358 2.319 0.547 0.126 0.027 64 6.2 precuneus 1298 923 2677 2.614 0.647 0.118 0.023 16 1.3 rostralanteriorcingulate 5659 4297 11095 2.199 0.591 0.136 0.030 71 7.0 rostralmiddlefrontal 11865 8719 24377 2.443 0.513 0.125 0.028 140 14.2 superiorfrontal 5413 3717 9221 2.148 0.532 0.117 0.021 53 4.7 superiorparietal 7559 5055 16206 2.758 0.648 0.110 0.026 69 8.1 superiortemporal 5267 3585 10042 2.460 0.611 0.109 0.020 45 4.3 supramarginal 598 371 927 2.431 0.462 0.121 0.022 6 0.5 transversetemporal 2860 1940 6169 3.152 0.772 0.102 0.023 19 2.5 insula @#@FSTIME 2021:05:08:18:22:49 mris_anatomical_stats N 14 e 14.38 S 0.13 U 14.22 P 99% M 481536 F 0 R 132586 W 0 c 759 w 1 I 0 O 24 L 1.74 1.53 1.48 @#@FSLOADPOST 2021:05:08:18:23:03 mris_anatomical_stats N 14 1.57 1.50 1.47 #-------------------------------------------- #@# ASeg Stats 2021��� 05��� 08��� ��������� 18:23:03 CST /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon 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/ASegStatsLUT.txt --subject pd_struc_recon setting seed for random number genererator to 1234 7.1.1 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/ASegStatsLUT.txt --subject pd_struc_recon sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1622534 mm^3 (det: 1.200656 ) Computing euler number orig.nofix lheno = -28, rheno = -4 orig.nofix lhholes = 15, rhholes = 3 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 2021:05:08:18:23:03 mri_segstats N 32 e 137.97 S 0.38 U 137.58 P 99% M 282548 F 0 R 766480 W 0 c 311 w 1 I 0 O 24 L 1.57 1.50 1.47 @#@FSLOADPOST 2021:05:08:18:25:21 mri_segstats N 32 1.68 1.57 1.49 /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /media/yelab/data/PD/PD_Nii/sub1/STRUC; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh 2021��� 05��� 08��� ��������� 18:25:21 CST mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA1_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4266 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:21 mri_label2label N 12 e 4.57 S 0.13 U 4.43 P 99% M 559080 F 0 R 163807 W 0 c 15 w 6 I 16184 O 272 L 1.63 1.56 1.49 @#@FSLOADPOST 2021:05:08:18:25:26 mri_label2label N 12 1.63 1.56 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA2_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8084 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:26 mri_label2label N 12 e 5.30 S 0.17 U 5.12 P 99% M 559476 F 0 R 163877 W 0 c 18 w 2 I 632 O 488 L 1.63 1.56 1.49 @#@FSLOADPOST 2021:05:08:18:25:31 mri_label2label N 12 1.66 1.56 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3a_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4160 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:31 mri_label2label N 12 e 4.57 S 0.17 U 4.40 P 100% M 559076 F 0 R 163807 W 0 c 8 w 2 I 320 O 248 L 1.66 1.56 1.49 @#@FSLOADPOST 2021:05:08:18:25:36 mri_label2label N 12 1.61 1.55 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3b_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6131 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:36 mri_label2label N 12 e 4.99 S 0.13 U 4.85 P 99% M 559176 F 0 R 163840 W 0 c 14 w 2 I 472 O 376 L 1.61 1.55 1.49 @#@FSLOADPOST 2021:05:08:18:25:41 mri_label2label N 12 1.56 1.54 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4a_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 340 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6124 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:41 mri_label2label N 12 e 4.88 S 0.14 U 4.74 P 99% M 559280 F 0 R 163836 W 0 c 10 w 2 I 456 O 408 L 1.56 1.54 1.49 @#@FSLOADPOST 2021:05:08:18:25:46 mri_label2label N 12 1.59 1.55 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4p_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 258 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4328 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:46 mri_label2label N 12 e 4.56 S 0.15 U 4.41 P 99% M 559256 F 0 R 163809 W 0 c 10 w 2 I 320 O 280 L 1.59 1.55 1.49 @#@FSLOADPOST 2021:05:08:18:25:50 mri_label2label N 12 1.55 1.54 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA6_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 1085 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14674 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:50 mri_label2label N 12 e 7.53 S 0.21 U 7.31 P 99% M 559712 F 0 R 163980 W 0 c 42 w 2 I 1056 O 1016 L 1.55 1.54 1.49 @#@FSLOADPOST 2021:05:08:18:25:58 mri_label2label N 12 1.78 1.59 1.50 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA44_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4390 mri_label2label: Done @#@FSTIME 2021:05:08:18:25:58 mri_label2label N 12 e 4.53 S 0.14 U 4.39 P 99% M 559208 F 0 R 163807 W 0 c 11 w 2 I 328 O 288 L 1.78 1.59 1.50 @#@FSLOADPOST 2021:05:08:18:26:02 mri_label2label N 12 1.79 1.60 1.51 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA45_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 794 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4216 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:02 mri_label2label N 12 e 4.48 S 0.18 U 4.30 P 100% M 559164 F 0 R 163797 W 0 c 13 w 2 I 272 O 328 L 1.79 1.60 1.51 @#@FSLOADPOST 2021:05:08:18:26:07 mri_label2label N 12 1.81 1.61 1.51 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V1_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 871 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5512 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:07 mri_label2label N 12 e 4.70 S 0.15 U 4.55 P 99% M 559236 F 0 R 163822 W 0 c 7 w 2 I 376 O 440 L 1.81 1.61 1.51 @#@FSLOADPOST 2021:05:08:18:26:11 mri_label2label N 12 1.75 1.60 1.51 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V2_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 1766 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9880 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:12 mri_label2label N 12 e 5.51 S 0.15 U 5.35 P 99% M 559268 F 0 R 163891 W 0 c 12 w 2 I 664 O 784 L 1.75 1.60 1.51 @#@FSLOADPOST 2021:05:08:18:26:17 mri_label2label N 12 1.69 1.58 1.50 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.MT_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2265 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:17 mri_label2label N 12 e 4.23 S 0.17 U 4.06 P 99% M 559020 F 0 R 160259 W 0 c 13 w 2 I 168 O 184 L 1.69 1.58 1.50 @#@FSLOADPOST 2021:05:08:18:26:21 mri_label2label N 12 1.63 1.58 1.50 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1442 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:21 mri_label2label N 12 e 4.15 S 0.18 U 3.96 P 99% M 559100 F 0 R 160242 W 0 c 13 w 2 I 120 O 104 L 1.63 1.58 1.50 @#@FSLOADPOST 2021:05:08:18:26:25 mri_label2label N 12 1.63 1.58 1.50 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject pd_struc_recon --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1310 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:26 mri_label2label N 12 e 4.13 S 0.15 U 3.98 P 99% M 558900 F 0 R 160243 W 0 c 10 w 2 I 112 O 96 L 1.63 1.58 1.50 @#@FSLOADPOST 2021:05:08:18:26:30 mri_label2label N 12 1.58 1.57 1.50 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 506 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:30 mri_label2label N 12 e 3.98 S 0.14 U 3.83 P 99% M 559008 F 0 R 160231 W 0 c 11 w 2 I 40 O 48 L 1.58 1.57 1.50 @#@FSLOADPOST 2021:05:08:18:26:34 mri_label2label N 12 1.53 1.56 1.50 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 816 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:34 mri_label2label N 12 e 4.08 S 0.15 U 3.92 P 99% M 559084 F 0 R 160237 W 0 c 11 w 2 I 72 O 72 L 1.53 1.56 1.50 @#@FSLOADPOST 2021:05:08:18:26:38 mri_label2label N 12 1.49 1.55 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 179 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 2052 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:38 mri_label2label N 12 e 4.24 S 0.11 U 4.13 P 100% M 559024 F 0 R 160258 W 0 c 9 w 2 I 176 O 160 L 1.49 1.55 1.49 @#@FSLOADPOST 2021:05:08:18:26:42 mri_label2label N 12 1.45 1.54 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2312 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:42 mri_label2label N 12 e 4.30 S 0.17 U 4.12 P 100% M 559056 F 0 R 160264 W 0 c 9 w 2 I 200 O 176 L 1.45 1.54 1.49 @#@FSLOADPOST 2021:05:08:18:26:46 mri_label2label N 12 1.41 1.53 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 738 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4615 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:46 mri_label2label N 12 e 4.54 S 0.14 U 4.40 P 99% M 559284 F 0 R 163808 W 0 c 9 w 2 I 360 O 368 L 1.41 1.53 1.49 @#@FSLOADPOST 2021:05:08:18:26:51 mri_label2label N 12 1.41 1.53 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 608 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3527 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:51 mri_label2label N 12 e 4.44 S 0.12 U 4.31 P 99% M 558872 F 0 R 160272 W 0 c 19 w 2 I 272 O 280 L 1.41 1.53 1.49 @#@FSLOADPOST 2021:05:08:18:26:55 mri_label2label N 12 1.46 1.54 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 409 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1695 mri_label2label: Done @#@FSTIME 2021:05:08:18:26:55 mri_label2label N 12 e 4.17 S 0.17 U 3.99 P 99% M 558912 F 0 R 163764 W 0 c 6 w 2 I 128 O 144 L 1.46 1.54 1.49 @#@FSLOADPOST 2021:05:08:18:27:00 mri_label2label N 12 1.42 1.53 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 340 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1346 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:00 mri_label2label N 12 e 4.12 S 0.17 U 3.94 P 99% M 558904 F 0 R 160244 W 0 c 273 w 2 I 96 O 120 L 1.42 1.53 1.49 @#@FSLOADPOST 2021:05:08:18:27:04 mri_label2label N 12 1.39 1.52 1.48 mris_label2annot --s pd_struc_recon --ctab /usr/local/freesurfer/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/average/colortable_vpnl.txt Number of ctab entries 9 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label cmdline mris_label2annot --s pd_struc_recon --ctab /usr/local/freesurfer/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 yelab-Precision-5820-Tower machine x86_64 user yelab subject pd_struc_recon hemi lh SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC ColorTable /usr/local/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 121762 unhit vertices Writing annot to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.mpm.vpnl.annot @#@FSTIME 2021:05:08:18:27:04 mris_label2annot N 26 e 0.68 S 0.03 U 0.64 P 99% M 159220 F 3 R 43509 W 0 c 4 w 6 I 1144 O 2144 L 1.39 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:27:05 mris_label2annot N 26 1.39 1.52 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1061 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:05 mri_label2label N 12 e 4.13 S 0.19 U 3.94 P 100% M 558756 F 0 R 163750 W 0 c 11 w 2 I 96 O 72 L 1.39 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:27:09 mri_label2label N 12 1.44 1.53 1.49 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2142 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:09 mri_label2label N 12 e 4.26 S 0.17 U 4.09 P 99% M 558896 F 0 R 163768 W 0 c 7 w 2 I 192 O 144 L 1.44 1.53 1.49 @#@FSLOADPOST 2021:05:08:18:27:13 mri_label2label N 12 1.40 1.52 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1529 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:13 mri_label2label N 12 e 4.21 S 0.17 U 4.04 P 99% M 559012 F 0 R 160250 W 0 c 10 w 2 I 136 O 88 L 1.40 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:27:17 mri_label2label N 12 1.37 1.51 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2050 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:17 mri_label2label N 12 e 4.29 S 0.17 U 4.11 P 99% M 558912 F 0 R 163764 W 0 c 26 w 2 I 184 O 136 L 1.37 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:27:22 mri_label2label N 12 1.42 1.52 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2456 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:22 mri_label2label N 12 e 4.28 S 0.12 U 4.16 P 99% M 559072 F 0 R 160268 W 0 c 11 w 2 I 208 O 160 L 1.42 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:27:26 mri_label2label N 12 1.42 1.52 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1631 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:26 mri_label2label N 12 e 4.19 S 0.17 U 4.01 P 99% M 558984 F 0 R 163760 W 0 c 7 w 2 I 144 O 112 L 1.42 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:27:30 mri_label2label N 12 1.39 1.51 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 586 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7621 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:30 mri_label2label N 12 e 5.11 S 0.16 U 4.94 P 99% M 559368 F 0 R 163863 W 0 c 19 w 2 I 616 O 528 L 1.39 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:27:35 mri_label2label N 12 1.44 1.52 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1979 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:35 mri_label2label N 12 e 4.22 S 0.15 U 4.06 P 99% M 558936 F 0 R 160254 W 0 c 273 w 2 I 168 O 128 L 1.44 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:27:40 mri_label2label N 12 1.40 1.51 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 309 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1460 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:40 mri_label2label N 12 e 4.17 S 0.17 U 4.00 P 99% M 558844 F 0 R 163757 W 0 c 6 w 2 I 104 O 120 L 1.40 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:27:44 mri_label2label N 12 1.37 1.50 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 620 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4025 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:44 mri_label2label N 12 e 4.51 S 0.13 U 4.37 P 99% M 558968 F 0 R 160289 W 0 c 22 w 2 I 304 O 328 L 1.37 1.50 1.48 @#@FSLOADPOST 2021:05:08:18:27:48 mri_label2label N 12 1.34 1.49 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 746 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4080 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:48 mri_label2label N 12 e 4.61 S 0.18 U 4.42 P 99% M 559072 F 0 R 163801 W 0 c 7 w 2 I 296 O 328 L 1.34 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:27:53 mri_label2label N 12 1.31 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 560 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:53 mri_label2label N 12 e 4.05 S 0.15 U 3.89 P 99% M 558728 F 0 R 163739 W 0 c 14 w 2 I 48 O 48 L 1.31 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:27:57 mri_label2label N 12 1.37 1.49 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 525 mri_label2label: Done @#@FSTIME 2021:05:08:18:27:57 mri_label2label N 12 e 4.16 S 0.15 U 4.00 P 99% M 558996 F 0 R 163743 W 0 c 10 w 2 I 48 O 40 L 1.37 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:28:01 mri_label2label N 12 1.34 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136905 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 503 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:01 mri_label2label N 12 e 4.05 S 0.17 U 3.87 P 99% M 558768 F 0 R 163744 W 0 c 10 w 2 I 48 O 40 L 1.34 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:05 mri_label2label N 12 1.34 1.48 1.47 mris_label2annot --s pd_struc_recon --hemi lh --ctab /usr/local/freesurfer/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/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label cmdline mris_label2annot --s pd_struc_recon --hemi lh --ctab /usr/local/freesurfer/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 yelab-Precision-5820-Tower machine x86_64 user yelab subject pd_struc_recon hemi lh SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 94092 unhit vertices Writing annot to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.BA_exvivo.annot @#@FSTIME 2021:05:08:18:28:05 mris_label2annot N 38 e 0.71 S 0.06 U 0.64 P 99% M 159640 F 0 R 43632 W 0 c 3 w 2 I 8 O 2144 L 1.34 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:06 mris_label2annot N 38 1.34 1.48 1.47 mris_label2annot --s pd_struc_recon --hemi lh --ctab /usr/local/freesurfer/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/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label cmdline mris_label2annot --s pd_struc_recon --hemi lh --ctab /usr/local/freesurfer/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 yelab-Precision-5820-Tower machine x86_64 user yelab subject pd_struc_recon hemi lh SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 111569 unhit vertices Writing annot to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2021:05:08:18:28:06 mris_label2annot N 38 e 0.68 S 0.05 U 0.62 P 99% M 159320 F 0 R 43654 W 0 c 46 w 1 I 0 O 2144 L 1.34 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:07 mris_label2annot N 38 1.39 1.49 1.47 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab pd_struc_recon lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254591 Total vertex volume 254335 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1622534 mm^3 (det: 1.200656 ) 1178 771 2577 2.480 0.529 0.119 0.032 14 1.3 BA1_exvivo 3815 2631 6230 2.204 0.542 0.113 0.021 34 3.6 BA2_exvivo 1088 745 1015 1.765 0.418 0.125 0.029 8 1.2 BA3a_exvivo 2506 1714 3809 1.932 0.604 0.109 0.025 22 2.4 BA3b_exvivo 1737 1049 3651 2.941 0.498 0.099 0.024 10 1.7 BA4a_exvivo 1559 972 2450 2.630 0.508 0.091 0.022 7 1.5 BA4p_exvivo 10709 7390 24041 2.715 0.610 0.115 0.026 89 11.6 BA6_exvivo 2319 1614 4472 2.495 0.400 0.101 0.021 20 1.7 BA44_exvivo 3433 2422 6777 2.405 0.500 0.122 0.027 38 3.6 BA45_exvivo 3480 2405 4386 1.739 0.483 0.121 0.029 41 4.0 V1_exvivo 7549 5340 12280 2.075 0.535 0.144 0.034 100 10.5 V2_exvivo 1952 1302 4006 2.505 0.698 0.109 0.023 18 1.9 MT_exvivo 781 558 2039 3.039 0.742 0.131 0.032 8 1.0 perirhinal_exvivo 707 525 1833 2.770 1.459 0.152 0.058 12 1.5 entorhinal_exvivo @#@FSTIME 2021:05:08:18:28:07 mris_anatomical_stats N 12 e 4.23 S 0.13 U 4.09 P 99% M 478364 F 0 R 135274 W 0 c 15 w 1 I 0 O 24 L 1.39 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:28:11 mris_anatomical_stats N 12 1.39 1.49 1.47 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab pd_struc_recon lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254591 Total vertex volume 254335 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1622534 mm^3 (det: 1.200656 ) 766 493 1607 2.407 0.517 0.136 0.038 11 1.0 BA1_exvivo 1545 1040 2724 2.233 0.566 0.105 0.021 13 1.4 BA2_exvivo 948 643 815 1.697 0.348 0.124 0.030 7 1.0 BA3a_exvivo 1539 1054 1797 1.616 0.348 0.089 0.016 7 1.1 BA3b_exvivo 1766 1057 3527 2.914 0.471 0.092 0.023 9 1.7 BA4a_exvivo 1201 777 1876 2.565 0.454 0.094 0.023 5 1.1 BA4p_exvivo 6098 4162 14094 2.779 0.627 0.116 0.028 51 7.1 BA6_exvivo 1452 1016 2887 2.495 0.413 0.100 0.022 13 1.0 BA44_exvivo 1378 1008 2998 2.465 0.496 0.140 0.035 22 1.8 BA45_exvivo 3667 2571 4798 1.756 0.486 0.124 0.031 43 4.6 V1_exvivo 3712 2633 5769 1.984 0.525 0.154 0.037 57 5.7 V2_exvivo 478 315 1061 2.653 0.772 0.102 0.019 4 0.3 MT_exvivo 349 242 829 2.887 0.805 0.139 0.034 4 0.5 perirhinal_exvivo 437 307 1357 3.240 1.101 0.110 0.038 4 0.6 entorhinal_exvivo @#@FSTIME 2021:05:08:18:28:11 mris_anatomical_stats N 12 e 4.25 S 0.13 U 4.11 P 99% M 478312 F 0 R 138786 W 0 c 8 w 1 I 0 O 24 L 1.39 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:28:15 mris_anatomical_stats N 12 1.36 1.48 1.47 #-------------------------------------------- #@# BA_exvivo Labels rh 2021��� 05��� 08��� ��������� 18:28:15 CST mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA1_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 230 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4192 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:15 mri_label2label N 12 e 4.53 S 0.15 U 4.38 P 99% M 558224 F 0 R 160099 W 0 c 10 w 5 I 16160 O 280 L 1.36 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:20 mri_label2label N 12 1.41 1.49 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA2_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6883 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:20 mri_label2label N 12 e 4.99 S 0.19 U 4.78 P 99% M 558500 F 0 R 160147 W 0 c 323 w 2 I 520 O 416 L 1.41 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:28:25 mri_label2label N 12 1.38 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3a_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4068 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:25 mri_label2label N 12 e 4.61 S 0.17 U 4.44 P 99% M 558280 F 0 R 160096 W 0 c 25 w 2 I 312 O 240 L 1.38 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:30 mri_label2label N 12 1.35 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3b_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 231 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4753 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:30 mri_label2label N 12 e 4.60 S 0.15 U 4.45 P 100% M 558300 F 0 R 160107 W 0 c 15 w 2 I 352 O 304 L 1.35 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:34 mri_label2label N 12 1.32 1.47 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4a_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5944 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:34 mri_label2label N 12 e 4.82 S 0.17 U 4.64 P 99% M 558348 F 0 R 160130 W 0 c 8 w 2 I 440 O 368 L 1.32 1.47 1.47 @#@FSLOADPOST 2021:05:08:18:28:39 mri_label2label N 12 1.37 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4p_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4635 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:39 mri_label2label N 12 e 4.61 S 0.17 U 4.43 P 99% M 558408 F 0 R 160104 W 0 c 14 w 2 I 344 O 280 L 1.37 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:28:44 mri_label2label N 12 1.34 1.47 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA6_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 352 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12608 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:44 mri_label2label N 12 e 6.69 S 0.12 U 6.56 P 99% M 558780 F 0 R 160243 W 0 c 19 w 2 I 936 O 760 L 1.34 1.47 1.47 @#@FSLOADPOST 2021:05:08:18:28:50 mri_label2label N 12 1.32 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA44_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 1328 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8240 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:50 mri_label2label N 12 e 5.05 S 0.14 U 4.90 P 100% M 558636 F 0 R 160161 W 0 c 8 w 2 I 528 O 616 L 1.32 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:28:55 mri_label2label N 12 1.37 1.47 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA45_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 1344 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6699 mri_label2label: Done @#@FSTIME 2021:05:08:18:28:56 mri_label2label N 12 e 4.79 S 0.18 U 4.59 P 99% M 558460 F 0 R 160135 W 0 c 312 w 2 I 416 O 528 L 1.37 1.47 1.47 @#@FSLOADPOST 2021:05:08:18:29:00 mri_label2label N 12 1.34 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V1_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 1136 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5863 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:00 mri_label2label N 12 e 4.68 S 0.16 U 4.52 P 99% M 558556 F 0 R 160120 W 0 c 11 w 2 I 376 O 472 L 1.34 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:29:05 mri_label2label N 12 1.55 1.50 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V2_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 1869 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9885 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:05 mri_label2label N 12 e 5.51 S 0.15 U 5.36 P 99% M 558936 F 0 R 160186 W 0 c 12 w 2 I 640 O 784 L 1.55 1.50 1.48 @#@FSLOADPOST 2021:05:08:18:29:11 mri_label2label N 12 1.59 1.51 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.MT_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 548 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2480 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:11 mri_label2label N 12 e 4.26 S 0.14 U 4.11 P 100% M 558460 F 0 R 163577 W 0 c 14 w 2 I 160 O 208 L 1.59 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:29:15 mri_label2label N 12 1.54 1.50 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1168 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:15 mri_label2label N 12 e 4.11 S 0.16 U 3.94 P 99% M 558420 F 0 R 160050 W 0 c 10 w 2 I 96 O 88 L 1.54 1.50 1.48 @#@FSLOADPOST 2021:05:08:18:29:19 mri_label2label N 12 1.58 1.51 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject pd_struc_recon --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 823 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:19 mri_label2label N 12 e 4.33 S 0.18 U 4.14 P 99% M 558184 F 0 R 160040 W 0 c 13 w 2 I 72 O 64 L 1.58 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:29:23 mri_label2label N 12 1.61 1.52 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 262 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 803 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:23 mri_label2label N 12 e 4.05 S 0.15 U 3.89 P 99% M 558120 F 0 R 163547 W 0 c 9 w 2 I 56 O 72 L 1.61 1.52 1.48 @#@FSLOADPOST 2021:05:08:18:29:27 mri_label2label N 12 1.56 1.51 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 308 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 1029 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:28 mri_label2label N 12 e 4.07 S 0.14 U 3.92 P 99% M 558372 F 0 R 163547 W 0 c 11 w 2 I 72 O 88 L 1.56 1.51 1.48 @#@FSLOADPOST 2021:05:08:18:29:32 mri_label2label N 12 1.52 1.50 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1760 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:32 mri_label2label N 12 e 4.17 S 0.15 U 4.01 P 99% M 558180 F 0 R 160058 W 0 c 13 w 2 I 144 O 144 L 1.52 1.50 1.48 @#@FSLOADPOST 2021:05:08:18:29:36 mri_label2label N 12 1.52 1.50 1.48 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1870 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:36 mri_label2label N 12 e 4.18 S 0.17 U 4.00 P 99% M 558256 F 0 R 160056 W 0 c 11 w 2 I 152 O 160 L 1.52 1.50 1.48 @#@FSLOADPOST 2021:05:08:18:29:40 mri_label2label N 12 1.48 1.49 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 934 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4601 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:40 mri_label2label N 12 e 4.56 S 0.16 U 4.39 P 99% M 558464 F 0 R 160103 W 0 c 10 w 2 I 328 O 376 L 1.48 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:29:45 mri_label2label N 12 1.44 1.49 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 630 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3349 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:45 mri_label2label N 12 e 4.35 S 0.15 U 4.18 P 99% M 558436 F 0 R 163585 W 0 c 281 w 2 I 248 O 272 L 1.44 1.49 1.47 @#@FSLOADPOST 2021:05:08:18:29:49 mri_label2label N 12 1.40 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 293 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1521 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:49 mri_label2label N 12 e 4.15 S 0.18 U 3.97 P 99% M 558144 F 0 R 163555 W 0 c 10 w 2 I 112 O 128 L 1.40 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:29:53 mri_label2label N 12 1.37 1.47 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject pd_struc_recon --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1369 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:53 mri_label2label N 12 e 4.12 S 0.14 U 3.97 P 99% M 558364 F 0 R 163558 W 0 c 8 w 2 I 96 O 120 L 1.37 1.47 1.47 @#@FSLOADPOST 2021:05:08:18:29:57 mri_label2label N 12 1.42 1.48 1.47 mris_label2annot --s pd_struc_recon --ctab /usr/local/freesurfer/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/average/colortable_vpnl.txt Number of ctab entries 9 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label cmdline mris_label2annot --s pd_struc_recon --ctab /usr/local/freesurfer/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 yelab-Precision-5820-Tower machine x86_64 user yelab subject pd_struc_recon hemi rh SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC ColorTable /usr/local/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 121443 unhit vertices Writing annot to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.mpm.vpnl.annot @#@FSTIME 2021:05:08:18:29:57 mris_label2annot N 26 e 0.67 S 0.04 U 0.62 P 100% M 158724 F 0 R 43433 W 0 c 2 w 1 I 0 O 2136 L 1.42 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:29:58 mris_label2annot N 26 1.42 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 91 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 967 mri_label2label: Done @#@FSTIME 2021:05:08:18:29:58 mri_label2label N 12 e 4.03 S 0.16 U 3.87 P 100% M 558388 F 0 R 163551 W 0 c 9 w 2 I 80 O 72 L 1.42 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:30:02 mri_label2label N 12 1.39 1.47 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2742 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:02 mri_label2label N 12 e 4.35 S 0.14 U 4.20 P 100% M 558464 F 0 R 160083 W 0 c 12 w 2 I 240 O 160 L 1.39 1.47 1.47 @#@FSLOADPOST 2021:05:08:18:30:06 mri_label2label N 12 1.36 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1715 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:07 mri_label2label N 12 e 4.24 S 0.18 U 4.06 P 99% M 558448 F 0 R 160063 W 0 c 18 w 2 I 152 O 96 L 1.36 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:11 mri_label2label N 12 1.36 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2276 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:11 mri_label2label N 12 e 4.26 S 0.14 U 4.11 P 99% M 558200 F 0 R 160068 W 0 c 10 w 2 I 192 O 152 L 1.36 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:15 mri_label2label N 12 1.41 1.47 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1437 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:15 mri_label2label N 12 e 4.16 S 0.14 U 4.01 P 100% M 558164 F 0 R 163555 W 0 c 7 w 2 I 120 O 96 L 1.41 1.47 1.47 @#@FSLOADPOST 2021:05:08:18:30:19 mri_label2label N 12 1.37 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1591 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:19 mri_label2label N 12 e 4.17 S 0.16 U 4.01 P 99% M 558420 F 0 R 160061 W 0 c 17 w 2 I 136 O 104 L 1.37 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:23 mri_label2label N 12 1.34 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7096 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:23 mri_label2label N 12 e 5.07 S 0.13 U 4.93 P 99% M 558612 F 0 R 160154 W 0 c 14 w 2 I 592 O 424 L 1.34 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:29 mri_label2label N 12 1.40 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 330 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1342 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:29 mri_label2label N 12 e 4.12 S 0.13 U 3.97 P 99% M 558448 F 0 R 160052 W 0 c 11 w 2 I 88 O 112 L 1.40 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:33 mri_label2label N 12 1.37 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 407 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1585 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:33 mri_label2label N 12 e 4.13 S 0.18 U 3.94 P 99% M 558220 F 0 R 163554 W 0 c 274 w 2 I 104 O 136 L 1.37 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:37 mri_label2label N 12 1.34 1.45 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 834 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4066 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:37 mri_label2label N 12 e 4.48 S 0.16 U 4.30 P 99% M 558484 F 0 R 160096 W 0 c 291 w 2 I 280 O 328 L 1.34 1.45 1.46 @#@FSLOADPOST 2021:05:08:18:30:41 mri_label2label N 12 1.39 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 821 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4258 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:41 mri_label2label N 12 e 4.48 S 0.14 U 4.34 P 99% M 558448 F 0 R 160097 W 0 c 9 w 2 I 296 O 344 L 1.39 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:46 mri_label2label N 12 1.39 1.46 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 361 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:46 mri_label2label N 12 e 4.00 S 0.17 U 3.82 P 100% M 558220 F 0 R 163536 W 0 c 8 w 2 I 24 O 32 L 1.39 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:30:50 mri_label2label N 12 1.44 1.47 1.46 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 779 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:50 mri_label2label N 12 e 4.06 S 0.13 U 3.92 P 99% M 558304 F 0 R 163544 W 0 c 14 w 2 I 64 O 64 L 1.44 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:30:54 mri_label2label N 12 1.48 1.48 1.47 mri_label2label --srcsubject fsaverage --srclabel /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject pd_struc_recon --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = pd_struc_recon 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 /media/yelab/data/PD/PD_Nii/sub1/STRUC FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white Reading target registration /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 136622 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 320 mri_label2label: Done @#@FSTIME 2021:05:08:18:30:54 mri_label2label N 12 e 4.13 S 0.17 U 3.96 P 99% M 558228 F 0 R 163540 W 0 c 12 w 2 I 32 O 32 L 1.48 1.48 1.47 @#@FSLOADPOST 2021:05:08:18:30:58 mri_label2label N 12 1.44 1.47 1.46 mris_label2annot --s pd_struc_recon --hemi rh --ctab /usr/local/freesurfer/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/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label cmdline mris_label2annot --s pd_struc_recon --hemi rh --ctab /usr/local/freesurfer/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 yelab-Precision-5820-Tower machine x86_64 user yelab subject pd_struc_recon hemi rh SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 93882 unhit vertices Writing annot to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.BA_exvivo.annot @#@FSTIME 2021:05:08:18:30:58 mris_label2annot N 38 e 0.71 S 0.05 U 0.65 P 100% M 159336 F 0 R 43525 W 0 c 4 w 1 I 0 O 2136 L 1.44 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:30:59 mris_label2annot N 38 1.44 1.47 1.46 mris_label2annot --s pd_struc_recon --hemi rh --ctab /usr/local/freesurfer/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/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label cmdline mris_label2annot --s pd_struc_recon --hemi rh --ctab /usr/local/freesurfer/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 yelab-Precision-5820-Tower machine x86_64 user yelab subject pd_struc_recon hemi rh SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/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 112526 unhit vertices Writing annot to /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2021:05:08:18:30:59 mris_label2annot N 38 e 0.67 S 0.05 U 0.61 P 99% M 158900 F 0 R 43464 W 0 c 3 w 1 I 0 O 2136 L 1.44 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:31:00 mris_label2annot N 38 1.44 1.47 1.46 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab pd_struc_recon rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 247033 Total vertex volume 246785 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1622534 mm^3 (det: 1.200656 ) 1064 653 2270 2.487 0.538 0.117 0.028 11 1.0 BA1_exvivo 3167 2071 4827 2.173 0.527 0.096 0.016 18 2.2 BA2_exvivo 1133 779 1129 1.731 0.416 0.110 0.023 6 1.1 BA3a_exvivo 2207 1448 3022 1.828 0.515 0.113 0.028 27 2.3 BA3b_exvivo 1708 1043 3459 2.770 0.478 0.097 0.026 12 1.7 BA4a_exvivo 1395 881 2199 2.583 0.515 0.091 0.020 6 1.1 BA4p_exvivo 7705 5374 15863 2.500 0.577 0.116 0.025 71 7.9 BA6_exvivo 4530 3115 8030 2.410 0.478 0.115 0.022 42 4.1 BA44_exvivo 4907 3593 9380 2.257 0.526 0.129 0.027 55 5.6 BA45_exvivo 3895 2705 5503 1.903 0.523 0.134 0.033 48 4.9 V1_exvivo 7621 5410 12513 2.131 0.536 0.145 0.035 106 10.5 V2_exvivo 2314 1590 3924 2.191 0.618 0.111 0.021 18 2.1 MT_exvivo 420 300 1224 3.382 0.649 0.116 0.024 3 0.4 perirhinal_exvivo 674 437 1842 2.988 1.195 0.107 0.048 11 1.2 entorhinal_exvivo @#@FSTIME 2021:05:08:18:31:00 mris_anatomical_stats N 12 e 4.24 S 0.10 U 4.14 P 100% M 477084 F 0 R 138475 W 0 c 11 w 1 I 0 O 24 L 1.44 1.47 1.46 @#@FSLOADPOST 2021:05:08:18:31:04 mris_anatomical_stats N 12 1.41 1.46 1.46 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab pd_struc_recon rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/mri/wm.mgz... reading input surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... reading input pial surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.pial... reading input white surface /media/yelab/data/PD/PD_Nii/sub1/STRUC/pd_struc_recon/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 247033 Total vertex volume 246785 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1622534 mm^3 (det: 1.200656 ) 763 453 1584 2.493 0.526 0.117 0.028 8 0.7 BA1_exvivo 1845 1205 3178 2.303 0.545 0.094 0.015 11 1.2 BA2_exvivo 1012 692 926 1.708 0.365 0.113 0.024 6 1.0 BA3a_exvivo 1701 1156 1981 1.649 0.359 0.103 0.019 11 1.5 BA3b_exvivo 1032 635 2143 2.740 0.561 0.107 0.030 9 1.1 BA4a_exvivo 1202 759 1923 2.628 0.518 0.089 0.018 5 0.9 BA4p_exvivo 4924 3396 10386 2.551 0.575 0.111 0.023 40 4.6 BA6_exvivo 1297 940 2764 2.498 0.345 0.114 0.023 15 1.3 BA44_exvivo 1527 1137 3099 2.278 0.461 0.142 0.032 22 1.9 BA45_exvivo 3786 2597 5062 1.867 0.522 0.134 0.032 48 4.8 V1_exvivo 3958 2875 6860 2.168 0.575 0.155 0.040 64 6.2 V2_exvivo 353 228 582 2.439 0.504 0.093 0.018 2 0.2 MT_exvivo 35 26 102 3.328 0.585 0.121 0.022 0 0.0 perirhinal_exvivo 661 428 1894 3.363 0.758 0.083 0.021 3 0.5 entorhinal_exvivo @#@FSTIME 2021:05:08:18:31:04 mris_anatomical_stats N 12 e 4.23 S 0.13 U 4.09 P 99% M 477280 F 0 R 134969 W 0 c 11 w 1 I 0 O 24 L 1.41 1.46 1.46 @#@FSLOADPOST 2021:05:08:18:31:08 mris_anatomical_stats N 12 1.46 1.47 1.46 Started at 2021��� 05��� 08��� ��������� 13:59:19 CST Ended at 2021��� 05��� 08��� ��������� 18:31:08 CST #@#%# recon-all-run-time-hours 4.530 recon-all -s pd_struc_recon finished without error at 2021��� 05��� 08��� ��������� 18:31:08 CST