Tue Jan 10 10:49:21 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/bin/recon-all -s Test_withT2 -i Test1/t1.nii.gz -T2 Test1/t2.nii.gz -all -parallel subjid Test_withT2 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer Actual FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 8223025 kbytes maxproc 256519 maxlocks unlimited maxsignal 256519 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 62Gi 10Gi 7.5Gi 104Mi 45Gi 51Gi Swap: 976Mi 142Mi 834Mi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/01/10-09:49:21-GMT BuildTime: Aug 4 2022 05:15:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2 mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test1/t1.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/001.mgz mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test1/t1.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/001.mgz reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test1/t1.nii.gz... INFO: This is an unsigined short. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00130218, -0.999999, 0.000694773) j_ras = (0.0980031, -0.000563811, -0.995186) k_ras = (0.995185, 0.001364, 0.0980023) writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Tue Jan 10 10:49:23 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2 mri_convert --no_scale 1 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test1/t2.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz mri_convert --no_scale 1 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test1/t2.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test1/t2.nii.gz... INFO: This is an unsigined short. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00118486, -0.999997, 0.00188591) j_ras = (0.0980046, -0.00176071, -0.995184) k_ras = (0.995185, 0.00136398, 0.0980023) writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Tue Jan 10 10:49:25 CET 2023 Found 1 runs /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/001.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/rawavg.mgz mri_info /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.000000, 1.000000, 1.000000 type: USHRT (10) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 0.0013, y_r = 0.0980, z_r = 0.9952, c_r = 3.2030 : x_a = -1.0000, y_a = -0.0006, z_a = 0.0014, c_a = -6.9160 : x_s = 0.0007, y_s = -0.9952, z_s = 0.0980, c_s = -8.9527 talairach xfm : Orientation : PIR Primary Slice Direction: sagittal voxel to ras transform: 0.0013 0.0980 0.9952 -97.0844 -1.0000 -0.0006 0.0014 121.0360 0.0007 -0.9952 0.0980 109.7180 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 0.0013 -1.0000 0.0007 121.0861 0.0980 -0.0006 -0.9952 118.7726 0.9952 0.0014 0.0980 85.6992 0.0000 0.0000 0.0000 1.0000 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2 mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz --conform mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz --conform reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00130218, -0.999999, 0.000694773) j_ras = (0.0980031, -0.000563811, -0.995186) k_ras = (0.995185, 0.001364, 0.0980023) changing data type from ushrt to uchar (noscale = 0)... MRIchangeType: Building histogram 0 2141 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz... mri_add_xform_to_header -c /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/talairach.xfm /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz INFO: extension is mgz mri_info /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz orig.mgz ======================================== Volume information for /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 3.2030 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -6.9160 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -8.9527 talairach xfm : /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 131.2030 0.0000 0.0000 1.0000 -134.9160 0.0000 -1.0000 0.0000 119.0473 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 131.2030 -0.0000 0.0000 -1.0000 119.0473 -0.0000 1.0000 -0.0000 134.9160 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Tue Jan 10 10:49:34 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 7.3.2 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux Tue Jan 10 10:49:34 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.702099 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.702099/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.702099/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.702099/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.702099/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 5.82077e-11) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Jan 10 10:51:59 CET 2023 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Tue Jan 10 10:51:59 CET 2023 Ended at Tue Jan 10 10:53:20 CET 2023 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.3.2 --src: orig.mgz src image (geometry). --trg: /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 1.29835 -0.05142 0.13846 -2.79659; -0.04885 1.08246 0.60331 -2.39490; -0.11777 -0.64842 1.22302 -38.72926; 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 Tue Jan 10 10:53:22 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2877, pval=0.0254 >= threshold=0.0050) awk -f /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/bin/extract_talairach_avi_QA.awk /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/talairach_avi.log tal_QC_AZS /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/talairach_avi.log TalAviQA: 0.96375 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Tue Jan 10 10:53:22 CET 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 7.3.2 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux Tue Jan 10 10:53:23 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.702629 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.702629/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.702629/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.702629/ones.mgz 7.3.2 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.702629/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.702629/ones.mgz sysname Linux hostname sharky machine x86_64 user brainstimmaps input ./tmp.mri_nu_correct.mni.702629/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.702629/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.702629/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.702629/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.702629/sum.junk --avgwf ./tmp.mri_nu_correct.mni.702629/input.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.702629/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.702629/sum.junk --avgwf ./tmp.mri_nu_correct.mni.702629/input.mean.dat sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.702629/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 Writing to ./tmp.mri_nu_correct.mni.702629/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.702629/ones.mgz --i ./tmp.mri_nu_correct.mni.702629/nu0.mgz --sum ./tmp.mri_nu_correct.mni.702629/sum.junk --avgwf ./tmp.mri_nu_correct.mni.702629/output.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.702629/ones.mgz --i ./tmp.mri_nu_correct.mni.702629/nu0.mgz --sum ./tmp.mri_nu_correct.mni.702629/sum.junk --avgwf ./tmp.mri_nu_correct.mni.702629/output.mean.dat sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.702629/ones.mgz Loading ./tmp.mri_nu_correct.mni.702629/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 Writing to ./tmp.mri_nu_correct.mni.702629/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.702629/nu0.mgz ./tmp.mri_nu_correct.mni.702629/nu0.mgz mul 1.19718070388619721578 Saving result to './tmp.mri_nu_correct.mni.702629/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.702629/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.702629/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.702629/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 5.82077e-11) 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 5 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 11, i2 = 42 #mri_make_uchar# mapping 27 104 to 3 110 : b -35.5774 m 1.4006 : thresh 25.4016 maxsat 207.467 : nzero 13378461 nsat 26237 Tue Jan 10 10:56:07 CET 2023 mri_nu_correct.mni done mri_add_xform_to_header -c /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Jan 10 10:56:07 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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... NOT doing gentle normalization with control points/label talairach transform 1.29835 -0.05142 0.13846 -2.79659; -0.04885 1.08246 0.60331 -2.39490; -0.11777 -0.64842 1.22302 -38.72926; 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 = 16 Starting OpenSpline(): npoints = 16 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 85 (85), valley at 58 (58) csf peak at 15, setting threshold to 61 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 80 (80), valley at 41 (41) csf peak at 13, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 33 seconds. #-------------------------------------------- #@# Skull Stripping Tue Jan 10 10:57:40 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_em_register -skull nu.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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=41.0 skull bounding box = (59, 23, 16) --> (202, 255, 237) finding center of left hemi white matter using (107, 100, 127) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (89,71,100) --> (124, 128,154) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 8.2 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.705 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.683581 @ (-10.526, 10.526, -10.526) max log p = -4.646956 @ (5.263, 5.263, 5.263) max log p = -4.613106 @ (-2.632, -7.895, 2.632) max log p = -4.594662 @ (-1.316, 6.579, -1.316) max log p = -4.579548 @ (0.658, -8.553, 1.974) max log p = -4.579548 @ (0.000, 0.000, 0.000) max log p = -4.579548 @ (0.000, 0.000, 0.000) max log p = -4.579548 @ (0.000, 0.000, 0.000) Found translation: (-8.6, 5.9, -2.0): log p = -4.580 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.265, old_max_log_p =-4.580 (thresh=-4.6) 1.14016 0.13740 0.05966 -43.05135; -0.16136 1.12194 0.48712 -18.79495; 0.00000 -0.36573 0.93367 49.92541; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.250, old_max_log_p =-4.265 (thresh=-4.3) 1.05465 0.12710 0.05518 -30.43981; -0.16136 1.12194 0.48712 -18.79495; 0.00000 -0.39316 1.00369 45.33225; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.250, old_max_log_p =-4.250 (thresh=-4.2) 1.05465 0.12710 0.05518 -30.43981; -0.16136 1.12194 0.48712 -18.79495; 0.00000 -0.39316 1.00369 45.33225; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.196, old_max_log_p =-4.250 (thresh=-4.2) 1.12497 0.03639 -0.02837 -23.45767; -0.05244 1.07440 0.50190 -32.68821; 0.04334 -0.41126 0.95041 45.60533; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.194, old_max_log_p =-4.196 (thresh=-4.2) 1.12270 0.07106 -0.01092 -29.16448; -0.08942 1.07846 0.54337 -33.00732; 0.04419 -0.43782 0.91598 50.60607; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.173, old_max_log_p =-4.194 (thresh=-4.2) 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.173, old_max_log_p =-4.173 (thresh=-4.2) 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.173 (old=-4.705) transform before final EM align: 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 808148 FSRUNTIME@ mri_em_register 0.0391 hours 4 threads registration took 2 minutes and 21 seconds. mri_watershed -T1 -brain_atlas /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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=132 y=99 z=105 r=86 first estimation of the main basin volume: 2667298 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=116, y=91, z=64, Imax=255 CSF=22, 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=8412966946 voxels, voxel volume =1.000 = 8412966946 mmm3 = 8412966.912 cm3 done. PostAnalyze...Basin Prior 1339 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=131,y=102, z=99, r=9057 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 44046 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 3006 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2502 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 18954 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 19044 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=20 , nb = 540 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 5, 53, 76 after analyzing : 3, 37, 53, 46 RIGHT_CER before analyzing : 4, 6, 53, 92 after analyzing : 4, 37, 53, 50 LEFT_CER before analyzing : 3, 5, 62, 90 after analyzing : 3, 43, 62, 54 RIGHT_BRAIN before analyzing : 3, 5, 53, 76 after analyzing : 3, 37, 53, 46 LEFT_BRAIN before analyzing : 3, 5, 54, 76 after analyzing : 3, 37, 54, 46 OTHER before analyzing : 20, 30, 65, 95 after analyzing : 20, 53, 65, 63 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.012 curvature mean = 66.514, std = 8.193 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.59, sigma = 12.74 after rotation: sse = 5.59, sigma = 12.74 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.50, its var is 22.70 before Erosion-Dilatation 9.22% 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...35 iterations mri_strip_skull: done peeling brain Brain Size = 1392599 voxels, voxel volume = 1.000 mm3 = 1392599 mmm3 = 1392.599 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Jan 10 11:00:13 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 = 4 == reading 1 input volumes... logging results to talairach.log reading '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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=29.9 skull bounding box = (69, 41, 37) --> (194, 171, 175) finding center of left hemi white matter using (111, 84, 106) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (96,68,89) --> (126, 99,122) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 4.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.334 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.215806 @ (-10.526, 10.526, -10.526) max log p = -4.037384 @ (5.263, 5.263, 5.263) max log p = -4.037384 @ (0.000, 0.000, 0.000) max log p = -4.035995 @ (-1.316, -1.316, 1.316) max log p = -4.009858 @ (0.658, 1.974, -0.658) max log p = -4.009858 @ (0.000, 0.000, 0.000) max log p = -4.009858 @ (0.000, 0.000, 0.000) max log p = -4.009858 @ (0.000, 0.000, 0.000) Found translation: (-5.9, 16.4, -4.6): log p = -4.010 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.669, old_max_log_p =-4.010 (thresh=-4.0) 1.14016 0.12059 0.04995 -42.67701; -0.16136 0.98467 0.40787 -0.02242; 0.00000 -0.38268 0.92388 50.49792; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.612, old_max_log_p =-3.669 (thresh=-3.7) 1.14016 0.12059 0.04995 -42.67701; -0.18557 1.13237 0.46905 -17.91932; 0.00000 -0.38268 0.92388 50.49792; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.612, old_max_log_p =-3.612 (thresh=-3.6) 1.14016 0.12059 0.04995 -42.67701; -0.18557 1.13237 0.46905 -17.91932; 0.00000 -0.38268 0.92388 50.49792; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.547, old_max_log_p =-3.612 (thresh=-3.6) 1.12827 0.04717 0.01499 -28.25086; -0.10607 1.06880 0.51070 -26.32786; 0.01259 -0.47302 0.92465 57.87077; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.533, old_max_log_p =-3.547 (thresh=-3.5) 1.10623 0.06031 -0.01550 -23.58337; -0.10643 1.08371 0.48018 -24.69410; 0.04603 -0.43602 0.94085 48.08654; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.533, old_max_log_p =-3.533 (thresh=-3.5) 1.10623 0.06031 -0.01550 -23.58337; -0.10643 1.08371 0.48018 -24.69410; 0.04603 -0.43602 0.94085 48.08654; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.521, old_max_log_p =-3.533 (thresh=-3.5) 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.521, old_max_log_p =-3.521 (thresh=-3.5) 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.521 (old=-4.334) transform before final EM align: 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 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) = 4.0 tol 0.000000 final transform: 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 795600 FSRUNTIME@ mri_em_register 0.0367 hours 4 threads registration took 2 minutes and 12 seconds. #-------------------------------------- #@# CA Normalize Tue Jan 10 11:02:25 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (69, 41, 37) --> (194, 171, 175) finding center of left hemi white matter using (111, 84, 106) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (96,68,89) --> (126, 99,122) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 4.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 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, 44, 31) --> (190, 154, 186) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 3803 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (73, 42, 32) --> (135, 144, 187) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 1 of 4230 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 123, 63) --> (174, 166, 114) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 25 of 90 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (90, 123, 62) --> (130, 161, 115) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 1 of 31 (3.2%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (116, 110, 94) --> (147, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 60 (0.0%) samples deleted using 8214 total control points for intensity normalization... bias field = 0.984 +- 0.055 78 of 8187 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 44, 31) --> (190, 154, 186) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 4071 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (73, 42, 32) --> (135, 144, 187) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 4464 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 123, 63) --> (174, 166, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 164 (9.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (90, 123, 62) --> (130, 161, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 100 (15.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (116, 110, 94) --> (147, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 48 of 119 (40.3%) samples deleted using 8918 total control points for intensity normalization... bias field = 1.021 +- 0.059 0 of 8747 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 44, 31) --> (190, 154, 186) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 4048 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (73, 42, 32) --> (135, 144, 187) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 4440 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 123, 63) --> (174, 166, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 162 (13.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (90, 123, 62) --> (130, 161, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 53 of 116 (45.7%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (116, 110, 94) --> (147, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 149 of 216 (69.0%) samples deleted using 8982 total control points for intensity normalization... bias field = 1.017 +- 0.055 2 of 8554 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 14 seconds. #-------------------------------------- #@# CA Reg Tue Jan 10 11:03:39 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 0.973061 #FOTS# QuadFit found better minimum quadopt=(dt=232.21,rms=0.920212) vs oldopt=(dt=369.92,rms=0.933193) #GCMRL# 0 dt 232.210101 rms 0.920 5.431% neg 0 invalid 762 tFOTS 6.3520 tGradient 5.1710 tsec 11.9720 #FOTS# QuadFit found better minimum quadopt=(dt=405.743,rms=0.897842) vs oldopt=(dt=369.92,rms=0.897895) #GCMRL# 1 dt 405.743274 rms 0.898 2.431% neg 0 invalid 762 tFOTS 7.2590 tGradient 5.0120 tsec 12.7850 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.894447) vs oldopt=(dt=92.48,rms=0.894501) #GCMRL# 2 dt 110.976000 rms 0.894 0.378% neg 0 invalid 762 tFOTS 7.1990 tGradient 5.0450 tsec 12.7490 #GCMRL# 3 dt 369.920000 rms 0.893 0.000% neg 0 invalid 762 tFOTS 7.1400 tGradient 4.9810 tsec 12.6450 #GCMRL# 4 dt 369.920000 rms 0.888 0.560% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0010 tsec 5.3940 #GCMRL# 5 dt 369.920000 rms 0.884 0.398% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0030 tsec 5.3980 #GCMRL# 6 dt 369.920000 rms 0.883 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9450 tsec 5.3420 #GCMRL# 7 dt 369.920000 rms 0.882 0.196% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9960 tsec 5.4360 #GCMRL# 8 dt 369.920000 rms 0.881 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0430 tsec 5.4330 #GCMRL# 9 dt 369.920000 rms 0.880 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9480 tsec 5.3360 #GCMRL# 10 dt 369.920000 rms 0.880 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9690 tsec 5.3910 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.879021) vs oldopt=(dt=92.48,rms=0.879022) #GCMRL# 11 dt 73.984000 rms 0.879 0.000% neg 0 invalid 762 tFOTS 5.2770 tGradient 4.9980 tsec 10.6900 #GCMRL# 12 dt 73.984000 rms 0.879 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0290 tsec 5.5320 #GCMRL# 13 dt 73.984000 rms 0.879 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0440 tsec 5.5450 #GCMRL# 14 dt 73.984000 rms 0.879 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9880 tsec 5.3780 #GCMRL# 15 dt 73.984000 rms 0.878 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0730 tsec 5.4750 #GCMRL# 16 dt 73.984000 rms 0.877 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1210 tsec 5.5170 #GCAMreg# pass 0 level1 5 level2 1 tsec 139.272 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 0.877305 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.874722) vs oldopt=(dt=92.48,rms=0.875015) #GCMRL# 18 dt 129.472000 rms 0.875 0.294% neg 0 invalid 762 tFOTS 5.3370 tGradient 4.9880 tsec 10.7260 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.874395) vs oldopt=(dt=92.48,rms=0.874428) #GCMRL# 19 dt 129.472000 rms 0.874 0.000% neg 0 invalid 762 tFOTS 5.3460 tGradient 4.9950 tsec 10.7630 #GCMRL# 20 dt 129.472000 rms 0.874 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9890 tsec 5.3860 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 0.887705 #FOTS# QuadFit found better minimum quadopt=(dt=65.2736,rms=0.881811) vs oldopt=(dt=103.68,rms=0.883454) #GCMRL# 22 dt 65.273632 rms 0.882 0.664% neg 0 invalid 762 tFOTS 5.2540 tGradient 3.5440 tsec 9.1910 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.865784) vs oldopt=(dt=414.72,rms=0.870859) #GCMRL# 23 dt 248.832000 rms 0.866 1.818% neg 0 invalid 762 tFOTS 7.0350 tGradient 3.5420 tsec 10.9750 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.864406) vs oldopt=(dt=25.92,rms=0.864428) #GCMRL# 24 dt 31.104000 rms 0.864 0.000% neg 0 invalid 762 tFOTS 7.1300 tGradient 3.4460 tsec 11.0970 #GCMRL# 25 dt 31.104000 rms 0.864 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4800 tsec 3.9390 #GCAMreg# pass 0 level1 4 level2 1 tsec 47.319 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 0.864497 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.86245) vs oldopt=(dt=25.92,rms=0.862702) #GCMRL# 27 dt 36.288000 rms 0.862 0.237% neg 0 invalid 762 tFOTS 7.0440 tGradient 3.4940 tsec 11.0420 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.862379) vs oldopt=(dt=6.48,rms=0.862397) #GCMRL# 28 dt 9.072000 rms 0.862 0.000% neg 0 invalid 762 tFOTS 6.2460 tGradient 3.4890 tsec 10.2110 #GCMRL# 29 dt 9.072000 rms 0.862 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5250 tsec 4.0250 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 0.885462 #FOTS# QuadFit found better minimum quadopt=(dt=13.2857,rms=0.881217) vs oldopt=(dt=8,rms=0.881623) #GCMRL# 31 dt 13.285714 rms 0.881 0.479% neg 0 invalid 762 tFOTS 6.5510 tGradient 2.6520 tsec 9.5940 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.87691) vs oldopt=(dt=32,rms=0.87713) #GCMRL# 32 dt 38.400000 rms 0.877 0.489% neg 0 invalid 762 tFOTS 6.9330 tGradient 2.5570 tsec 9.8820 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.873796) vs oldopt=(dt=32,rms=0.874021) #GCMRL# 33 dt 44.800000 rms 0.874 0.355% neg 0 invalid 762 tFOTS 6.7090 tGradient 2.6630 tsec 9.7740 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.873665) vs oldopt=(dt=8,rms=0.873671) #GCMRL# 34 dt 6.400000 rms 0.874 0.000% neg 0 invalid 762 tFOTS 6.6970 tGradient 2.5500 tsec 9.6710 #GCMRL# 35 dt 6.400000 rms 0.874 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5550 tsec 3.0670 #GCAMreg# pass 0 level1 3 level2 1 tsec 53.52 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 0.874052 #GCMRL# 37 dt 0.000000 rms 0.874 0.047% neg 0 invalid 762 tFOTS 6.6700 tGradient 2.5450 tsec 9.6120 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 0.905529 #FOTS# QuadFit found better minimum quadopt=(dt=0.216,rms=0.90508) vs oldopt=(dt=0.18,rms=0.905081) #GCMRL# 39 dt 0.216000 rms 0.905 0.049% neg 0 invalid 762 tFOTS 6.5140 tGradient 2.0210 tsec 8.9330 #FOTS# QuadFit found better minimum quadopt=(dt=0.063,rms=0.905074) vs oldopt=(dt=0.045,rms=0.905075) #GCMRL# 40 dt 0.063000 rms 0.905 0.000% neg 0 invalid 762 tFOTS 6.0520 tGradient 2.0030 tsec 8.4690 #GCAMreg# pass 0 level1 2 level2 1 tsec 28.305 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 0.905469 #FOTS# QuadFit found better minimum quadopt=(dt=0.00675,rms=0.905075) vs oldopt=(dt=0.01125,rms=0.905075) #GCMRL# 42 dt 0.006750 rms 0.905 0.043% neg 0 invalid 762 tFOTS 6.3420 tGradient 2.0300 tsec 8.7760 #FOTS# QuadFit found better minimum quadopt=(dt=0.000421875,rms=0.905076) vs oldopt=(dt=0.000703125,rms=0.905076) 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 0.965325 #FOTS# QuadFit found better minimum quadopt=(dt=0.505076,rms=0.957562) vs oldopt=(dt=0.32,rms=0.958943) #GCMRL# 44 dt 0.505076 rms 0.958 0.804% neg 0 invalid 762 tFOTS 6.7470 tGradient 1.6570 tsec 8.8020 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.953522) vs oldopt=(dt=0.32,rms=0.953867) #GCMRL# 45 dt 0.448000 rms 0.954 0.422% neg 0 invalid 762 tFOTS 6.7360 tGradient 1.6250 tsec 8.7620 #GCMRL# 46 dt 0.320000 rms 0.950 0.331% neg 0 invalid 762 tFOTS 6.7330 tGradient 1.6240 tsec 8.7590 #GCMRL# 47 dt 0.320000 rms 0.949 0.000% neg 0 invalid 762 tFOTS 6.6640 tGradient 1.6440 tsec 8.7320 #GCMRL# 48 dt 0.320000 rms 0.947 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6310 tsec 2.1430 #GCMRL# 49 dt 0.320000 rms 0.945 0.216% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6330 tsec 2.1580 #GCMRL# 50 dt 0.320000 rms 0.943 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6390 tsec 2.1640 #GCMRL# 51 dt 0.320000 rms 0.943 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6320 tsec 2.1750 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.940839) vs oldopt=(dt=0.32,rms=0.941091) #GCMRL# 52 dt 0.448000 rms 0.941 0.204% neg 0 invalid 762 tFOTS 6.5820 tGradient 1.6370 tsec 8.6180 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.94038) vs oldopt=(dt=0.08,rms=0.940467) #GCMRL# 53 dt 0.112000 rms 0.940 0.000% neg 0 invalid 762 tFOTS 6.3660 tGradient 1.6310 tsec 8.4080 #GCMRL# 54 dt 0.112000 rms 0.940 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5940 tsec 2.0960 #GCMRL# 55 dt 0.112000 rms 0.940 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6060 tsec 2.1140 #GCMRL# 56 dt 0.112000 rms 0.939 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6180 tsec 2.1300 #GCMRL# 57 dt 0.112000 rms 0.939 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5630 tsec 2.0630 #GCMRL# 58 dt 0.112000 rms 0.938 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6050 tsec 2.1310 #GCMRL# 59 dt 0.112000 rms 0.938 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6580 tsec 2.1510 #GCAMreg# pass 0 level1 1 level2 1 tsec 83.629 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 0.937514 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.936529) vs oldopt=(dt=0.32,rms=0.936575) #GCMRL# 61 dt 0.448000 rms 0.937 0.105% neg 0 invalid 762 tFOTS 6.5860 tGradient 1.5970 tsec 8.6960 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.936193) vs oldopt=(dt=0.32,rms=0.936215) #GCMRL# 62 dt 0.256000 rms 0.936 0.000% neg 0 invalid 762 tFOTS 6.6840 tGradient 1.5960 tsec 8.7020 #GCMRL# 63 dt 0.256000 rms 0.936 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5930 tsec 2.1120 #GCMRL# 64 dt 0.256000 rms 0.935 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6210 tsec 2.1520 #GCMRL# 65 dt 0.256000 rms 0.935 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6220 tsec 2.1550 #GCMRL# 66 dt 0.256000 rms 0.934 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6400 tsec 2.1720 #GCMRL# 67 dt 0.256000 rms 0.934 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6270 tsec 2.1550 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 0.912733 #FOTS# QuadFit found better minimum quadopt=(dt=0.336415,rms=0.902018) vs oldopt=(dt=0.32,rms=0.902083) #GCMRL# 69 dt 0.336415 rms 0.902 1.174% neg 0 invalid 762 tFOTS 4.9740 tGradient 1.2320 tsec 6.6080 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.901555) vs oldopt=(dt=0.02,rms=0.901615) #GCMRL# 70 dt 0.028000 rms 0.902 0.000% neg 0 invalid 762 tFOTS 5.0270 tGradient 1.2460 tsec 6.6920 #GCAMreg# pass 0 level1 0 level2 1 tsec 23.236 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 0.901926 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.901349) vs oldopt=(dt=0.02,rms=0.901359) #GCMRL# 72 dt 0.024000 rms 0.901 0.064% neg 0 invalid 762 tFOTS 4.9940 tGradient 1.2190 tsec 6.6170 #FOTS# QuadFit found better minimum quadopt=(dt=0.00175,rms=0.901349) vs oldopt=(dt=0.00125,rms=0.901349) GCAMregister done in 8.80752 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.23588 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (822 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (822 voxels, peak = 5), gca=6.4 gca peak = 0.17690 (16) mri peak = 0.19356 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (375 voxels, overlap=0.035) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (375 voxels, peak = 7), gca=7.0 gca peak = 0.28275 (96) mri peak = 0.13191 (94) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (782 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (782 voxels, peak = 95), gca=94.6 gca peak = 0.18948 (93) mri peak = 0.11240 (94) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (597 voxels, overlap=1.001) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (597 voxels, peak = 93), gca=92.5 gca peak = 0.20755 (55) mri peak = 0.10151 (74) Right_Hippocampus (53): linear fit = 1.24 x + 0.0 (718 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.24 x + 0.0 (718 voxels, peak = 68), gca=67.9 gca peak = 0.31831 (58) mri peak = 0.12195 (69) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (612 voxels, overlap=0.063) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (612 voxels, peak = 68), gca=67.6 gca peak = 0.11957 (102) mri peak = 0.06560 (109) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (53864 voxels, overlap=0.645) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (53864 voxels, peak = 110), gca=109.7 gca peak = 0.11429 (102) mri peak = 0.06787 (106) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (55813 voxels, overlap=0.663) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (55813 voxels, peak = 109), gca=108.6 gca peak = 0.14521 (59) mri peak = 0.04901 (75) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (15129 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (15129 voxels, peak = 76), gca=76.4 gca peak = 0.14336 (58) mri peak = 0.04166 (75) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (16802 voxels, overlap=0.011) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (16802 voxels, peak = 71), gca=71.1 gca peak = 0.13305 (70) mri peak = 0.17512 (81) Right_Caudate (50): linear fit = 1.22 x + 0.0 (398 voxels, overlap=0.011) Right_Caudate (50): linear fit = 1.22 x + 0.0 (398 voxels, peak = 85), gca=85.1 gca peak = 0.15761 (71) mri peak = 0.11950 (88) Left_Caudate (11): linear fit = 1.23 x + 0.0 (879 voxels, overlap=0.021) Left_Caudate (11): linear fit = 1.23 x + 0.0 (879 voxels, peak = 87), gca=87.0 gca peak = 0.13537 (57) mri peak = 0.06499 (77) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (19309 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (19309 voxels, peak = 76), gca=75.5 gca peak = 0.13487 (56) mri peak = 0.06519 (77) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (23533 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (23533 voxels, peak = 75), gca=74.8 gca peak = 0.19040 (84) mri peak = 0.08638 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (7726 voxels, overlap=0.512) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (7726 voxels, peak = 93), gca=92.8 gca peak = 0.18871 (83) mri peak = 0.09992 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6223 voxels, overlap=0.937) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6223 voxels, peak = 88), gca=87.6 gca peak = 0.24248 (57) mri peak = 0.11015 (69) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (316 voxels, overlap=0.042) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (316 voxels, peak = 68), gca=67.5 gca peak = 0.35833 (56) mri peak = 0.10667 (65) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (375 voxels, overlap=0.163) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (375 voxels, peak = 64), gca=63.6 gca peak = 0.12897 (85) mri peak = 0.09218 (92) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4503 voxels, overlap=0.760) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4503 voxels, peak = 91), gca=90.5 gca peak = 0.13127 (83) mri peak = 0.09268 (89) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3498 voxels, overlap=0.682) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3498 voxels, peak = 88), gca=88.4 gca peak = 0.12974 (78) mri peak = 0.09969 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1947 voxels, overlap=0.026) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1947 voxels, peak = 90), gca=90.1 gca peak = 0.17796 (79) mri peak = 0.09490 (94) Right_Putamen (51): linear fit = 1.20 x + 0.0 (1863 voxels, overlap=0.060) Right_Putamen (51): linear fit = 1.20 x + 0.0 (1863 voxels, peak = 94), gca=94.4 gca peak = 0.10999 (80) mri peak = 0.11000 (87) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9578 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9578 voxels, peak = 88), gca=88.4 gca peak = 0.13215 (88) mri peak = 0.09125 (93) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (869 voxels, overlap=0.577) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (869 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.08513 (92) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1070 voxels, overlap=0.638) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1070 voxels, peak = 93), gca=93.0 gca peak = 0.20775 (25) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13297 (21) mri peak = 0.13890 (11) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (229 voxels, overlap=0.506) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (229 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 1.21 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 0.42 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 2.92007 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 0.897575 #FOTS# QuadFit found better minimum quadopt=(dt=198.857,rms=0.868808) vs oldopt=(dt=92.48,rms=0.876485) #GCMRL# 74 dt 198.857143 rms 0.869 3.205% neg 0 invalid 762 tFOTS 5.2890 tGradient 3.2140 tsec 8.9020 #GCMRL# 75 dt 369.920000 rms 0.850 2.158% neg 0 invalid 762 tFOTS 5.2150 tGradient 3.2110 tsec 8.8190 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.847187) vs oldopt=(dt=92.48,rms=0.847455) #GCMRL# 76 dt 129.472000 rms 0.847 0.338% neg 0 invalid 762 tFOTS 5.2280 tGradient 3.1570 tsec 8.7790 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.839849) vs oldopt=(dt=1479.68,rms=0.840574) #GCMRL# 77 dt 1183.744000 rms 0.840 0.866% neg 0 invalid 762 tFOTS 5.2250 tGradient 3.2020 tsec 8.8220 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.834892) vs oldopt=(dt=369.92,rms=0.83569) #GCMRL# 78 dt 295.936000 rms 0.835 0.590% neg 0 invalid 762 tFOTS 5.2880 tGradient 3.1770 tsec 8.8590 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.834096) vs oldopt=(dt=92.48,rms=0.834112) #GCMRL# 79 dt 110.976000 rms 0.834 0.095% neg 0 invalid 762 tFOTS 5.2550 tGradient 3.2010 tsec 8.8540 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.832332) vs oldopt=(dt=369.92,rms=0.832596) #GCMRL# 80 dt 517.888000 rms 0.832 0.212% neg 0 invalid 762 tFOTS 5.2250 tGradient 3.3370 tsec 8.9570 #GCMRL# 81 dt 369.920000 rms 0.830 0.290% neg 0 invalid 762 tFOTS 5.2340 tGradient 3.2270 tsec 8.8570 #GCMRL# 82 dt 92.480000 rms 0.830 0.000% neg 0 invalid 762 tFOTS 5.2600 tGradient 3.2150 tsec 8.8890 #GCMRL# 83 dt 92.480000 rms 0.829 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2320 tsec 3.6260 #GCMRL# 84 dt 92.480000 rms 0.829 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2210 tsec 3.7260 #GCMRL# 85 dt 92.480000 rms 0.828 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2020 tsec 3.5950 #GCMRL# 86 dt 92.480000 rms 0.827 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1650 tsec 3.5590 #GCMRL# 87 dt 92.480000 rms 0.826 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1780 tsec 3.6840 #GCMRL# 88 dt 92.480000 rms 0.824 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1580 tsec 3.5490 #GCMRL# 89 dt 92.480000 rms 0.823 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1670 tsec 3.6660 #GCMRL# 90 dt 92.480000 rms 0.822 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1730 tsec 3.6730 #GCMRL# 91 dt 92.480000 rms 0.821 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1960 tsec 3.6970 #GCMRL# 92 dt 92.480000 rms 0.820 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1790 tsec 3.6850 #GCMRL# 93 dt 92.480000 rms 0.819 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1890 tsec 3.5800 #GCMRL# 94 dt 92.480000 rms 0.818 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1360 tsec 3.6370 #GCMRL# 95 dt 92.480000 rms 0.817 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1830 tsec 3.6850 #GCMRL# 96 dt 92.480000 rms 0.816 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1590 tsec 3.6620 #GCMRL# 97 dt 92.480000 rms 0.815 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1970 tsec 3.7000 #GCMRL# 98 dt 92.480000 rms 0.814 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2270 tsec 3.7250 #GCMRL# 99 dt 92.480000 rms 0.813 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2090 tsec 3.7040 #GCMRL# 100 dt 92.480000 rms 0.812 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1980 tsec 3.6990 #GCMRL# 101 dt 92.480000 rms 0.811 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2250 tsec 3.6180 #GCMRL# 102 dt 92.480000 rms 0.810 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1250 tsec 3.6260 #GCMRL# 103 dt 92.480000 rms 0.809 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1660 tsec 3.6740 #GCMRL# 104 dt 92.480000 rms 0.808 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2470 tsec 3.7520 #GCMRL# 105 dt 92.480000 rms 0.807 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2630 tsec 3.6640 #GCMRL# 106 dt 92.480000 rms 0.806 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1970 tsec 3.5950 #GCMRL# 107 dt 92.480000 rms 0.806 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2410 tsec 3.7430 #GCMRL# 108 dt 92.480000 rms 0.805 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2780 tsec 3.7830 #GCMRL# 109 dt 92.480000 rms 0.804 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2500 tsec 3.7560 #GCMRL# 110 dt 92.480000 rms 0.803 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2530 tsec 3.7530 #GCMRL# 111 dt 92.480000 rms 0.802 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2140 tsec 3.7210 #GCMRL# 112 dt 92.480000 rms 0.802 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2040 tsec 3.6020 #GCMRL# 113 dt 92.480000 rms 0.801 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1640 tsec 3.5610 #GCMRL# 114 dt 92.480000 rms 0.801 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2190 tsec 3.7060 #GCMRL# 115 dt 92.480000 rms 0.801 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1520 tsec 3.6600 #GCMRL# 116 dt 92.480000 rms 0.800 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2300 tsec 3.7410 #GCMRL# 117 dt 92.480000 rms 0.799 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2220 tsec 3.7140 #GCMRL# 118 dt 92.480000 rms 0.799 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2320 tsec 3.7350 #GCMRL# 119 dt 92.480000 rms 0.798 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2580 tsec 3.7570 #GCMRL# 120 dt 92.480000 rms 0.798 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2540 tsec 3.6530 #GCMRL# 121 dt 92.480000 rms 0.798 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2630 tsec 3.7500 #GCMRL# 122 dt 92.480000 rms 0.797 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2610 tsec 3.7470 #GCMRL# 123 dt 92.480000 rms 0.797 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2150 tsec 3.6030 #GCMRL# 124 dt 92.480000 rms 0.796 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2660 tsec 3.7710 #GCMRL# 125 dt 92.480000 rms 0.796 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2990 tsec 3.7380 #GCMRL# 126 dt 92.480000 rms 0.795 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3360 tsec 3.8270 #GCMRL# 127 dt 92.480000 rms 0.795 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3220 tsec 3.7670 #GCMRL# 128 dt 92.480000 rms 0.795 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2330 tsec 3.7260 #GCMRL# 129 dt 92.480000 rms 0.794 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3190 tsec 3.8050 #GCMRL# 130 dt 92.480000 rms 0.794 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2690 tsec 3.7700 #GCMRL# 131 dt 92.480000 rms 0.794 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1920 tsec 3.5960 #GCMRL# 132 dt 92.480000 rms 0.793 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2390 tsec 3.6320 #GCMRL# 133 dt 92.480000 rms 0.793 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2120 tsec 3.7220 #GCMRL# 134 dt 92.480000 rms 0.793 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2640 tsec 3.6590 #GCMRL# 135 dt 92.480000 rms 0.792 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2190 tsec 3.7280 #GCMRL# 136 dt 92.480000 rms 0.792 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3560 tsec 3.8810 #GCMRL# 137 dt 92.480000 rms 0.792 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4990 tsec 3.9990 #GCMRL# 138 dt 92.480000 rms 0.791 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3200 tsec 3.8210 #GCMRL# 139 dt 92.480000 rms 0.791 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2060 tsec 3.5980 #GCMRL# 140 dt 92.480000 rms 0.791 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1990 tsec 3.7050 #GCMRL# 141 dt 92.480000 rms 0.791 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2190 tsec 3.6120 #GCMRL# 142 dt 92.480000 rms 0.790 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2170 tsec 3.7260 #GCMRL# 143 dt 92.480000 rms 0.790 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2440 tsec 3.7540 #GCMRL# 144 dt 92.480000 rms 0.790 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2420 tsec 3.6360 #GCMRL# 145 dt 92.480000 rms 0.790 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2030 tsec 3.7200 #GCMRL# 146 dt 92.480000 rms 0.789 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2470 tsec 3.6420 #GCMRL# 147 dt 92.480000 rms 0.789 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2200 tsec 3.6160 #GCMRL# 148 dt 92.480000 rms 0.789 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2220 tsec 3.7380 #GCMRL# 149 dt 92.480000 rms 0.789 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2040 tsec 3.7170 #GCMRL# 150 dt 92.480000 rms 0.789 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2110 tsec 3.6050 #GCMRL# 151 dt 92.480000 rms 0.788 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2420 tsec 3.6360 #GCMRL# 152 dt 92.480000 rms 0.788 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2130 tsec 3.7240 #GCMRL# 153 dt 92.480000 rms 0.788 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2380 tsec 3.7680 #FOTS# QuadFit found better minimum quadopt=(dt=-0.0961538,rms=0.788135) vs oldopt=(dt=0.36125,rms=0.788135) #GCAMreg# pass 0 level1 5 level2 1 tsec 360.722 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 0.788702 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.78789) vs oldopt=(dt=92.48,rms=0.787945) #GCMRL# 155 dt 73.984000 rms 0.788 0.103% neg 0 invalid 762 tFOTS 5.0220 tGradient 3.2220 tsec 8.6430 #GCMRL# 156 dt 23.120000 rms 0.788 0.000% neg 0 invalid 762 tFOTS 5.6040 tGradient 3.2440 tsec 9.5650 #GCMRL# 157 dt 23.120000 rms 0.788 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2000 tsec 3.5930 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 0.790113 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.779506) vs oldopt=(dt=414.72,rms=0.781896) #GCMRL# 159 dt 248.832000 rms 0.780 1.343% neg 0 invalid 762 tFOTS 4.9520 tGradient 2.4850 tsec 7.8470 #FOTS# QuadFit found better minimum quadopt=(dt=68.5128,rms=0.774609) vs oldopt=(dt=25.92,rms=0.77615) #GCMRL# 160 dt 68.512821 rms 0.775 0.628% neg 0 invalid 762 tFOTS 5.2930 tGradient 2.4880 tsec 8.1780 #FOTS# QuadFit found better minimum quadopt=(dt=117.096,rms=0.770793) vs oldopt=(dt=103.68,rms=0.770808) #GCMRL# 161 dt 117.096296 rms 0.771 0.493% neg 0 invalid 762 tFOTS 5.1930 tGradient 2.4420 tsec 8.0280 #FOTS# QuadFit found better minimum quadopt=(dt=66.2857,rms=0.768359) vs oldopt=(dt=25.92,rms=0.768953) #GCMRL# 162 dt 66.285714 rms 0.768 0.316% neg 0 invalid 762 tFOTS 5.2120 tGradient 2.4690 tsec 8.0760 #FOTS# QuadFit found better minimum quadopt=(dt=98.7884,rms=0.765757) vs oldopt=(dt=103.68,rms=0.76578) #GCMRL# 163 dt 98.788382 rms 0.766 0.339% neg 0 invalid 762 tFOTS 5.2080 tGradient 2.5060 tsec 8.1070 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.764231) vs oldopt=(dt=25.92,rms=0.764515) #GCMRL# 164 dt 36.288000 rms 0.764 0.199% neg 0 invalid 762 tFOTS 5.1860 tGradient 2.4970 tsec 8.0750 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.758294) vs oldopt=(dt=414.72,rms=0.758609) #GCMRL# 165 dt 580.608000 rms 0.758 0.777% neg 0 invalid 762 tFOTS 4.9310 tGradient 2.4950 tsec 7.8210 #FOTS# QuadFit found better minimum quadopt=(dt=54.7009,rms=0.753736) vs oldopt=(dt=25.92,rms=0.754599) #GCMRL# 166 dt 54.700855 rms 0.754 0.601% neg 0 invalid 762 tFOTS 4.9030 tGradient 2.4380 tsec 7.7320 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.752963) vs oldopt=(dt=25.92,rms=0.753077) #GCMRL# 167 dt 36.288000 rms 0.753 0.103% neg 0 invalid 762 tFOTS 6.7640 tGradient 2.4360 tsec 9.6050 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.74792) vs oldopt=(dt=414.72,rms=0.749111) #GCMRL# 168 dt 580.608000 rms 0.748 0.670% neg 0 invalid 762 tFOTS 5.0370 tGradient 2.4680 tsec 7.9020 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.747212) vs oldopt=(dt=25.92,rms=0.747348) #GCMRL# 169 dt 36.288000 rms 0.747 0.095% neg 0 invalid 762 tFOTS 4.6620 tGradient 2.4880 tsec 7.5500 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.74611) vs oldopt=(dt=414.72,rms=0.746356) #GCMRL# 170 dt 248.832000 rms 0.746 0.148% neg 0 invalid 762 tFOTS 4.9950 tGradient 2.4890 tsec 7.8870 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.745543) vs oldopt=(dt=25.92,rms=0.745652) #GCMRL# 171 dt 36.288000 rms 0.746 0.076% neg 0 invalid 762 tFOTS 7.0480 tGradient 2.5140 tsec 9.9640 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.744298) vs oldopt=(dt=414.72,rms=0.744458) #GCMRL# 172 dt 331.776000 rms 0.744 0.167% neg 0 invalid 762 tFOTS 4.9580 tGradient 2.5030 tsec 7.8590 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.743452) vs oldopt=(dt=25.92,rms=0.743512) #GCMRL# 173 dt 36.288000 rms 0.743 0.114% neg 0 invalid 762 tFOTS 6.5580 tGradient 2.4780 tsec 9.4410 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.743155) vs oldopt=(dt=103.68,rms=0.743179) #GCMRL# 174 dt 82.944000 rms 0.743 0.000% neg 0 invalid 762 tFOTS 4.7130 tGradient 2.4990 tsec 7.6310 #GCMRL# 175 dt 82.944000 rms 0.743 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5490 tsec 2.9440 #GCMRL# 176 dt 82.944000 rms 0.742 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5190 tsec 3.0210 #GCMRL# 177 dt 82.944000 rms 0.742 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4920 tsec 3.0800 #GCMRL# 178 dt 82.944000 rms 0.741 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4840 tsec 2.8820 #GCMRL# 179 dt 10.368000 rms 0.741 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5190 tsec 3.6530 #GCMRL# 180 dt 5.184000 rms 0.741 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4780 tsec 3.2640 #GCMRL# 181 dt 1.620000 rms 0.741 0.000% neg 0 invalid 762 tFOTS 4.0880 tGradient 2.5140 tsec 7.0220 #GCMRL# 182 dt 0.202500 rms 0.741 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4900 tsec 3.6220 #GCMRL# 183 dt 0.050625 rms 0.741 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4760 tsec 3.4280 #GCAMreg# pass 0 level1 4 level2 1 tsec 176.232 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 0.741367 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.740433) vs oldopt=(dt=25.92,rms=0.740464) #GCMRL# 185 dt 36.288000 rms 0.740 0.126% neg 0 invalid 762 tFOTS 4.9460 tGradient 2.4700 tsec 7.8120 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.739818) vs oldopt=(dt=103.68,rms=0.739976) #GCMRL# 186 dt 82.944000 rms 0.740 0.083% neg 0 invalid 762 tFOTS 5.2790 tGradient 2.5140 tsec 8.1860 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.738191) vs oldopt=(dt=414.72,rms=0.738511) #GCMRL# 187 dt 331.776000 rms 0.738 0.220% neg 0 invalid 762 tFOTS 5.2750 tGradient 2.5500 tsec 8.2220 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.737378) vs oldopt=(dt=25.92,rms=0.737466) #GCMRL# 188 dt 36.288000 rms 0.737 0.110% neg 0 invalid 762 tFOTS 5.2630 tGradient 2.4160 tsec 8.0730 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.736898) vs oldopt=(dt=103.68,rms=0.73695) #GCMRL# 189 dt 145.152000 rms 0.737 0.065% neg 0 invalid 762 tFOTS 5.2860 tGradient 2.4240 tsec 8.1030 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.734033) vs oldopt=(dt=414.72,rms=0.734344) #GCMRL# 190 dt 331.776000 rms 0.734 0.389% neg 0 invalid 762 tFOTS 5.2790 tGradient 2.4750 tsec 8.1530 #FOTS# QuadFit found better minimum quadopt=(dt=21.8734,rms=0.733497) vs oldopt=(dt=25.92,rms=0.733516) #GCMRL# 191 dt 21.873418 rms 0.733 0.073% neg 0 invalid 762 tFOTS 5.3180 tGradient 2.4740 tsec 8.1970 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.73348) vs oldopt=(dt=1.62,rms=0.733481) #GCMRL# 192 dt 2.268000 rms 0.733 0.000% neg 0 invalid 762 tFOTS 5.2810 tGradient 2.4960 tsec 8.1990 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 0.741573 #FOTS# QuadFit found better minimum quadopt=(dt=78.4724,rms=0.724624) vs oldopt=(dt=32,rms=0.729226) #GCMRL# 194 dt 78.472362 rms 0.725 2.286% neg 0 invalid 762 tFOTS 4.9470 tGradient 2.1240 tsec 7.4780 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.71483) vs oldopt=(dt=32,rms=0.715215) #GCMRL# 195 dt 25.600000 rms 0.715 1.352% neg 0 invalid 762 tFOTS 5.0240 tGradient 2.1450 tsec 7.5710 #FOTS# QuadFit found better minimum quadopt=(dt=20.8619,rms=0.710579) vs oldopt=(dt=32,rms=0.711355) #GCMRL# 196 dt 20.861878 rms 0.711 0.595% neg 0 invalid 762 tFOTS 4.9880 tGradient 2.0980 tsec 7.4820 #GCMRL# 197 dt 32.000000 rms 0.708 0.433% neg 0 invalid 762 tFOTS 4.9700 tGradient 2.0980 tsec 7.4590 #FOTS# QuadFit found better minimum quadopt=(dt=25.1429,rms=0.704997) vs oldopt=(dt=8,rms=0.705568) #GCMRL# 198 dt 25.142857 rms 0.705 0.354% neg 0 invalid 762 tFOTS 4.9320 tGradient 2.0550 tsec 7.3890 #FOTS# QuadFit found better minimum quadopt=(dt=20.2222,rms=0.702497) vs oldopt=(dt=8,rms=0.703002) #GCMRL# 199 dt 20.222222 rms 0.702 0.355% neg 0 invalid 762 tFOTS 5.0070 tGradient 2.1010 tsec 7.5150 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.700721) vs oldopt=(dt=8,rms=0.701093) #GCMRL# 200 dt 11.200000 rms 0.701 0.253% neg 0 invalid 762 tFOTS 5.0230 tGradient 2.1020 tsec 7.5260 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.69685) vs oldopt=(dt=32,rms=0.697949) #GCMRL# 201 dt 44.800000 rms 0.697 0.552% neg 0 invalid 762 tFOTS 4.6860 tGradient 2.1160 tsec 7.1990 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.695971) vs oldopt=(dt=8,rms=0.696205) #GCMRL# 202 dt 11.200000 rms 0.696 0.126% neg 0 invalid 762 tFOTS 4.6460 tGradient 2.1370 tsec 7.1810 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.695202) vs oldopt=(dt=8,rms=0.695419) #GCMRL# 203 dt 11.200000 rms 0.695 0.110% neg 0 invalid 762 tFOTS 4.6390 tGradient 2.1220 tsec 7.1570 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.694548) vs oldopt=(dt=8,rms=0.694659) #GCMRL# 204 dt 9.600000 rms 0.695 0.094% neg 0 invalid 762 tFOTS 4.6360 tGradient 2.1410 tsec 7.1730 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.694533) vs oldopt=(dt=0.125,rms=0.694536) #GCMRL# 205 dt 0.175000 rms 0.695 0.000% neg 0 invalid 762 tFOTS 3.7200 tGradient 2.1670 tsec 6.3070 #GCMRL# 206 dt 0.175000 rms 0.695 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1500 tsec 2.5490 #GCMRL# 207 dt 0.021875 rms 0.695 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1430 tsec 3.2830 #GCMRL# 208 dt 0.010937 rms 0.695 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1570 tsec 2.9490 #FOTS# QuadFit found better minimum quadopt=(dt=0.009375,rms=0.694519) vs oldopt=(dt=0.0078125,rms=0.694519) #GCAMreg# pass 0 level1 3 level2 1 tsec 109.715 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 0.695032 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.693709) vs oldopt=(dt=8,rms=0.693856) #GCMRL# 210 dt 11.200000 rms 0.694 0.190% neg 0 invalid 762 tFOTS 5.2730 tGradient 2.1480 tsec 7.8420 #FOTS# QuadFit found better minimum quadopt=(dt=25.0435,rms=0.692956) vs oldopt=(dt=32,rms=0.693096) #GCMRL# 211 dt 25.043478 rms 0.693 0.109% neg 0 invalid 762 tFOTS 5.3560 tGradient 2.2170 tsec 7.9690 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.691331) vs oldopt=(dt=32,rms=0.691641) #GCMRL# 212 dt 44.800000 rms 0.691 0.235% neg 0 invalid 762 tFOTS 5.2230 tGradient 2.0830 tsec 7.7070 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.690523) vs oldopt=(dt=32,rms=0.690663) #GCMRL# 213 dt 44.800000 rms 0.691 0.117% neg 0 invalid 762 tFOTS 5.2880 tGradient 2.1170 tsec 7.8450 #FOTS# QuadFit found better minimum quadopt=(dt=93.0909,rms=0.687736) vs oldopt=(dt=32,rms=0.688266) #GCMRL# 214 dt 93.090909 rms 0.688 0.404% neg 0 invalid 762 tFOTS 6.0360 tGradient 2.2990 tsec 8.7760 #FOTS# QuadFit found better minimum quadopt=(dt=17.2174,rms=0.685405) vs oldopt=(dt=8,rms=0.685837) #GCMRL# 215 dt 17.217391 rms 0.685 0.339% neg 0 invalid 762 tFOTS 6.0030 tGradient 2.1710 tsec 8.6530 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.684547) vs oldopt=(dt=32,rms=0.68459) #GCMRL# 216 dt 25.600000 rms 0.685 0.125% neg 0 invalid 762 tFOTS 6.0220 tGradient 2.4040 tsec 8.8440 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.683624) vs oldopt=(dt=32,rms=0.683633) #GCMRL# 217 dt 25.600000 rms 0.684 0.135% neg 0 invalid 762 tFOTS 5.5770 tGradient 2.1130 tsec 8.0980 #FOTS# QuadFit found better minimum quadopt=(dt=24,rms=0.682825) vs oldopt=(dt=32,rms=0.683003) #GCMRL# 218 dt 24.000000 rms 0.683 0.117% neg 0 invalid 762 tFOTS 6.1660 tGradient 2.0950 tsec 8.7290 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.68189) vs oldopt=(dt=32,rms=0.68196) #GCMRL# 219 dt 25.600000 rms 0.682 0.137% neg 0 invalid 762 tFOTS 7.7460 tGradient 2.1180 tsec 10.2850 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.681321) vs oldopt=(dt=8,rms=0.681436) #GCMRL# 220 dt 11.200000 rms 0.681 0.083% neg 0 invalid 762 tFOTS 5.8660 tGradient 2.0980 tsec 8.3810 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.677104) vs oldopt=(dt=128,rms=0.678135) #GCMRL# 221 dt 179.200000 rms 0.677 0.619% neg 0 invalid 762 tFOTS 5.0820 tGradient 2.1380 tsec 7.6350 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.676113) vs oldopt=(dt=32,rms=0.676277) #GCMRL# 222 dt 19.200000 rms 0.676 0.146% neg 0 invalid 762 tFOTS 5.3130 tGradient 2.1920 tsec 7.9080 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.675539) vs oldopt=(dt=32,rms=0.675563) #GCMRL# 223 dt 25.600000 rms 0.676 0.085% neg 0 invalid 762 tFOTS 5.4140 tGradient 2.1910 tsec 8.0150 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.674798) vs oldopt=(dt=32,rms=0.674836) #GCMRL# 224 dt 25.600000 rms 0.675 0.110% neg 0 invalid 762 tFOTS 5.4670 tGradient 2.0720 tsec 7.9360 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.674412) vs oldopt=(dt=8,rms=0.674484) #GCMRL# 225 dt 11.200000 rms 0.674 0.057% neg 0 invalid 762 tFOTS 5.2470 tGradient 2.1950 tsec 7.8450 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.671199) vs oldopt=(dt=128,rms=0.671895) #GCMRL# 226 dt 179.200000 rms 0.671 0.476% neg 0 invalid 762 tFOTS 5.2530 tGradient 2.1290 tsec 7.8200 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.670666) vs oldopt=(dt=8,rms=0.670799) #GCMRL# 227 dt 11.200000 rms 0.671 0.079% neg 0 invalid 762 tFOTS 5.4540 tGradient 2.1860 tsec 8.0590 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.670375) vs oldopt=(dt=32,rms=0.670421) #GCMRL# 228 dt 19.200000 rms 0.670 0.000% neg 0 invalid 762 tFOTS 5.1870 tGradient 2.1550 tsec 7.7620 #GCMRL# 229 dt 19.200000 rms 0.670 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1520 tsec 2.5640 #GCMRL# 230 dt 19.200000 rms 0.670 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1100 tsec 2.5200 #GCMRL# 231 dt 19.200000 rms 0.669 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0850 tsec 2.4800 #GCMRL# 232 dt 19.200000 rms 0.668 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1180 tsec 2.5630 #GCMRL# 233 dt 19.200000 rms 0.667 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1530 tsec 2.5940 #GCMRL# 234 dt 19.200000 rms 0.666 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1530 tsec 2.5670 #GCMRL# 235 dt 19.200000 rms 0.664 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1100 tsec 2.5150 #GCMRL# 236 dt 19.200000 rms 0.663 0.212% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1850 tsec 2.5870 #GCMRL# 237 dt 19.200000 rms 0.661 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2610 tsec 2.6900 #GCMRL# 238 dt 19.200000 rms 0.660 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1530 tsec 2.5670 #GCMRL# 239 dt 19.200000 rms 0.659 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1480 tsec 2.5570 #GCMRL# 240 dt 19.200000 rms 0.657 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1330 tsec 2.5370 #GCMRL# 241 dt 19.200000 rms 0.656 0.225% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0770 tsec 2.4740 #GCMRL# 242 dt 19.200000 rms 0.654 0.203% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0870 tsec 2.4890 #GCMRL# 243 dt 19.200000 rms 0.653 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0770 tsec 2.4770 #GCMRL# 244 dt 19.200000 rms 0.652 0.173% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0630 tsec 2.5910 #GCMRL# 245 dt 19.200000 rms 0.651 0.180% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2210 tsec 2.6380 #GCMRL# 246 dt 19.200000 rms 0.650 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1770 tsec 2.6070 #GCMRL# 247 dt 19.200000 rms 0.649 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1540 tsec 2.5660 #GCMRL# 248 dt 19.200000 rms 0.648 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0610 tsec 2.4860 #GCMRL# 249 dt 19.200000 rms 0.647 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3290 tsec 3.0820 #GCMRL# 250 dt 19.200000 rms 0.646 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0680 tsec 2.4870 #GCMRL# 251 dt 19.200000 rms 0.645 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0510 tsec 2.4480 #GCMRL# 252 dt 19.200000 rms 0.645 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0840 tsec 2.4860 #GCMRL# 253 dt 19.200000 rms 0.644 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0610 tsec 2.4620 #GCMRL# 254 dt 19.200000 rms 0.644 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0490 tsec 2.4530 #GCMRL# 255 dt 19.200000 rms 0.643 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0580 tsec 2.4530 #GCMRL# 256 dt 19.200000 rms 0.642 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0230 tsec 2.7270 #GCMRL# 257 dt 19.200000 rms 0.642 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9040 tsec 3.7960 #GCMRL# 258 dt 19.200000 rms 0.641 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8070 tsec 3.6850 #GCMRL# 259 dt 19.200000 rms 0.641 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8200 tsec 3.5500 #GCMRL# 260 dt 19.200000 rms 0.640 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7330 tsec 3.2240 #GCMRL# 261 dt 19.200000 rms 0.640 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1760 tsec 2.7430 #GCMRL# 262 dt 19.200000 rms 0.639 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3720 tsec 2.9900 #GCMRL# 263 dt 19.200000 rms 0.639 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5710 tsec 3.2240 #GCMRL# 264 dt 19.200000 rms 0.639 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5780 tsec 3.2320 #GCMRL# 265 dt 19.200000 rms 0.638 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6130 tsec 3.2480 #GCMRL# 266 dt 19.200000 rms 0.638 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5480 tsec 3.2020 #GCMRL# 267 dt 19.200000 rms 0.638 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4420 tsec 3.0840 #GCMRL# 268 dt 19.200000 rms 0.637 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4000 tsec 3.0410 #GCMRL# 269 dt 19.200000 rms 0.637 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3800 tsec 3.0140 #GCMRL# 270 dt 19.200000 rms 0.637 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4130 tsec 3.0620 #GCMRL# 271 dt 19.200000 rms 0.637 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4240 tsec 3.0870 #GCMRL# 272 dt 19.200000 rms 0.636 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5210 tsec 2.9490 #GCMRL# 273 dt 19.200000 rms 0.636 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9930 tsec 2.3940 #GCMRL# 274 dt 19.200000 rms 0.636 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9990 tsec 2.3950 #GCMRL# 275 dt 19.200000 rms 0.635 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9590 tsec 2.3480 #GCMRL# 276 dt 19.200000 rms 0.635 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9540 tsec 2.3580 #GCMRL# 277 dt 19.200000 rms 0.635 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9840 tsec 2.3830 #GCMRL# 278 dt 19.200000 rms 0.635 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9640 tsec 2.3650 #GCMRL# 279 dt 19.200000 rms 0.634 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3940 tsec 2.9640 #GCMRL# 280 dt 19.200000 rms 0.634 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0690 tsec 3.6760 #GCMRL# 281 dt 19.200000 rms 0.634 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1630 tsec 2.7230 #GCMRL# 282 dt 19.200000 rms 0.634 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0940 tsec 2.5420 #GCMRL# 283 dt 19.200000 rms 0.633 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0560 tsec 2.5070 #GCMRL# 284 dt 19.200000 rms 0.633 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1970 tsec 2.6570 #GCMRL# 285 dt 19.200000 rms 0.633 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0740 tsec 2.5340 #GCMRL# 286 dt 19.200000 rms 0.633 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0370 tsec 2.5840 #GCMRL# 287 dt 19.200000 rms 0.632 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1030 tsec 2.5710 #GCMRL# 288 dt 19.200000 rms 0.632 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0460 tsec 2.5170 #GCMRL# 289 dt 19.200000 rms 0.632 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0570 tsec 2.5800 #GCMRL# 290 dt 19.200000 rms 0.632 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0990 tsec 2.5620 #GCMRL# 291 dt 19.200000 rms 0.631 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1230 tsec 2.5820 #GCMRL# 292 dt 19.200000 rms 0.631 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0990 tsec 2.5610 #GCMRL# 293 dt 19.200000 rms 0.631 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0760 tsec 2.5140 #GCMRL# 294 dt 19.200000 rms 0.631 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1120 tsec 2.6130 #GCMRL# 295 dt 19.200000 rms 0.631 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1230 tsec 2.5850 #GCMRL# 296 dt 19.200000 rms 0.631 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0890 tsec 2.5780 #GCMRL# 297 dt 32.000000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 5.8230 tGradient 2.0250 tsec 8.3440 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 0.654368 #GCMRL# 299 dt 0.000000 rms 0.654 0.095% neg 0 invalid 762 tFOTS 5.3470 tGradient 1.8600 tsec 7.6750 #GCMRL# 300 dt 0.150000 rms 0.654 0.000% neg 0 invalid 762 tFOTS 5.4480 tGradient 1.8900 tsec 8.1870 #GCAMreg# pass 0 level1 2 level2 1 tsec 24.238 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 0.654368 #GCMRL# 302 dt 0.000000 rms 0.654 0.095% neg 0 invalid 762 tFOTS 5.8500 tGradient 1.8600 tsec 8.2180 #GCMRL# 303 dt 0.150000 rms 0.654 0.000% neg 0 invalid 762 tFOTS 5.7920 tGradient 1.9270 tsec 8.6050 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 0.701111 #FOTS# QuadFit found better minimum quadopt=(dt=0.786184,rms=0.698582) vs oldopt=(dt=1.28,rms=0.698924) #GCMRL# 305 dt 0.786184 rms 0.699 0.361% neg 0 invalid 762 tFOTS 5.6150 tGradient 1.6610 tsec 7.6750 #GCMRL# 306 dt 0.320000 rms 0.698 0.000% neg 0 invalid 762 tFOTS 5.7000 tGradient 1.7560 tsec 7.9580 #GCAMreg# pass 0 level1 1 level2 1 tsec 23.607 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 0.698959 #FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.697351) vs oldopt=(dt=1.28,rms=0.697594) #GCMRL# 308 dt 0.768000 rms 0.697 0.230% neg 0 invalid 762 tFOTS 5.7030 tGradient 1.7410 tsec 7.9290 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.697109) vs oldopt=(dt=0.32,rms=0.697139) #GCMRL# 309 dt 0.448000 rms 0.697 0.000% neg 0 invalid 762 tFOTS 5.6510 tGradient 1.7140 tsec 7.8310 #GCMRL# 310 dt 0.448000 rms 0.697 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7420 tsec 2.1860 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 0.643583 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.619219) vs oldopt=(dt=0.32,rms=0.625791) #GCMRL# 312 dt 0.448000 rms 0.619 3.786% neg 0 invalid 762 tFOTS 5.2220 tGradient 1.2960 tsec 6.9880 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.608906) vs oldopt=(dt=0.32,rms=0.611821) #GCMRL# 313 dt 0.448000 rms 0.609 1.666% neg 0 invalid 762 tFOTS 5.3140 tGradient 1.3180 tsec 7.1240 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.602571) vs oldopt=(dt=0.32,rms=0.604388) #GCMRL# 314 dt 0.448000 rms 0.603 1.040% neg 0 invalid 762 tFOTS 5.3160 tGradient 1.3040 tsec 7.0760 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.59948) vs oldopt=(dt=0.32,rms=0.600374) #GCMRL# 315 dt 0.448000 rms 0.599 0.513% neg 0 invalid 762 tFOTS 5.4090 tGradient 1.5600 tsec 7.4410 #GCMRL# 316 dt 0.320000 rms 0.598 0.250% neg 0 invalid 762 tFOTS 5.2610 tGradient 1.3530 tsec 7.0590 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.596487) vs oldopt=(dt=0.32,rms=0.596921) #GCMRL# 317 dt 0.448000 rms 0.596 0.250% neg 0 invalid 762 tFOTS 5.2580 tGradient 1.3060 tsec 7.0320 #FOTS# QuadFit found better minimum quadopt=(dt=0.388889,rms=0.59575) vs oldopt=(dt=0.32,rms=0.595874) #GCMRL# 318 dt 0.388889 rms 0.596 0.123% neg 0 invalid 762 tFOTS 5.2760 tGradient 1.3240 tsec 7.0690 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.595117) vs oldopt=(dt=0.32,rms=0.595272) #GCMRL# 319 dt 0.448000 rms 0.595 0.106% neg 0 invalid 762 tFOTS 5.3570 tGradient 1.3290 tsec 7.2050 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.594604) vs oldopt=(dt=0.32,rms=0.594714) #GCMRL# 320 dt 0.448000 rms 0.595 0.086% neg 0 invalid 762 tFOTS 5.2970 tGradient 1.2740 tsec 7.0580 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.594247) vs oldopt=(dt=0.32,rms=0.594309) #GCMRL# 321 dt 0.448000 rms 0.594 0.060% neg 0 invalid 762 tFOTS 5.2790 tGradient 1.3030 tsec 7.1040 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.593919) vs oldopt=(dt=0.32,rms=0.593971) #GCMRL# 322 dt 0.448000 rms 0.594 0.055% neg 0 invalid 762 tFOTS 5.3350 tGradient 1.2860 tsec 7.0960 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.593688) vs oldopt=(dt=0.32,rms=0.59371) #GCMRL# 323 dt 0.448000 rms 0.594 0.000% neg 0 invalid 762 tFOTS 5.2880 tGradient 1.2560 tsec 7.0680 #GCMRL# 324 dt 0.448000 rms 0.593 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2880 tsec 1.7190 #GCMRL# 325 dt 0.448000 rms 0.593 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3470 tsec 1.8480 #GCMRL# 326 dt 0.224000 rms 0.593 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3150 tsec 2.1790 #GCMRL# 327 dt 0.224000 rms 0.593 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3200 tsec 1.7360 #GCMRL# 328 dt 0.224000 rms 0.592 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3000 tsec 1.7460 #GCMRL# 329 dt 0.224000 rms 0.592 -0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3200 tsec 2.3450 #FOTS# QuadFit found better minimum quadopt=(dt=0,rms=0.592279) vs oldopt=(dt=0,rms=0.592279) #GCAMreg# pass 0 level1 0 level2 1 tsec 109.507 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 0.592963 #GCMRL# 331 dt 0.320000 rms 0.583 1.646% neg 0 invalid 762 tFOTS 5.5330 tGradient 1.3280 tsec 7.2710 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.577233) vs oldopt=(dt=0.32,rms=0.578213) #GCMRL# 332 dt 0.384000 rms 0.577 1.024% neg 0 invalid 762 tFOTS 5.3640 tGradient 1.2650 tsec 7.0560 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.574666) vs oldopt=(dt=0.32,rms=0.575078) #GCMRL# 333 dt 0.384000 rms 0.575 0.445% neg 0 invalid 762 tFOTS 5.4000 tGradient 1.2800 tsec 7.0960 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.572923) vs oldopt=(dt=0.32,rms=0.5732) #GCMRL# 334 dt 0.384000 rms 0.573 0.303% neg 0 invalid 762 tFOTS 5.4520 tGradient 1.3100 tsec 7.1720 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.572056) vs oldopt=(dt=0.32,rms=0.572185) #GCMRL# 335 dt 0.384000 rms 0.572 0.151% neg 0 invalid 762 tFOTS 5.3700 tGradient 1.3160 tsec 7.1340 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.57136) vs oldopt=(dt=0.32,rms=0.571456) #GCMRL# 336 dt 0.384000 rms 0.571 0.122% neg 0 invalid 762 tFOTS 5.3750 tGradient 1.3030 tsec 7.1290 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.571118) vs oldopt=(dt=0.32,rms=0.571141) #GCMRL# 337 dt 0.384000 rms 0.571 0.000% neg 0 invalid 762 tFOTS 5.3150 tGradient 1.3030 tsec 7.1140 #GCMRL# 338 dt 0.384000 rms 0.571 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3270 tsec 1.7380 #GCMRL# 339 dt 0.384000 rms 0.570 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2920 tsec 1.7670 #GCMRL# 340 dt 0.384000 rms 0.570 -0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2760 tsec 2.4160 #FOTS# QuadFit found better minimum quadopt=(dt=1e-05,rms=0.570316) vs oldopt=(dt=1.25e-05,rms=0.570316) #GCMRL# 341 dt 0.000010 rms 0.570 0.000% neg 0 invalid 762 tFOTS 7.2310 tGradient 1.3190 tsec 8.9670 GCAMregister done in 22.8663 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 0.568393 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.567505) vs oldopt=(dt=23.12,rms=0.567531) #GCMRL# 343 dt 32.368000 rms 0.568 0.156% neg 0 invalid 762 tFOTS 8.8970 tGradient 2.9850 tsec 12.4840 #FOTS# QuadFit found better minimum quadopt=(dt=0.00108375,rms=0.56751) vs oldopt=(dt=0.000903125,rms=0.56751) #GCAMreg# pass 0 level1 5 level2 1 tsec 34.204 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 0.568225 #GCMRL# 345 dt 0.000000 rms 0.568 0.126% neg 0 invalid 762 tFOTS 7.8350 tGradient 3.1500 tsec 11.5160 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 0.568255 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.567301) vs oldopt=(dt=6.48,rms=0.567348) #GCMRL# 347 dt 9.072000 rms 0.567 0.168% neg 0 invalid 762 tFOTS 8.9470 tGradient 2.4300 tsec 11.9680 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.567231) vs oldopt=(dt=6.48,rms=0.567237) #GCMRL# 348 dt 9.072000 rms 0.567 0.000% neg 0 invalid 762 tFOTS 8.7870 tGradient 2.3940 tsec 11.7960 #GCAMreg# pass 0 level1 4 level2 1 tsec 33.564 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 0.567952 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.56704) vs oldopt=(dt=6.48,rms=0.567076) #GCMRL# 350 dt 9.072000 rms 0.567 0.161% neg 0 invalid 762 tFOTS 8.9470 tGradient 2.4190 tsec 11.8560 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.566963) vs oldopt=(dt=6.48,rms=0.566974) #GCMRL# 351 dt 9.072000 rms 0.567 0.000% neg 0 invalid 762 tFOTS 8.3970 tGradient 2.3740 tsec 11.3440 #GCMRL# 352 dt 9.072000 rms 0.567 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3620 tsec 2.8740 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 0.567734 #FOTS# QuadFit found better minimum quadopt=(dt=22.5882,rms=0.562946) vs oldopt=(dt=8,rms=0.564118) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 354 dt 22.588235 rms 0.563 0.819% neg 0 invalid 762 tFOTS 8.6490 tGradient 2.1050 tsec 12.5350 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.5628) vs oldopt=(dt=8,rms=0.562802) iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 355 dt 9.600000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 8.8860 tGradient 1.9790 tsec 12.2930 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 38.119 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 0.563511 #FOTS# QuadFit found better minimum quadopt=(dt=25.1733,rms=0.558593) vs oldopt=(dt=8,rms=0.559935) iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 357 dt 25.173333 rms 0.559 0.843% neg 0 invalid 762 tFOTS 9.5490 tGradient 1.9840 tsec 16.2180 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 358 dt 32.000000 rms 0.555 0.753% neg 0 invalid 762 tFOTS 8.5010 tGradient 2.1000 tsec 12.0310 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.553266) vs oldopt=(dt=8,rms=0.553301) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 359 dt 9.600000 rms 0.553 0.000% neg 0 invalid 762 tFOTS 8.5120 tGradient 2.0120 tsec 12.0540 #GCMRL# 360 dt 9.600000 rms 0.553 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9590 tsec 2.5390 #GCMRL# 361 dt 9.600000 rms 0.552 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9940 tsec 2.5130 #GCMRL# 362 dt 9.600000 rms 0.551 0.205% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9870 tsec 2.4990 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 363 dt 9.600000 rms 0.549 0.271% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9260 tsec 4.1670 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 364 dt 9.600000 rms 0.548 0.275% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9350 tsec 4.5840 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 365 dt 9.600000 rms 0.547 0.259% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9520 tsec 3.8660 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 366 dt 9.600000 rms 0.545 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9870 tsec 4.1360 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 367 dt 9.600000 rms 0.544 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0160 tsec 4.6800 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 368 dt 9.600000 rms 0.543 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9690 tsec 4.9780 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 369 dt 9.600000 rms 0.543 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9670 tsec 7.5290 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 370 dt 9.600000 rms 0.542 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3930 tsec 4.1490 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 371 dt 9.600000 rms 0.541 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0530 tsec 4.7170 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 372 dt 9.600000 rms 0.540 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0600 tsec 5.9750 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 373 dt 9.600000 rms 0.540 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9760 tsec 5.5070 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 374 dt 9.600000 rms 0.539 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0560 tsec 4.3260 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.538774) vs oldopt=(dt=32,rms=0.538779) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 375 dt 38.400000 rms 0.539 0.000% neg 0 invalid 762 tFOTS 8.8290 tGradient 2.0290 tsec 12.2520 iter 0, gcam->neg = 2 after 0 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_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 0.543874 #FOTS# QuadFit found better minimum quadopt=(dt=5.45455,rms=0.540932) vs oldopt=(dt=2.88,rms=0.541427) iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 377 dt 5.454545 rms 0.541 0.540% neg 0 invalid 762 tFOTS 8.9210 tGradient 1.7140 tsec 14.1360 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.540894) vs oldopt=(dt=0.72,rms=0.540903) iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 378 dt 1.008000 rms 0.541 0.000% neg 0 invalid 762 tFOTS 8.6060 tGradient 2.1030 tsec 13.3580 #GCMRL# 379 dt 1.008000 rms 0.541 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7320 tsec 2.2720 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 41.678 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 0.541628 #FOTS# QuadFit found better minimum quadopt=(dt=6.05128,rms=0.539565) vs oldopt=(dt=2.88,rms=0.53991) #GCMRL# 381 dt 6.051282 rms 0.540 0.381% neg 0 invalid 762 tFOTS 8.5310 tGradient 1.8190 tsec 10.7870 #FOTS# QuadFit found better minimum quadopt=(dt=13.824,rms=0.537702) vs oldopt=(dt=11.52,rms=0.537754) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 382 dt 13.824000 rms 0.538 0.345% neg 0 invalid 762 tFOTS 8.7620 tGradient 1.9180 tsec 12.6670 #FOTS# QuadFit found better minimum quadopt=(dt=22.087,rms=0.535029) vs oldopt=(dt=11.52,rms=0.535589) iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 383 dt 22.086957 rms 0.535 0.498% neg 0 invalid 762 tFOTS 8.6760 tGradient 1.7270 tsec 12.6800 #FOTS# QuadFit found better minimum quadopt=(dt=6.912,rms=0.532627) vs oldopt=(dt=11.52,rms=0.53334) #GCMRL# 384 dt 6.912000 rms 0.533 0.449% neg 0 invalid 762 tFOTS 8.7910 tGradient 2.0920 tsec 11.2860 #FOTS# QuadFit found better minimum quadopt=(dt=4.54545,rms=0.532104) vs oldopt=(dt=2.88,rms=0.532172) #GCMRL# 385 dt 4.545455 rms 0.532 0.000% neg 0 invalid 762 tFOTS 8.4460 tGradient 1.7160 tsec 10.5900 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 386 dt 4.545455 rms 0.532 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7880 tsec 4.2390 #GCMRL# 387 dt 4.545455 rms 0.531 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8800 tsec 2.3920 #GCMRL# 388 dt 4.545455 rms 0.529 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7200 tsec 2.2680 #GCMRL# 389 dt 4.545455 rms 0.528 0.257% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0000 tsec 2.5850 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 390 dt 4.545455 rms 0.527 0.275% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2870 tsec 3.5820 #GCMRL# 391 dt 4.545455 rms 0.525 0.289% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7670 tsec 2.2790 #GCMRL# 392 dt 4.545455 rms 0.524 0.279% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9070 tsec 2.5140 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 393 dt 4.545455 rms 0.522 0.249% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0840 tsec 4.0230 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 394 dt 4.545455 rms 0.521 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7630 tsec 3.9780 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 395 dt 4.545455 rms 0.520 0.193% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2540 tsec 3.4930 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 396 dt 4.545455 rms 0.519 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7400 tsec 2.9970 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 397 dt 4.545455 rms 0.519 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9090 tsec 5.3350 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 398 dt 4.545455 rms 0.518 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7420 tsec 5.3130 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 399 dt 4.545455 rms 0.517 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1700 tsec 6.8370 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 400 dt 4.545455 rms 0.517 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2420 tsec 7.7050 #GCMRL# 401 dt 11.520000 rms 0.517 0.000% neg 0 invalid 762 tFOTS 8.3670 tGradient 2.3470 tsec 11.1330 iter 0, gcam->neg = 4 after 3 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 0.523557 #GCMRL# 403 dt 0.000000 rms 0.523 0.140% neg 0 invalid 762 tFOTS 7.9000 tGradient 1.6040 tsec 9.9040 #GCAMreg# pass 0 level1 1 level2 1 tsec 27.953 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 0.523557 #GCMRL# 405 dt 0.000000 rms 0.523 0.140% neg 0 invalid 762 tFOTS 7.4160 tGradient 1.5900 tsec 9.4090 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 0.51366 #FOTS# QuadFit found better minimum quadopt=(dt=1.49611,rms=0.481296) vs oldopt=(dt=1.28,rms=0.482049) iter 0, gcam->neg = 1386 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 407 dt 1.496112 rms 0.490 4.690% neg 0 invalid 762 tFOTS 5.9770 tGradient 1.2020 tsec 13.1010 #GCMRL# 408 dt 0.000013 rms 0.490 0.000% neg 0 invalid 762 tFOTS 7.6020 tGradient 1.1790 tsec 9.2150 #GCAMreg# pass 0 level1 0 level2 1 tsec 32.22 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 0.490433 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.488417) vs oldopt=(dt=0.08,rms=0.488638) #GCMRL# 410 dt 0.112000 rms 0.488 0.411% neg 0 invalid 762 tFOTS 6.0210 tGradient 1.1760 tsec 7.5890 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.487903) vs oldopt=(dt=0.08,rms=0.487972) #GCMRL# 411 dt 0.112000 rms 0.488 0.000% neg 0 invalid 762 tFOTS 6.5440 tGradient 1.1710 tsec 8.5800 #GCMRL# 412 dt 0.112000 rms 0.488 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7580 tsec 2.3270 label assignment complete, 0 changed (0.00%) GCAMregister done in 9.46978 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 0.4838 #GCMRL# 414 dt 5.780000 rms 0.484 0.002% neg 0 invalid 762 tFOTS 7.9300 tGradient 2.6720 tsec 10.9890 #FOTS# QuadFit found better minimum quadopt=(dt=0.00338672,rms=0.483792) vs oldopt=(dt=0.00564453,rms=0.483792) #GCMRL# 415 dt 0.003387 rms 0.484 0.000% neg 0 invalid 762 tFOTS 9.8650 tGradient 2.3330 tsec 12.6300 #GCAMreg# pass 0 level1 5 level2 1 tsec 33.258 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 0.483792 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 0.483848 #GCAMreg# pass 0 level1 4 level2 1 tsec 18.163 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 0.483848 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 0.484061 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.483899) vs oldopt=(dt=2,rms=0.483924) #GCMRL# 420 dt 2.800000 rms 0.484 0.033% neg 0 invalid 762 tFOTS 8.0450 tGradient 1.5910 tsec 10.0430 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.483891) vs oldopt=(dt=0.5,rms=0.483892) #GCMRL# 421 dt 0.700000 rms 0.484 0.000% neg 0 invalid 762 tFOTS 7.1350 tGradient 1.5480 tsec 9.1010 #GCAMreg# pass 0 level1 3 level2 1 tsec 29.07 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 0.483891 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.483168) vs oldopt=(dt=8,rms=0.483286) #GCMRL# 423 dt 11.200000 rms 0.483 0.149% neg 0 invalid 762 tFOTS 8.9460 tGradient 1.5640 tsec 10.9880 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.482199) vs oldopt=(dt=32,rms=0.482207) #GCMRL# 424 dt 38.400000 rms 0.482 0.200% neg 0 invalid 762 tFOTS 6.5870 tGradient 1.6720 tsec 8.6570 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.480649) vs oldopt=(dt=32,rms=0.480832) #GCMRL# 425 dt 44.800000 rms 0.481 0.321% neg 0 invalid 762 tFOTS 6.1990 tGradient 1.4920 tsec 8.0880 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.480145) vs oldopt=(dt=8,rms=0.480204) #GCMRL# 426 dt 11.200000 rms 0.480 0.000% neg 0 invalid 762 tFOTS 8.0010 tGradient 1.6330 tsec 10.0450 #GCMRL# 427 dt 11.200000 rms 0.480 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4160 tsec 1.9110 #GCMRL# 428 dt 11.200000 rms 0.480 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4200 tsec 1.9160 #GCMRL# 429 dt 11.200000 rms 0.480 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4480 tsec 1.9700 #GCMRL# 430 dt 11.200000 rms 0.479 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4800 tsec 1.9740 #GCMRL# 431 dt 11.200000 rms 0.478 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4060 tsec 1.8450 #GCMRL# 432 dt 11.200000 rms 0.478 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4220 tsec 1.9200 #GCMRL# 433 dt 11.200000 rms 0.477 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4190 tsec 1.9310 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 0.478978 #FOTS# QuadFit found better minimum quadopt=(dt=2.75,rms=0.478507) vs oldopt=(dt=2.88,rms=0.478509) #GCMRL# 435 dt 2.750000 rms 0.479 0.098% neg 0 invalid 762 tFOTS 7.7030 tGradient 1.2500 tsec 9.3320 #GCAMreg# pass 0 level1 2 level2 1 tsec 26.797 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 0.478507 #FOTS# QuadFit found better minimum quadopt=(dt=11.8319,rms=0.476535) vs oldopt=(dt=11.52,rms=0.476536) #GCMRL# 437 dt 11.831933 rms 0.477 0.412% neg 0 invalid 762 tFOTS 7.7670 tGradient 1.2530 tsec 9.4030 #FOTS# QuadFit found better minimum quadopt=(dt=15.4315,rms=0.473586) vs oldopt=(dt=11.52,rms=0.473766) iter 0, gcam->neg = 11 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 438 dt 15.431472 rms 0.474 0.602% neg 0 invalid 762 tFOTS 7.7620 tGradient 1.2520 tsec 13.7740 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.472906) vs oldopt=(dt=2.88,rms=0.472959) #GCMRL# 439 dt 4.032000 rms 0.473 0.000% neg 0 invalid 762 tFOTS 5.6200 tGradient 1.2460 tsec 7.2640 #GCMRL# 440 dt 4.032000 rms 0.473 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2610 tsec 1.6520 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 441 dt 4.032000 rms 0.472 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2600 tsec 2.4820 #GCMRL# 442 dt 4.032000 rms 0.471 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2600 tsec 1.7560 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 443 dt 4.032000 rms 0.470 0.210% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2480 tsec 5.2860 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 444 dt 4.032000 rms 0.469 0.213% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2470 tsec 3.5460 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 445 dt 4.032000 rms 0.469 0.194% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2590 tsec 3.5920 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 446 dt 4.032000 rms 0.468 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2860 tsec 3.1350 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 447 dt 4.032000 rms 0.467 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2460 tsec 3.5250 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 448 dt 4.032000 rms 0.466 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2570 tsec 5.9590 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 449 dt 4.032000 rms 0.466 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2450 tsec 3.8620 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 450 dt 4.032000 rms 0.465 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2590 tsec 3.9800 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.465332) vs oldopt=(dt=2.88,rms=0.46534) iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 451 dt 4.032000 rms 0.465 0.000% neg 0 invalid 762 tFOTS 7.5970 tGradient 1.2530 tsec 10.8190 #GCMRL# 452 dt 4.032000 rms 0.465 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2620 tsec 1.7530 #GCMRL# 453 dt 4.032000 rms 0.465 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2670 tsec 1.7640 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 0.468914 #GCAMreg# pass 0 level1 1 level2 1 tsec 15.203 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 0.468914 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 0.462883 #FOTS# QuadFit found better minimum quadopt=(dt=1.10552,rms=0.449105) vs oldopt=(dt=1.28,rms=0.449427) iter 0, gcam->neg = 805 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 457 dt 1.105516 rms 0.455 1.649% neg 0 invalid 762 tFOTS 5.7160 tGradient 0.7320 tsec 13.7830 #FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.455249) vs oldopt=(dt=1.95313e-05,rms=0.455249) #GCMRL# 458 dt 0.000023 rms 0.455 0.000% neg 0 invalid 762 tFOTS 7.2070 tGradient 0.7230 tsec 8.3330 #GCAMreg# pass 0 level1 0 level2 1 tsec 31.537 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 0.455249 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.453271) vs oldopt=(dt=0.32,rms=0.453294) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 460 dt 0.256000 rms 0.453 0.435% neg 0 invalid 762 tFOTS 5.7080 tGradient 0.7270 tsec 7.9910 #FOTS# QuadFit found better minimum quadopt=(dt=0.511905,rms=0.450053) vs oldopt=(dt=0.32,rms=0.450666) iter 0, gcam->neg = 14 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 461 dt 0.511905 rms 0.450 0.698% neg 0 invalid 762 tFOTS 5.6000 tGradient 0.7140 tsec 8.1940 #FOTS# QuadFit found better minimum quadopt=(dt=0.62,rms=0.446491) vs oldopt=(dt=0.32,rms=0.447535) iter 0, gcam->neg = 116 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 462 dt 0.620000 rms 0.447 0.649% neg 0 invalid 762 tFOTS 5.6410 tGradient 0.7220 tsec 11.8180 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 463 dt 0.320000 rms 0.446 0.256% neg 0 invalid 762 tFOTS 5.6510 tGradient 0.7300 tsec 7.5880 #FOTS# QuadFit found better minimum quadopt=(dt=0.521277,rms=0.444001) vs oldopt=(dt=0.32,rms=0.444467) iter 0, gcam->neg = 41 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 464 dt 0.521277 rms 0.444 0.348% neg 0 invalid 762 tFOTS 5.6170 tGradient 0.7120 tsec 11.0880 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.444313) vs oldopt=(dt=0.08,rms=0.444335) #GCMRL# 465 dt 0.112000 rms 0.444 0.000% neg 0 invalid 762 tFOTS 5.6790 tGradient 0.7280 tsec 6.8140 #GCMRL# 466 dt 0.112000 rms 0.444 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7330 tsec 1.1150 #GCMRL# 467 dt 0.112000 rms 0.444 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7340 tsec 1.1180 #GCMRL# 468 dt 0.112000 rms 0.444 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7500 tsec 1.1350 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 469 dt 0.112000 rms 0.443 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7320 tsec 2.3370 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 470 dt 0.112000 rms 0.442 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7270 tsec 1.9450 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 471 dt 0.112000 rms 0.442 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7310 tsec 1.9650 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 472 dt 0.112000 rms 0.442 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7240 tsec 2.3840 #FOTS# QuadFit found better minimum quadopt=(dt=0.004,rms=0.441676) vs oldopt=(dt=0.005,rms=0.441676) #GCMRL# 473 dt 0.004000 rms 0.442 0.000% neg 0 invalid 762 tFOTS 5.6560 tGradient 0.7170 tsec 6.7730 GCAMregister done in 6.88652 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 3949 tmin = 3.65843 Calls to gcamLabelEnergy 3287 tmin = 0.8445 Calls to gcamJacobianEnergy 3949 tmin = 2.1083 Calls to gcamSmoothnessEnergy 3949 tmin = 8.16905 Calls to gcamLogLikelihoodTerm 475 tmin = 1.30045 Calls to gcamLabelTerm 414 tmin = 3.70933 Calls to gcamJacobianTerm 475 tmin = 2.49655 Calls to gcamSmoothnessTerm 475 tmin = 1.22738 Calls to gcamComputeGradient 475 tmin = 18.2038 Calls to gcamComputeMetricProperties 5540 tmin = 4.59105 mri_ca_register took 0 hours, 51 minutes and 7 seconds. #VMPC# mri_ca_register VmPeak 2306084 FSRUNTIME@ mri_ca_register 0.8521 hours 4 threads #-------------------------------------- #@# SubCort Seg Tue Jan 10 11:54:47 CET 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname sharky machine x86_64 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 = 4 == reading 1 input volumes reading classifier array from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 5.82 Atlas used for the 3D morph was /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 = 0.14999 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.29 x + 0.0 (1385 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1385 voxels, peak = 6), gca=8.0 gca peak = 0.20380 (13) mri peak = 0.14964 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.47 x + 0.0 (810 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.47 x + 0.0 (810 voxels, peak = 6), gca=6.0 gca peak = 0.26283 (96) mri peak = 0.11820 (100) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (423 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (423 voxels, peak = 97), gca=97.4 gca peak = 0.15814 (97) mri peak = 0.12253 (97) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (501 voxels, overlap=0.833) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (501 voxels, peak = 99), gca=99.4 gca peak = 0.27624 (56) mri peak = 0.11045 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (584 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (584 voxels, peak = 69), gca=68.6 gca peak = 0.28723 (59) mri peak = 0.13407 (69) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (540 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (540 voxels, peak = 70), gca=69.9 gca peak = 0.07623 (103) mri peak = 0.07867 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (34922 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (34922 voxels, peak = 109), gca=108.7 gca peak = 0.07837 (105) mri peak = 0.07601 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (34085 voxels, overlap=0.620) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (34085 voxels, peak = 110), gca=109.7 gca peak = 0.10165 (58) mri peak = 0.04929 (75) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (22723 voxels, overlap=0.055) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (22723 voxels, peak = 73), gca=72.8 gca peak = 0.11113 (58) mri peak = 0.04865 (71) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (22186 voxels, overlap=0.350) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (22186 voxels, peak = 71), gca=71.1 gca peak = 0.27796 (67) mri peak = 0.10595 (84) Right_Caudate (50): linear fit = 1.25 x + 0.0 (537 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.25 x + 0.0 (537 voxels, peak = 83), gca=83.4 gca peak = 0.14473 (69) mri peak = 0.15469 (88) Left_Caudate (11): linear fit = 1.13 x + 0.0 (626 voxels, overlap=0.018) Left_Caudate (11): linear fit = 1.13 x + 0.0 (626 voxels, peak = 78), gca=78.3 gca peak = 0.14301 (56) mri peak = 0.07191 (77) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (22864 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (22864 voxels, peak = 76), gca=75.9 gca peak = 0.14610 (55) mri peak = 0.07495 (77) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (22972 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (22972 voxels, peak = 73), gca=73.4 gca peak = 0.16309 (85) mri peak = 0.10769 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (5362 voxels, overlap=0.427) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (5362 voxels, peak = 93), gca=93.1 gca peak = 0.15172 (84) mri peak = 0.12295 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5859 voxels, overlap=0.354) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5859 voxels, peak = 92), gca=92.0 gca peak = 0.30461 (58) mri peak = 0.15974 (69) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (313 voxels, overlap=0.048) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (313 voxels, peak = 69), gca=69.3 gca peak = 0.32293 (57) mri peak = 0.11202 (73) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (309 voxels, overlap=0.043) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (309 voxels, peak = 70), gca=70.4 gca peak = 0.11083 (90) mri peak = 0.09037 (92) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (4397 voxels, overlap=0.804) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (4397 voxels, peak = 93), gca=93.1 gca peak = 0.11393 (83) mri peak = 0.08423 (89) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (4199 voxels, overlap=0.670) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (4199 voxels, peak = 90), gca=90.1 gca peak = 0.08575 (81) mri peak = 0.12928 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1050 voxels, overlap=0.125) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1050 voxels, peak = 94), gca=93.6 gca peak = 0.08618 (78) mri peak = 0.10660 (92) Right_Putamen (51): linear fit = 1.16 x + 0.0 (993 voxels, overlap=0.179) Right_Putamen (51): linear fit = 1.16 x + 0.0 (993 voxels, peak = 91), gca=90.9 gca peak = 0.08005 (78) mri peak = 0.09865 (87) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12109 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12109 voxels, peak = 83), gca=83.1 gca peak = 0.12854 (88) mri peak = 0.10531 (91) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1260 voxels, overlap=0.671) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1260 voxels, peak = 93), gca=92.8 gca peak = 0.15703 (87) mri peak = 0.08775 (92) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1280 voxels, overlap=0.816) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1280 voxels, peak = 93), gca=92.7 gca peak = 0.17522 (25) mri peak = 0.06842 ( 4) gca peak = 0.17113 (14) mri peak = 0.15518 (13) Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (236 voxels, overlap=0.476) Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (236 voxels, peak = 10), gca=10.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) 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 1.22 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.53 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31708 ( 7) mri peak = 0.14999 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.71 x + 0.0 (1385 voxels, overlap=0.497) Left_Lateral_Ventricle (4): linear fit = 0.71 x + 0.0 (1385 voxels, peak = 5), gca=5.0 gca peak = 0.33113 ( 6) mri peak = 0.14964 ( 9) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (810 voxels, overlap=0.809) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (810 voxels, peak = 7), gca=6.5 gca peak = 0.21938 (97) mri peak = 0.11820 (100) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (423 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (423 voxels, peak = 96), gca=95.5 gca peak = 0.16529 (99) mri peak = 0.12253 (97) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (501 voxels, overlap=0.976) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (501 voxels, peak = 99), gca=99.5 gca peak = 0.24482 (68) mri peak = 0.11045 (70) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (584 voxels, overlap=0.966) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (584 voxels, peak = 68), gca=68.0 gca peak = 0.32843 (67) mri peak = 0.13407 (69) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (540 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (540 voxels, peak = 68), gca=68.0 gca peak = 0.07413 (109) mri peak = 0.07867 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34922 voxels, overlap=0.829) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34922 voxels, peak = 109), gca=109.0 gca peak = 0.07449 (109) mri peak = 0.07601 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34085 voxels, overlap=0.809) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34085 voxels, peak = 109), gca=109.0 gca peak = 0.08198 (73) mri peak = 0.04929 (75) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (22723 voxels, overlap=0.961) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (22723 voxels, peak = 73), gca=73.0 gca peak = 0.09254 (71) mri peak = 0.04865 (71) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22186 voxels, overlap=0.974) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22186 voxels, peak = 71), gca=71.0 gca peak = 0.20518 (82) mri peak = 0.10595 (84) Right_Caudate (50): linear fit = 1.01 x + 0.0 (537 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.01 x + 0.0 (537 voxels, peak = 83), gca=83.2 gca peak = 0.15916 (88) mri peak = 0.15469 (88) Left_Caudate (11): linear fit = 0.99 x + 0.0 (626 voxels, overlap=0.832) Left_Caudate (11): linear fit = 0.99 x + 0.0 (626 voxels, peak = 87), gca=86.7 gca peak = 0.09990 (76) mri peak = 0.07191 (77) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (22864 voxels, overlap=0.957) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (22864 voxels, peak = 75), gca=74.9 gca peak = 0.11962 (74) mri peak = 0.07495 (77) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22972 voxels, overlap=0.906) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22972 voxels, peak = 73), gca=72.9 gca peak = 0.14900 (93) mri peak = 0.10769 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5362 voxels, overlap=0.953) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5362 voxels, peak = 93), gca=92.5 gca peak = 0.13878 (92) mri peak = 0.12295 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5859 voxels, overlap=0.909) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5859 voxels, peak = 92), gca=91.5 gca peak = 0.28856 (69) mri peak = 0.15974 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (313 voxels, overlap=0.942) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (313 voxels, peak = 69), gca=69.0 gca peak = 0.30235 (71) mri peak = 0.11202 (73) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (309 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (309 voxels, peak = 69), gca=69.2 gca peak = 0.10724 (93) mri peak = 0.09037 (92) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4397 voxels, overlap=0.939) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4397 voxels, peak = 93), gca=92.5 gca peak = 0.10473 (90) mri peak = 0.08423 (89) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4199 voxels, overlap=0.954) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4199 voxels, peak = 90), gca=89.6 gca peak = 0.08806 (87) mri peak = 0.12928 (92) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1050 voxels, overlap=0.736) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1050 voxels, peak = 87), gca=86.6 gca peak = 0.07835 (93) mri peak = 0.10660 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (993 voxels, overlap=0.903) Right_Putamen (51): linear fit = 1.00 x + 0.0 (993 voxels, peak = 93), gca=92.5 gca peak = 0.07384 (86) mri peak = 0.09865 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12109 voxels, overlap=0.739) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12109 voxels, peak = 86), gca=85.6 gca peak = 0.12598 (89) mri peak = 0.10531 (91) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1260 voxels, overlap=0.796) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1260 voxels, peak = 88), gca=87.7 gca peak = 0.14510 (91) mri peak = 0.08775 (92) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1280 voxels, overlap=0.853) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1280 voxels, peak = 90), gca=89.6 gca peak = 0.25694 (13) mri peak = 0.06842 ( 4) gca peak = 0.21036 (12) mri peak = 0.15518 (13) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (236 voxels, overlap=0.858) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (236 voxels, peak = 12), gca=12.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.15108 (33) gca peak Third_Ventricle = 0.25694 (13) gca peak CSF = 0.30158 (19) gca peak Left_Accumbens_area = 0.58924 (71) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.22810 (28) gca peak Right_Accumbens_area = 0.28338 (82) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.91795 (17) gca peak WM_hypointensities = 0.11613 (80) gca peak non_WM_hypointensities = 0.11377 (43) gca peak Optic_Chiasm = 0.51672 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 68789 voxels changed in iteration 0 of unlikely voxel relabeling 272 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 54 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 69140 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 578 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 72161 changed. image ll: -2.171, PF=0.500 pass 2: 16371 changed. image ll: -2.169, PF=0.500 pass 3: 4617 changed. 47995 voxels changed in iteration 0 of unlikely voxel relabeling 274 voxels changed in iteration 1 of unlikely voxel relabeling 28 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5843 voxels changed in iteration 0 of unlikely voxel relabeling 66 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5830 voxels changed in iteration 0 of unlikely voxel relabeling 50 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 4559 voxels changed in iteration 0 of unlikely voxel relabeling 33 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 6483 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 4922 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 361 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1872.913188 mri_ca_label stimesec 0.791941 mri_ca_label ru_maxrss 2127820 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 428714 mri_ca_label ru_majflt 16 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2696 mri_ca_label ru_oublock 632 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 600 mri_ca_label ru_nivcsw 4934 auto-labeling took 30 minutes and 23 seconds. #-------------------------------------- #@# CC Seg Tue Jan 10 12:25:10 CET 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/cc_up.lta Test_withT2 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/cc_up.lta reading aseg from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/aseg.auto_noCCseg.mgz reading norm from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/norm.mgz 57485 voxels in left wm, 93161 in right wm, xrange [123, 139] searching rotation angles z=[-11 3], y=[-6 8] searching scale 1 Z rot -10.9 searching scale 1 Z rot -10.7 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.2 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 global minimum found at slice 133.0, rotations (0.56, -4.92) final transformation (x=133.0, yr=0.563, zr=-4.922): 0.99626 0.08580 0.00979 -12.59451; -0.08580 0.99631 -0.00084 56.80095; -0.00983 0.00000 0.99995 30.31233; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 131] in xformed coordinates best xformed slice 127 min_x_fornix = 122 min_x_fornix = 121 min_x_fornix = 121 min_x_fornix = 121 min_x_fornix = 121 cc center is found at 127 83 99 eigenvectors: 0.00223 0.01087 0.99994; -0.29135 -0.95655 0.01104; 0.95661 -0.29136 0.00104; writing aseg with callosum to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #VMPC# mri_cc VmPeak 460152 mri_cc done #-------------------------------------- #@# Merge ASeg Tue Jan 10 12:25:49 CET 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Jan 10 12:25:49 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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... Reading aseg aseg.presurf.mgz normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 367 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 80 (80), valley at 22 (22) csf peak at 10, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 79 (79), valley at 19 (19) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 31 seconds. #-------------------------------------------- #@# Mask BFS Tue Jan 10 12:28:21 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1291345 voxels in mask (pct= 7.70) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Jan 10 12:28:22 CET 2023 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 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 (102.0): 103.3 +- 6.8 [79.0 --> 125.0] CCS GM (77.0) : 74.4 +- 13.4 [30.0 --> 95.0] white_mean 103.309 white_sigma 6.81111 gray_mean 74.4249 gray_sigma 13.3689 setting bottom of white matter range wm_low to 87.8 setting top of gray matter range gray_hi to 101.2 wm_low 87.7939 wm_hi 125 gray_low 30 gray_hi 101.163 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 87.7939 wm_hi 125 gray_low 30 gray_hi 101.163 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 101.163, wm_low = 87.7939 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=101.163, wmlow=87.7939 163023 voxels processed (0.97%) 69508 voxels white (0.41%) 93515 voxels non-white (0.56%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=82.7939, gray_hi=101.163, wsize=13 350704 voxels tested (2.09%) 63182 voxels changed (0.38%) 79727 multi-scale searches (0.48%) Recovering bright white MRIrecoverBrightWhite() wm_low 87.7939 wm_hi 125 slack 6.81111 pct_thresh 0.33 intensity_thresh 131.811 nvox_thresh 8.58 3870 voxels tested (0.02%) 2265 voxels changed (0.01%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=82.7939, hithr=101.163 smoothing input volume with sigma = 0.250 148462 voxels tested (0.88%) 20523 voxels changed (0.12%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 15089 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 4025 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3329 filled MRIfindBrightNonWM(): 23269 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.42 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 5293 additional wm voxels added 0 additional wm voxels added SEG EDIT: 47098 voxels turned on, 11700 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 63 found - 63 modified | TOTAL: 63 pass 2 (xy+): 0 found - 63 modified | TOTAL: 63 pass 1 (xy-): 64 found - 64 modified | TOTAL: 127 pass 2 (xy-): 0 found - 64 modified | TOTAL: 127 pass 1 (yz+): 53 found - 53 modified | TOTAL: 180 pass 2 (yz+): 0 found - 53 modified | TOTAL: 180 pass 1 (yz-): 56 found - 56 modified | TOTAL: 236 pass 2 (yz-): 0 found - 56 modified | TOTAL: 236 pass 1 (xz+): 40 found - 40 modified | TOTAL: 276 pass 2 (xz+): 0 found - 40 modified | TOTAL: 276 pass 1 (xz-): 40 found - 40 modified | TOTAL: 316 pass 2 (xz-): 0 found - 40 modified | TOTAL: 316 Iteration Number : 1 pass 1 (+++): 115 found - 115 modified | TOTAL: 115 pass 2 (+++): 0 found - 115 modified | TOTAL: 115 pass 1 (+++): 145 found - 145 modified | TOTAL: 260 pass 2 (+++): 0 found - 145 modified | TOTAL: 260 pass 1 (+++): 98 found - 98 modified | TOTAL: 358 pass 2 (+++): 0 found - 98 modified | TOTAL: 358 pass 1 (+++): 91 found - 91 modified | TOTAL: 449 pass 2 (+++): 0 found - 91 modified | TOTAL: 449 Iteration Number : 1 pass 1 (++): 152 found - 152 modified | TOTAL: 152 pass 2 (++): 0 found - 152 modified | TOTAL: 152 pass 1 (+-): 91 found - 91 modified | TOTAL: 243 pass 2 (+-): 0 found - 91 modified | TOTAL: 243 pass 1 (--): 157 found - 157 modified | TOTAL: 400 pass 2 (--): 0 found - 157 modified | TOTAL: 400 pass 1 (-+): 88 found - 88 modified | TOTAL: 488 pass 2 (-+): 0 found - 88 modified | TOTAL: 488 Iteration Number : 2 pass 1 (xy+): 25 found - 25 modified | TOTAL: 25 pass 2 (xy+): 0 found - 25 modified | TOTAL: 25 pass 1 (xy-): 17 found - 17 modified | TOTAL: 42 pass 2 (xy-): 0 found - 17 modified | TOTAL: 42 pass 1 (yz+): 21 found - 21 modified | TOTAL: 63 pass 2 (yz+): 0 found - 21 modified | TOTAL: 63 pass 1 (yz-): 14 found - 14 modified | TOTAL: 77 pass 2 (yz-): 0 found - 14 modified | TOTAL: 77 pass 1 (xz+): 19 found - 19 modified | TOTAL: 96 pass 2 (xz+): 0 found - 19 modified | TOTAL: 96 pass 1 (xz-): 13 found - 13 modified | TOTAL: 109 pass 2 (xz-): 0 found - 13 modified | TOTAL: 109 Iteration Number : 2 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 6 found - 6 modified | TOTAL: 16 pass 2 (+++): 0 found - 6 modified | TOTAL: 16 pass 1 (+++): 4 found - 4 modified | TOTAL: 20 pass 2 (+++): 0 found - 4 modified | TOTAL: 20 pass 1 (+++): 4 found - 4 modified | TOTAL: 24 pass 2 (+++): 0 found - 4 modified | TOTAL: 24 Iteration Number : 2 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 14 found - 14 modified | TOTAL: 27 pass 2 (+-): 0 found - 14 modified | TOTAL: 27 pass 1 (--): 11 found - 11 modified | TOTAL: 38 pass 2 (--): 0 found - 11 modified | TOTAL: 38 pass 1 (-+): 9 found - 9 modified | TOTAL: 47 pass 2 (-+): 0 found - 9 modified | TOTAL: 47 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 5 found - 5 modified | TOTAL: 5 pass 2 (xy-): 0 found - 5 modified | TOTAL: 5 pass 1 (yz+): 1 found - 1 modified | TOTAL: 6 pass 2 (yz+): 0 found - 1 modified | TOTAL: 6 pass 1 (yz-): 5 found - 5 modified | TOTAL: 11 pass 2 (yz-): 0 found - 5 modified | TOTAL: 11 pass 1 (xz+): 2 found - 2 modified | TOTAL: 13 pass 2 (xz+): 0 found - 2 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 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 (--): 4 found - 4 modified | TOTAL: 4 pass 2 (--): 0 found - 4 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 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 = 1451 (out of 481238: 0.301514) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Jan 10 12:30:32 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.11217 0.03154 -0.04637 -18.33588; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21301; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.11217 0.03154 -0.04637 -18.33588; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21301; 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] = 1795 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) need search nearby using seed (124, 120, 151), TAL = (4.0, 23.0, 8.0) talairach voxel to voxel transform 0.89598 -0.00769 0.04752 14.15422; 0.07011 0.76997 -0.37292 39.51464; -0.02809 0.33928 0.88620 -29.06593; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 120, 151) --> (4.0, 23.0, 8.0) done. filling took 1.1 minutes talairach cc position changed to (4.00, 23.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 23.00, 8.00) SRC: (115.38, 83.03, 142.49) search lh wm seed point around talairach space (-14.00, 23.00, 8.00), SRC: (147.64, 85.56, 141.47) 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 ... Embedding colortable mri_fill done, writing output to filled.mgz... cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Tue Jan 10 12:31:41 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 9 found - 9 modified | TOTAL: 14 pass 2 (xy-): 0 found - 9 modified | TOTAL: 14 pass 1 (yz+): 10 found - 10 modified | TOTAL: 24 pass 2 (yz+): 0 found - 10 modified | TOTAL: 24 pass 1 (yz-): 5 found - 5 modified | TOTAL: 29 pass 2 (yz-): 0 found - 5 modified | TOTAL: 29 pass 1 (xz+): 3 found - 3 modified | TOTAL: 32 pass 2 (xz+): 0 found - 3 modified | TOTAL: 32 pass 1 (xz-): 1 found - 1 modified | TOTAL: 33 pass 2 (xz-): 0 found - 1 modified | TOTAL: 33 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 1 found - 1 modified | TOTAL: 6 pass 2 (+-): 0 found - 1 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 53 (out of 231176: 0.022926) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 30: 23 vertices, 32 faces slice 40: 5295 vertices, 5583 faces slice 50: 15245 vertices, 15644 faces slice 60: 25697 vertices, 26118 faces slice 70: 36554 vertices, 37037 faces slice 80: 47216 vertices, 47677 faces slice 90: 58129 vertices, 58667 faces slice 100: 69147 vertices, 69655 faces slice 110: 79303 vertices, 79809 faces slice 120: 87834 vertices, 88330 faces slice 130: 96620 vertices, 97111 faces slice 140: 104146 vertices, 104608 faces slice 150: 111159 vertices, 111580 faces slice 160: 116501 vertices, 116875 faces slice 170: 120856 vertices, 121193 faces slice 180: 123144 vertices, 123408 faces slice 190: 123264 vertices, 123486 faces slice 200: 123264 vertices, 123486 faces slice 210: 123264 vertices, 123486 faces slice 220: 123264 vertices, 123486 faces slice 230: 123264 vertices, 123486 faces slice 240: 123264 vertices, 123486 faces slice 250: 123264 vertices, 123486 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 123256 voxel in cpt #1: X=-224 [v=123256,e=370440,f=246960] located at (-27.949211, -33.008633, 30.394667) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-4.000000, 2.000000, 34.000000) For the whole surface: X=-222 [v=123264,e=370458,f=246972] 2 components have been found keeping component #1 with 123256 vertices done #-------------------------------------------- #@# Tessellate rh Tue Jan 10 12:31:45 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 14 found - 14 modified | TOTAL: 20 pass 2 (xy-): 0 found - 14 modified | TOTAL: 20 pass 1 (yz+): 9 found - 9 modified | TOTAL: 29 pass 2 (yz+): 0 found - 9 modified | TOTAL: 29 pass 1 (yz-): 13 found - 13 modified | TOTAL: 42 pass 2 (yz-): 0 found - 13 modified | TOTAL: 42 pass 1 (xz+): 7 found - 7 modified | TOTAL: 49 pass 2 (xz+): 0 found - 7 modified | TOTAL: 49 pass 1 (xz-): 2 found - 2 modified | TOTAL: 51 pass 2 (xz-): 0 found - 2 modified | TOTAL: 51 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 1 found - 1 modified | TOTAL: 5 pass 2 (+++): 0 found - 1 modified | TOTAL: 5 pass 1 (+++): 2 found - 2 modified | TOTAL: 7 pass 2 (+++): 0 found - 2 modified | TOTAL: 7 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 4 found - 4 modified | TOTAL: 9 pass 2 (+-): 0 found - 4 modified | TOTAL: 9 pass 1 (--): 2 found - 2 modified | TOTAL: 11 pass 2 (--): 0 found - 2 modified | TOTAL: 11 pass 1 (-+): 0 found - 0 modified | TOTAL: 11 Iteration Number : 2 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 : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 70 (out of 228304: 0.030661) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 40: 3731 vertices, 3933 faces slice 50: 11617 vertices, 12029 faces slice 60: 24236 vertices, 24787 faces slice 70: 37038 vertices, 37572 faces slice 80: 48900 vertices, 49449 faces slice 90: 59407 vertices, 59960 faces slice 100: 70281 vertices, 70848 faces slice 110: 79982 vertices, 80530 faces slice 120: 89032 vertices, 89571 faces slice 130: 98132 vertices, 98661 faces slice 140: 106144 vertices, 106623 faces slice 150: 113156 vertices, 113625 faces slice 160: 118546 vertices, 118950 faces slice 170: 122305 vertices, 122662 faces slice 180: 124344 vertices, 124619 faces slice 190: 124470 vertices, 124716 faces slice 200: 124470 vertices, 124716 faces slice 210: 124470 vertices, 124716 faces slice 220: 124470 vertices, 124716 faces slice 230: 124470 vertices, 124716 faces slice 240: 124470 vertices, 124716 faces slice 250: 124470 vertices, 124716 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 124470 voxel in cpt #1: X=-246 [v=124470,e=374148,f=249432] located at (20.403656, -32.920368, 35.060471) For the whole surface: X=-246 [v=124470,e=374148,f=249432] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Jan 10 12:31:49 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Tue Jan 10 12:31:49 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 737618 of (737618 737621) to complete... Waiting for PID 737621 of (737618 737621) to complete... 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... 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... PIDs (737618 737621) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Tue Jan 10 12:31:52 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Tue Jan 10 12:31:52 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 737670 of (737670 737673) to complete... Waiting for PID 737673 of (737670 737673) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.8 mm, total surface area = 63374 mm^2 step 000: RMS=0.175 (target=0.015) step 005: RMS=0.135 (target=0.015) step 010: RMS=0.108 (target=0.015) step 015: RMS=0.099 (target=0.015) step 020: RMS=0.093 (target=0.015) step 025: RMS=0.088 (target=0.015) step 030: RMS=0.083 (target=0.015) step 035: RMS=0.081 (target=0.015) step 040: RMS=0.078 (target=0.015) step 045: RMS=0.078 (target=0.015) step 050: RMS=0.077 (target=0.015) step 055: RMS=0.078 (target=0.015) step 060: RMS=0.079 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 29.212422 mris_inflate stimesec 0.807127 mris_inflate ru_maxrss 198912 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 423485 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 360 mris_inflate ru_oublock 8680 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1573 mris_inflate ru_nivcsw 126 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.1 mm, total surface area = 63475 mm^2 step 000: RMS=0.176 (target=0.015) step 005: RMS=0.135 (target=0.015) step 010: RMS=0.112 (target=0.015) step 015: RMS=0.104 (target=0.015) step 020: RMS=0.097 (target=0.015) step 025: RMS=0.093 (target=0.015) step 030: RMS=0.090 (target=0.015) step 035: RMS=0.087 (target=0.015) step 040: RMS=0.085 (target=0.015) step 045: RMS=0.084 (target=0.015) step 050: RMS=0.083 (target=0.015) step 055: RMS=0.085 (target=0.015) step 060: RMS=0.086 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 29.470503 mris_inflate stimesec 0.858248 mris_inflate ru_maxrss 200768 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 426463 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 56 mris_inflate ru_oublock 8768 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1605 mris_inflate ru_nivcsw 160 PIDs (737670 737673) completed and logs appended. #-------------------------------------------- #@# QSphere lh Tue Jan 10 12:32:05 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Tue Jan 10 12:32:05 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 737722 of (737722 737725) to complete... Waiting for PID 737725 of (737722 737725) to complete... 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: 7.3.2 available threads: 4 scaling brain by 0.346... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.65 (0.00-->6.46) (max @ vno 91904 --> 91905) face area 0.03 +- 0.04 (-0.25-->0.66) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.643, avgs=0 005/300: dt: 0.9000, rms radial error=175.387, avgs=0 010/300: dt: 0.9000, rms radial error=174.837, avgs=0 015/300: dt: 0.9000, rms radial error=174.116, avgs=0 020/300: dt: 0.9000, rms radial error=173.294, avgs=0 025/300: dt: 0.9000, rms radial error=172.415, avgs=0 030/300: dt: 0.9000, rms radial error=171.502, avgs=0 035/300: dt: 0.9000, rms radial error=170.572, avgs=0 040/300: dt: 0.9000, rms radial error=169.633, avgs=0 045/300: dt: 0.9000, rms radial error=168.693, avgs=0 050/300: dt: 0.9000, rms radial error=167.754, avgs=0 055/300: dt: 0.9000, rms radial error=166.815, avgs=0 060/300: dt: 0.9000, rms radial error=165.880, avgs=0 065/300: dt: 0.9000, rms radial error=164.948, avgs=0 070/300: dt: 0.9000, rms radial error=164.018, avgs=0 075/300: dt: 0.9000, rms radial error=163.093, avgs=0 080/300: dt: 0.9000, rms radial error=162.173, avgs=0 085/300: dt: 0.9000, rms radial error=161.257, avgs=0 090/300: dt: 0.9000, rms radial error=160.345, avgs=0 095/300: dt: 0.9000, rms radial error=159.437, avgs=0 100/300: dt: 0.9000, rms radial error=158.534, avgs=0 105/300: dt: 0.9000, rms radial error=157.635, avgs=0 110/300: dt: 0.9000, rms radial error=156.749, avgs=0 115/300: dt: 0.9000, rms radial error=155.867, avgs=0 120/300: dt: 0.9000, rms radial error=154.990, avgs=0 125/300: dt: 0.9000, rms radial error=154.118, avgs=0 130/300: dt: 0.9000, rms radial error=153.250, avgs=0 135/300: dt: 0.9000, rms radial error=152.388, avgs=0 140/300: dt: 0.9000, rms radial error=151.531, avgs=0 145/300: dt: 0.9000, rms radial error=150.678, avgs=0 150/300: dt: 0.9000, rms radial error=149.829, avgs=0 155/300: dt: 0.9000, rms radial error=148.985, avgs=0 160/300: dt: 0.9000, rms radial error=148.146, avgs=0 165/300: dt: 0.9000, rms radial error=147.312, avgs=0 170/300: dt: 0.9000, rms radial error=146.482, avgs=0 175/300: dt: 0.9000, rms radial error=145.656, avgs=0 180/300: dt: 0.9000, rms radial error=144.835, avgs=0 185/300: dt: 0.9000, rms radial error=144.019, avgs=0 190/300: dt: 0.9000, rms radial error=143.208, avgs=0 195/300: dt: 0.9000, rms radial error=142.401, avgs=0 200/300: dt: 0.9000, rms radial error=141.598, avgs=0 205/300: dt: 0.9000, rms radial error=140.800, avgs=0 210/300: dt: 0.9000, rms radial error=140.006, avgs=0 215/300: dt: 0.9000, rms radial error=139.217, avgs=0 220/300: dt: 0.9000, rms radial error=138.432, avgs=0 225/300: dt: 0.9000, rms radial error=137.651, avgs=0 230/300: dt: 0.9000, rms radial error=136.875, avgs=0 235/300: dt: 0.9000, rms radial error=136.103, avgs=0 240/300: dt: 0.9000, rms radial error=135.336, avgs=0 245/300: dt: 0.9000, rms radial error=134.573, avgs=0 250/300: dt: 0.9000, rms radial error=133.814, avgs=0 255/300: dt: 0.9000, rms radial error=133.059, avgs=0 260/300: dt: 0.9000, rms radial error=132.309, avgs=0 265/300: dt: 0.9000, rms radial error=131.562, avgs=0 270/300: dt: 0.9000, rms radial error=130.820, avgs=0 275/300: dt: 0.9000, rms radial error=130.081, avgs=0 280/300: dt: 0.9000, rms radial error=129.347, avgs=0 285/300: dt: 0.9000, rms radial error=128.617, avgs=0 290/300: dt: 0.9000, rms radial error=127.890, avgs=0 295/300: dt: 0.9000, rms radial error=127.168, avgs=0 300/300: dt: 0.9000, rms radial error=126.450, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14065.16 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00039 epoch 2 (K=40.0), pass 1, starting sse = 2282.13 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00047 epoch 3 (K=160.0), pass 1, starting sse = 269.31 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/14 = 0.00363 epoch 4 (K=640.0), pass 1, starting sse = 38.39 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/18 = 0.00486 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0185 hours FSRUNTIME@ mris_sphere 0.0185 hours 4 threads #VMPC# mris_sphere VmPeak 778060 mris_sphere done 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: 7.3.2 available threads: 4 scaling brain by 0.344... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.66 (0.00-->8.47) (max @ vno 100446 --> 100447) face area 0.03 +- 0.04 (-0.31-->0.77) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.706, avgs=0 005/300: dt: 0.9000, rms radial error=175.452, avgs=0 010/300: dt: 0.9000, rms radial error=174.906, avgs=0 015/300: dt: 0.9000, rms radial error=174.188, avgs=0 020/300: dt: 0.9000, rms radial error=173.370, avgs=0 025/300: dt: 0.9000, rms radial error=172.494, avgs=0 030/300: dt: 0.9000, rms radial error=171.586, avgs=0 035/300: dt: 0.9000, rms radial error=170.656, avgs=0 040/300: dt: 0.9000, rms radial error=169.717, avgs=0 045/300: dt: 0.9000, rms radial error=168.774, avgs=0 050/300: dt: 0.9000, rms radial error=167.832, avgs=0 055/300: dt: 0.9000, rms radial error=166.891, avgs=0 060/300: dt: 0.9000, rms radial error=165.954, avgs=0 065/300: dt: 0.9000, rms radial error=165.020, avgs=0 070/300: dt: 0.9000, rms radial error=164.090, avgs=0 075/300: dt: 0.9000, rms radial error=163.164, avgs=0 080/300: dt: 0.9000, rms radial error=162.243, avgs=0 085/300: dt: 0.9000, rms radial error=161.326, avgs=0 090/300: dt: 0.9000, rms radial error=160.420, avgs=0 095/300: dt: 0.9000, rms radial error=159.518, avgs=0 100/300: dt: 0.9000, rms radial error=158.621, avgs=0 105/300: dt: 0.9000, rms radial error=157.729, avgs=0 110/300: dt: 0.9000, rms radial error=156.841, avgs=0 115/300: dt: 0.9000, rms radial error=155.958, avgs=0 120/300: dt: 0.9000, rms radial error=155.079, avgs=0 125/300: dt: 0.9000, rms radial error=154.204, avgs=0 130/300: dt: 0.9000, rms radial error=153.334, avgs=0 135/300: dt: 0.9000, rms radial error=152.469, avgs=0 140/300: dt: 0.9000, rms radial error=151.607, avgs=0 145/300: dt: 0.9000, rms radial error=150.750, avgs=0 150/300: dt: 0.9000, rms radial error=149.900, avgs=0 155/300: dt: 0.9000, rms radial error=149.056, avgs=0 160/300: dt: 0.9000, rms radial error=148.217, avgs=0 165/300: dt: 0.9000, rms radial error=147.382, avgs=0 170/300: dt: 0.9000, rms radial error=146.552, avgs=0 175/300: dt: 0.9000, rms radial error=145.727, avgs=0 180/300: dt: 0.9000, rms radial error=144.905, avgs=0 185/300: dt: 0.9000, rms radial error=144.089, avgs=0 190/300: dt: 0.9000, rms radial error=143.277, avgs=0 195/300: dt: 0.9000, rms radial error=142.469, avgs=0 200/300: dt: 0.9000, rms radial error=141.667, avgs=0 205/300: dt: 0.9000, rms radial error=140.868, avgs=0 210/300: dt: 0.9000, rms radial error=140.074, avgs=0 215/300: dt: 0.9000, rms radial error=139.285, avgs=0 220/300: dt: 0.9000, rms radial error=138.499, avgs=0 225/300: dt: 0.9000, rms radial error=137.719, avgs=0 230/300: dt: 0.9000, rms radial error=136.942, avgs=0 235/300: dt: 0.9000, rms radial error=136.170, avgs=0 240/300: dt: 0.9000, rms radial error=135.402, avgs=0 245/300: dt: 0.9000, rms radial error=134.638, avgs=0 250/300: dt: 0.9000, rms radial error=133.878, avgs=0 255/300: dt: 0.9000, rms radial error=133.123, avgs=0 260/300: dt: 0.9000, rms radial error=132.372, avgs=0 265/300: dt: 0.9000, rms radial error=131.625, avgs=0 270/300: dt: 0.9000, rms radial error=130.882, avgs=0 275/300: dt: 0.9000, rms radial error=130.143, avgs=0 280/300: dt: 0.9000, rms radial error=129.408, avgs=0 285/300: dt: 0.9000, rms radial error=128.678, avgs=0 290/300: dt: 0.9000, rms radial error=127.952, avgs=0 295/300: dt: 0.9000, rms radial error=127.229, avgs=0 300/300: dt: 0.9000, rms radial error=126.511, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14240.30 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00036 epoch 2 (K=40.0), pass 1, starting sse = 2326.57 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00042 epoch 3 (K=160.0), pass 1, starting sse = 287.05 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/13 = 0.00383 epoch 4 (K=640.0), pass 1, starting sse = 44.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/16 = 0.00447 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0185 hours FSRUNTIME@ mris_sphere 0.0185 hours 4 threads #VMPC# mris_sphere VmPeak 779056 mris_sphere done PIDs (737722 737725) completed and logs appended. #@# Fix Topology lh Tue Jan 10 12:33:12 CET 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test_withT2 lh #@# Fix Topology rh Tue Jan 10 12:33:12 CET 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test_withT2 rh Waiting for PID 737782 of (737782 737785) to complete... Waiting for PID 737785 of (737782 737785) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test_withT2 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' 7.3.2 7.3.2 before topology correction, eno=-224 (nv=123256, nf=246960, ne=370440, g=113) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 24468 ambiguous faces found in tessellation segmenting defects... 102 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 22 -merging segment 30 into 29 -merging segment 45 into 39 -merging segment 67 into 57 -merging segment 65 into 59 -merging segment 73 into 60 96 defects to be corrected 0 vertices coincident reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.6270 (-4.3135) -vertex loglikelihood: -6.0766 (-3.0383) -normal dot loglikelihood: -3.5835 (-3.5835) -quad curv loglikelihood: -6.1487 (-3.0744) Total Loglikelihood : -24.4358 CORRECTING DEFECT 0 (vertices=28, convex hull=53, v0=0) After retessellation of defect 0 (v0=0), euler #=-96 (109387,324789,215306) : difference with theory (-93) = 3 CORRECTING DEFECT 1 (vertices=10, convex hull=19, v0=13) After retessellation of defect 1 (v0=13), euler #=-95 (109388,324798,215315) : difference with theory (-92) = 3 CORRECTING DEFECT 2 (vertices=181, convex hull=118, v0=23) After retessellation of defect 2 (v0=23), euler #=-94 (109433,324987,215460) : difference with theory (-91) = 3 CORRECTING DEFECT 3 (vertices=24, convex hull=35, v0=178) After retessellation of defect 3 (v0=178), euler #=-93 (109439,325016,215484) : difference with theory (-90) = 3 CORRECTING DEFECT 4 (vertices=49, convex hull=71, v0=267) After retessellation of defect 4 (v0=267), euler #=-92 (109452,325086,215542) : difference with theory (-89) = 3 CORRECTING DEFECT 5 (vertices=7, convex hull=17, v0=1113) After retessellation of defect 5 (v0=1113), euler #=-91 (109453,325093,215549) : difference with theory (-88) = 3 CORRECTING DEFECT 6 (vertices=88, convex hull=113, v0=1295) After retessellation of defect 6 (v0=1295), euler #=-90 (109494,325265,215681) : difference with theory (-87) = 3 CORRECTING DEFECT 7 (vertices=30, convex hull=30, v0=1301) After retessellation of defect 7 (v0=1301), euler #=-89 (109500,325291,215702) : difference with theory (-86) = 3 CORRECTING DEFECT 8 (vertices=7, convex hull=17, v0=1855) After retessellation of defect 8 (v0=1855), euler #=-88 (109500,325295,215707) : difference with theory (-85) = 3 CORRECTING DEFECT 9 (vertices=322, convex hull=137, v0=1950) After retessellation of defect 9 (v0=1950), euler #=-87 (109518,325412,215807) : difference with theory (-84) = 3 CORRECTING DEFECT 10 (vertices=203, convex hull=139, v0=2032) After retessellation of defect 10 (v0=2032), euler #=-86 (109584,325673,216003) : difference with theory (-83) = 3 CORRECTING DEFECT 11 (vertices=179, convex hull=130, v0=2205) After retessellation of defect 11 (v0=2205), euler #=-85 (109622,325847,216140) : difference with theory (-82) = 3 CORRECTING DEFECT 12 (vertices=15, convex hull=19, v0=2367) After retessellation of defect 12 (v0=2367), euler #=-84 (109622,325851,216145) : difference with theory (-81) = 3 CORRECTING DEFECT 13 (vertices=245, convex hull=103, v0=3404) After retessellation of defect 13 (v0=3404), euler #=-83 (109630,325920,216207) : difference with theory (-80) = 3 CORRECTING DEFECT 14 (vertices=800, convex hull=279, v0=3554) After retessellation of defect 14 (v0=3554), euler #=-82 (109653,326127,216392) : difference with theory (-79) = 3 CORRECTING DEFECT 15 (vertices=341, convex hull=65, v0=4778) After retessellation of defect 15 (v0=4778), euler #=-81 (109676,326221,216464) : difference with theory (-78) = 3 CORRECTING DEFECT 16 (vertices=135, convex hull=95, v0=8600) After retessellation of defect 16 (v0=8600), euler #=-80 (109712,326373,216581) : difference with theory (-77) = 3 CORRECTING DEFECT 17 (vertices=191, convex hull=77, v0=9050) After retessellation of defect 17 (v0=9050), euler #=-79 (109744,326500,216677) : difference with theory (-76) = 3 CORRECTING DEFECT 18 (vertices=60, convex hull=31, v0=9330) After retessellation of defect 18 (v0=9330), euler #=-78 (109750,326527,216699) : difference with theory (-75) = 3 CORRECTING DEFECT 19 (vertices=84, convex hull=30, v0=9814) After retessellation of defect 19 (v0=9814), euler #=-77 (109753,326543,216713) : difference with theory (-74) = 3 CORRECTING DEFECT 20 (vertices=47, convex hull=27, v0=10264) After retessellation of defect 20 (v0=10264), euler #=-76 (109756,326559,216727) : difference with theory (-73) = 3 CORRECTING DEFECT 21 (vertices=81, convex hull=104, v0=11186) After retessellation of defect 21 (v0=11186), euler #=-75 (109766,326640,216799) : difference with theory (-72) = 3 CORRECTING DEFECT 22 (vertices=22, convex hull=46, v0=12010) After retessellation of defect 22 (v0=12010), euler #=-73 (109770,326669,216826) : difference with theory (-71) = 2 CORRECTING DEFECT 23 (vertices=108, convex hull=51, v0=13338) After retessellation of defect 23 (v0=13338), euler #=-72 (109785,326736,216879) : difference with theory (-70) = 2 CORRECTING DEFECT 24 (vertices=25, convex hull=23, v0=13685) After retessellation of defect 24 (v0=13685), euler #=-71 (109786,326747,216890) : difference with theory (-69) = 2 CORRECTING DEFECT 25 (vertices=41, convex hull=71, v0=14387) After retessellation of defect 25 (v0=14387), euler #=-70 (109809,326846,216967) : difference with theory (-68) = 2 CORRECTING DEFECT 26 (vertices=214, convex hull=108, v0=15729) After retessellation of defect 26 (v0=15729), euler #=-69 (109827,326945,217049) : difference with theory (-67) = 2 CORRECTING DEFECT 27 (vertices=25, convex hull=61, v0=16344) After retessellation of defect 27 (v0=16344), euler #=-68 (109839,327006,217099) : difference with theory (-66) = 2 CORRECTING DEFECT 28 (vertices=351, convex hull=270, v0=16871) After retessellation of defect 28 (v0=16871), euler #=-66 (109935,327446,217445) : difference with theory (-65) = 1 CORRECTING DEFECT 29 (vertices=198, convex hull=82, v0=20320) After retessellation of defect 29 (v0=20320), euler #=-65 (109953,327541,217523) : difference with theory (-64) = 1 CORRECTING DEFECT 30 (vertices=33, convex hull=29, v0=23372) After retessellation of defect 30 (v0=23372), euler #=-64 (109956,327560,217540) : difference with theory (-63) = 1 CORRECTING DEFECT 31 (vertices=82, convex hull=57, v0=23795) After retessellation of defect 31 (v0=23795), euler #=-63 (109974,327637,217600) : difference with theory (-62) = 1 CORRECTING DEFECT 32 (vertices=22, convex hull=45, v0=25337) After retessellation of defect 32 (v0=25337), euler #=-62 (109986,327691,217643) : difference with theory (-61) = 1 CORRECTING DEFECT 33 (vertices=67, convex hull=53, v0=26540) After retessellation of defect 33 (v0=26540), euler #=-61 (109995,327738,217682) : difference with theory (-60) = 1 CORRECTING DEFECT 34 (vertices=28, convex hull=31, v0=26566) After retessellation of defect 34 (v0=26566), euler #=-60 (110000,327766,217706) : difference with theory (-59) = 1 CORRECTING DEFECT 35 (vertices=1368, convex hull=245, v0=26766) After retessellation of defect 35 (v0=26766), euler #=-59 (110149,328328,218120) : difference with theory (-58) = 1 CORRECTING DEFECT 36 (vertices=209, convex hull=61, v0=27445) After retessellation of defect 36 (v0=27445), euler #=-58 (110165,328400,218177) : difference with theory (-57) = 1 CORRECTING DEFECT 37 (vertices=190, convex hull=135, v0=27497) After retessellation of defect 37 (v0=27497), euler #=-56 (110228,328661,218377) : difference with theory (-56) = 0 CORRECTING DEFECT 38 (vertices=107, convex hull=87, v0=27609) After retessellation of defect 38 (v0=27609), euler #=-55 (110257,328784,218472) : difference with theory (-55) = 0 CORRECTING DEFECT 39 (vertices=43, convex hull=30, v0=29708) After retessellation of defect 39 (v0=29708), euler #=-54 (110263,328811,218494) : difference with theory (-54) = 0 CORRECTING DEFECT 40 (vertices=17, convex hull=25, v0=30030) After retessellation of defect 40 (v0=30030), euler #=-53 (110265,328825,218507) : difference with theory (-53) = 0 CORRECTING DEFECT 41 (vertices=101, convex hull=65, v0=30157) After retessellation of defect 41 (v0=30157), euler #=-52 (110281,328900,218567) : difference with theory (-52) = 0 CORRECTING DEFECT 42 (vertices=109, convex hull=60, v0=34121) After retessellation of defect 42 (v0=34121), euler #=-51 (110303,328985,218631) : difference with theory (-51) = 0 CORRECTING DEFECT 43 (vertices=56, convex hull=76, v0=35484) After retessellation of defect 43 (v0=35484), euler #=-50 (110331,329100,218719) : difference with theory (-50) = 0 CORRECTING DEFECT 44 (vertices=215, convex hull=76, v0=36022) After retessellation of defect 44 (v0=36022), euler #=-49 (110358,329211,218804) : difference with theory (-49) = 0 CORRECTING DEFECT 45 (vertices=22, convex hull=51, v0=38942) After retessellation of defect 45 (v0=38942), euler #=-48 (110372,329271,218851) : difference with theory (-48) = 0 CORRECTING DEFECT 46 (vertices=69, convex hull=50, v0=39690) After retessellation of defect 46 (v0=39690), euler #=-47 (110389,329344,218908) : difference with theory (-47) = 0 CORRECTING DEFECT 47 (vertices=74, convex hull=80, v0=39760) After retessellation of defect 47 (v0=39760), euler #=-46 (110416,329459,218997) : difference with theory (-46) = 0 CORRECTING DEFECT 48 (vertices=38, convex hull=47, v0=41586) After retessellation of defect 48 (v0=41586), euler #=-45 (110427,329507,219035) : difference with theory (-45) = 0 CORRECTING DEFECT 49 (vertices=15, convex hull=36, v0=42248) After retessellation of defect 49 (v0=42248), euler #=-44 (110429,329528,219055) : difference with theory (-44) = 0 CORRECTING DEFECT 50 (vertices=23, convex hull=32, v0=43161) After retessellation of defect 50 (v0=43161), euler #=-43 (110433,329551,219075) : difference with theory (-43) = 0 CORRECTING DEFECT 51 (vertices=10, convex hull=21, v0=45479) After retessellation of defect 51 (v0=45479), euler #=-42 (110434,329558,219082) : difference with theory (-42) = 0 CORRECTING DEFECT 52 (vertices=38, convex hull=45, v0=45996) After retessellation of defect 52 (v0=45996), euler #=-41 (110443,329598,219114) : difference with theory (-41) = 0 CORRECTING DEFECT 53 (vertices=15, convex hull=19, v0=46291) After retessellation of defect 53 (v0=46291), euler #=-40 (110445,329612,219127) : difference with theory (-40) = 0 CORRECTING DEFECT 54 (vertices=3641, convex hull=1051, v0=48001) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 54 (v0=48001), euler #=-41 (111591,333654,222022) : difference with theory (-39) = 2 CORRECTING DEFECT 55 (vertices=51, convex hull=80, v0=48079) After retessellation of defect 55 (v0=48079), euler #=-40 (111629,333800,222131) : difference with theory (-38) = 2 CORRECTING DEFECT 56 (vertices=388, convex hull=205, v0=50647) After retessellation of defect 56 (v0=50647), euler #=-38 (111673,334035,222324) : difference with theory (-37) = 1 CORRECTING DEFECT 57 (vertices=481, convex hull=108, v0=52808) v 120811 (69428) --> 120951 (72721), len = 95.743 INFLATED: (-59.5, -28.5, 49.5) --> (-54.5, -25.5, 45.5), len = 7.07 CANON: (-82.7, -24.5, 50.6) --> (-81.8, -19.5, 54.1), len = 6.17 CURRENT: (-59.5, -28.5, 49.5) --> (-54.5, -25.5, 45.5), len = 7.07 ORIG: (-59.2, -28.3, 49.9) --> (-54.3, -25.6, 45.6), len = 7.07 After retessellation of defect 57 (v0=52808), euler #=-36 (111695,334165,222434) : difference with theory (-36) = 0 CORRECTING DEFECT 58 (vertices=9, convex hull=24, v0=57448) After retessellation of defect 58 (v0=57448), euler #=-35 (111696,334174,222443) : difference with theory (-35) = 0 CORRECTING DEFECT 59 (vertices=20, convex hull=24, v0=57896) After retessellation of defect 59 (v0=57896), euler #=-34 (111699,334190,222457) : difference with theory (-34) = 0 CORRECTING DEFECT 60 (vertices=50, convex hull=51, v0=62316) After retessellation of defect 60 (v0=62316), euler #=-33 (111709,334237,222495) : difference with theory (-33) = 0 CORRECTING DEFECT 61 (vertices=38, convex hull=80, v0=63380) After retessellation of defect 61 (v0=63380), euler #=-32 (111727,334324,222565) : difference with theory (-32) = 0 CORRECTING DEFECT 62 (vertices=196, convex hull=40, v0=64246) After retessellation of defect 62 (v0=64246), euler #=-31 (111737,334367,222599) : difference with theory (-31) = 0 CORRECTING DEFECT 63 (vertices=63, convex hull=79, v0=66279) After retessellation of defect 63 (v0=66279), euler #=-30 (111751,334441,222660) : difference with theory (-30) = 0 CORRECTING DEFECT 64 (vertices=8, convex hull=8, v0=66290) After retessellation of defect 64 (v0=66290), euler #=-29 (111752,334445,222664) : difference with theory (-29) = 0 CORRECTING DEFECT 65 (vertices=17, convex hull=31, v0=70310) After retessellation of defect 65 (v0=70310), euler #=-28 (111755,334463,222680) : difference with theory (-28) = 0 CORRECTING DEFECT 66 (vertices=335, convex hull=85, v0=70639) After retessellation of defect 66 (v0=70639), euler #=-27 (111773,334552,222752) : difference with theory (-27) = 0 CORRECTING DEFECT 67 (vertices=45, convex hull=75, v0=72307) After retessellation of defect 67 (v0=72307), euler #=-26 (111789,334631,222816) : difference with theory (-26) = 0 CORRECTING DEFECT 68 (vertices=11, convex hull=27, v0=72791) After retessellation of defect 68 (v0=72791), euler #=-25 (111796,334658,222837) : difference with theory (-25) = 0 CORRECTING DEFECT 69 (vertices=65, convex hull=76, v0=73040) After retessellation of defect 69 (v0=73040), euler #=-24 (111813,334743,222906) : difference with theory (-24) = 0 CORRECTING DEFECT 70 (vertices=28, convex hull=64, v0=74348) After retessellation of defect 70 (v0=74348), euler #=-23 (111830,334817,222964) : difference with theory (-23) = 0 CORRECTING DEFECT 71 (vertices=21, convex hull=49, v0=79567) After retessellation of defect 71 (v0=79567), euler #=-22 (111839,334860,222999) : difference with theory (-22) = 0 CORRECTING DEFECT 72 (vertices=37, convex hull=70, v0=81742) After retessellation of defect 72 (v0=81742), euler #=-21 (111863,334961,223077) : difference with theory (-21) = 0 CORRECTING DEFECT 73 (vertices=74, convex hull=73, v0=83078) After retessellation of defect 73 (v0=83078), euler #=-20 (111898,335097,223179) : difference with theory (-20) = 0 CORRECTING DEFECT 74 (vertices=26, convex hull=69, v0=91263) After retessellation of defect 74 (v0=91263), euler #=-19 (111915,335174,223240) : difference with theory (-19) = 0 CORRECTING DEFECT 75 (vertices=36, convex hull=76, v0=91819) After retessellation of defect 75 (v0=91819), euler #=-18 (111939,335273,223316) : difference with theory (-18) = 0 CORRECTING DEFECT 76 (vertices=218, convex hull=166, v0=92025) After retessellation of defect 76 (v0=92025), euler #=-17 (112035,335640,223588) : difference with theory (-17) = 0 CORRECTING DEFECT 77 (vertices=24, convex hull=40, v0=94399) After retessellation of defect 77 (v0=94399), euler #=-16 (112048,335694,223630) : difference with theory (-16) = 0 CORRECTING DEFECT 78 (vertices=98, convex hull=47, v0=97181) After retessellation of defect 78 (v0=97181), euler #=-15 (112057,335741,223669) : difference with theory (-15) = 0 CORRECTING DEFECT 79 (vertices=33, convex hull=59, v0=97194) After retessellation of defect 79 (v0=97194), euler #=-14 (112070,335809,223725) : difference with theory (-14) = 0 CORRECTING DEFECT 80 (vertices=8, convex hull=13, v0=98443) After retessellation of defect 80 (v0=98443), euler #=-13 (112071,335815,223731) : difference with theory (-13) = 0 CORRECTING DEFECT 81 (vertices=12, convex hull=15, v0=99584) After retessellation of defect 81 (v0=99584), euler #=-12 (112072,335824,223740) : difference with theory (-12) = 0 CORRECTING DEFECT 82 (vertices=41, convex hull=75, v0=100321) After retessellation of defect 82 (v0=100321), euler #=-11 (112096,335928,223821) : difference with theory (-11) = 0 CORRECTING DEFECT 83 (vertices=24, convex hull=61, v0=101985) After retessellation of defect 83 (v0=101985), euler #=-10 (112107,335984,223867) : difference with theory (-10) = 0 CORRECTING DEFECT 84 (vertices=10, convex hull=14, v0=102296) After retessellation of defect 84 (v0=102296), euler #=-9 (112109,335994,223876) : difference with theory (-9) = 0 CORRECTING DEFECT 85 (vertices=58, convex hull=104, v0=103938) After retessellation of defect 85 (v0=103938), euler #=-8 (112122,336085,223955) : difference with theory (-8) = 0 CORRECTING DEFECT 86 (vertices=168, convex hull=39, v0=103951) After retessellation of defect 86 (v0=103951), euler #=-7 (112131,336126,223988) : difference with theory (-7) = 0 CORRECTING DEFECT 87 (vertices=6, convex hull=25, v0=105252) After retessellation of defect 87 (v0=105252), euler #=-6 (112133,336140,224001) : difference with theory (-6) = 0 CORRECTING DEFECT 88 (vertices=36, convex hull=32, v0=105485) After retessellation of defect 88 (v0=105485), euler #=-5 (112136,336163,224022) : difference with theory (-5) = 0 CORRECTING DEFECT 89 (vertices=26, convex hull=63, v0=109409) After retessellation of defect 89 (v0=109409), euler #=-4 (112145,336213,224064) : difference with theory (-4) = 0 CORRECTING DEFECT 90 (vertices=249, convex hull=158, v0=113733) After retessellation of defect 90 (v0=113733), euler #=-3 (112182,336402,224217) : difference with theory (-3) = 0 CORRECTING DEFECT 91 (vertices=36, convex hull=63, v0=117760) After retessellation of defect 91 (v0=117760), euler #=-2 (112197,336475,224276) : difference with theory (-2) = 0 CORRECTING DEFECT 92 (vertices=24, convex hull=57, v0=119758) After retessellation of defect 92 (v0=119758), euler #=-1 (112206,336523,224316) : difference with theory (-1) = 0 CORRECTING DEFECT 93 (vertices=28, convex hull=69, v0=120635) After retessellation of defect 93 (v0=120635), euler #=0 (112221,336596,224375) : difference with theory (0) = 0 CORRECTING DEFECT 94 (vertices=41, convex hull=80, v0=120866) After retessellation of defect 94 (v0=120866), euler #=1 (112247,336709,224463) : difference with theory (1) = 0 CORRECTING DEFECT 95 (vertices=32, convex hull=65, v0=122732) After retessellation of defect 95 (v0=122732), euler #=2 (112263,336783,224522) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.28 (0.03-->10.22) (max @ vno 3348 --> 3908) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.28 (0.03-->10.22) (max @ vno 3348 --> 3908) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 361 mutations (35.0%), 669 crossovers (65.0%), 777 vertices were eliminated building final representation... 10993 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=112263, nf=224522, ne=336783, g=0) writing corrected surface to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 1441 intersecting 001: 208 intersecting 002: 79 intersecting 003: 73 intersecting step 1 with no progress (num=88, old_num=73) 004: 88 intersecting step 2 with no progress (num=89, old_num=88) 005: 89 intersecting 006: 70 intersecting step 1 with no progress (num=70, old_num=70) 007: 70 intersecting step 2 with no progress (num=70, old_num=70) 008: 70 intersecting step 3 with no progress (num=70, old_num=70) 009: 70 intersecting step 4 with no progress (num=70, old_num=70) 010: 70 intersecting step 5 with no progress (num=70, old_num=70) 011: 70 intersecting step 6 with no progress (num=70, old_num=70) 012: 70 intersecting step 7 with no progress (num=70, old_num=70) 013: 70 intersecting step 8 with no progress (num=70, old_num=70) 014: 70 intersecting step 9 with no progress (num=70, old_num=70) 015: 70 intersecting step 10 with no progress (num=70, old_num=70) 016: 70 intersecting step 11 with no progress (num=70, old_num=70) 017: 70 intersecting step 12 with no progress (num=70, old_num=70) 018: 70 intersecting step 13 with no progress (num=70, old_num=70) 019: 70 intersecting step 14 with no progress (num=70, old_num=70) 020: 70 intersecting step 15 with no progress (num=70, old_num=70) 021: 70 intersecting step 16 with no progress (num=70, old_num=70) terminating search with 70 intersecting topology fixing took 7.2 minutes FSRUNTIME@ mris_fix_topology lh 0.1195 hours 4 threads #VMPC# mris_fix_topology VmPeak 959164 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test_withT2 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' 7.3.2 7.3.2 before topology correction, eno=-246 (nv=124470, nf=249432, ne=374148, g=124) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 31175 ambiguous faces found in tessellation segmenting defects... 83 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 4 -merging segment 7 into 6 -merging segment 16 into 13 -merging segment 67 into 69 -merging segment 78 into 77 78 defects to be corrected 0 vertices coincident reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7535 (-4.3767) -vertex loglikelihood: -6.0721 (-3.0361) -normal dot loglikelihood: -3.5467 (-3.5467) -quad curv loglikelihood: -6.0469 (-3.0235) Total Loglikelihood : -24.4193 CORRECTING DEFECT 0 (vertices=9, convex hull=28, v0=48) After retessellation of defect 0 (v0=48), euler #=-71 (107141,317893,210681) : difference with theory (-75) = -4 CORRECTING DEFECT 1 (vertices=18, convex hull=40, v0=95) After retessellation of defect 1 (v0=95), euler #=-70 (107150,317935,210715) : difference with theory (-74) = -4 CORRECTING DEFECT 2 (vertices=31, convex hull=43, v0=199) After retessellation of defect 2 (v0=199), euler #=-69 (107158,317977,210750) : difference with theory (-73) = -4 CORRECTING DEFECT 3 (vertices=147, convex hull=165, v0=201) After retessellation of defect 3 (v0=201), euler #=-68 (107180,318126,210878) : difference with theory (-72) = -4 CORRECTING DEFECT 4 (vertices=213, convex hull=152, v0=335) After retessellation of defect 4 (v0=335), euler #=-66 (107201,318259,210992) : difference with theory (-71) = -5 CORRECTING DEFECT 5 (vertices=62, convex hull=90, v0=384) After retessellation of defect 5 (v0=384), euler #=-64 (107225,318366,211077) : difference with theory (-70) = -6 CORRECTING DEFECT 6 (vertices=37, convex hull=75, v0=1803) After retessellation of defect 6 (v0=1803), euler #=-63 (107234,318424,211127) : difference with theory (-69) = -6 CORRECTING DEFECT 7 (vertices=80, convex hull=39, v0=2065) After retessellation of defect 7 (v0=2065), euler #=-62 (107240,318454,211152) : difference with theory (-68) = -6 CORRECTING DEFECT 8 (vertices=34, convex hull=36, v0=2563) After retessellation of defect 8 (v0=2563), euler #=-61 (107245,318483,211177) : difference with theory (-67) = -6 CORRECTING DEFECT 9 (vertices=50, convex hull=30, v0=2766) After retessellation of defect 9 (v0=2766), euler #=-60 (107248,318501,211193) : difference with theory (-66) = -6 CORRECTING DEFECT 10 (vertices=26, convex hull=58, v0=3182) After retessellation of defect 10 (v0=3182), euler #=-59 (107263,318567,211245) : difference with theory (-65) = -6 CORRECTING DEFECT 11 (vertices=430, convex hull=276, v0=3638) After retessellation of defect 11 (v0=3638), euler #=-57 (107279,318763,211427) : difference with theory (-64) = -7 CORRECTING DEFECT 12 (vertices=6, convex hull=21, v0=3904) After retessellation of defect 12 (v0=3904), euler #=-56 (107280,318771,211435) : difference with theory (-63) = -7 CORRECTING DEFECT 13 (vertices=1383, convex hull=757, v0=4708) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 13 (v0=4708), euler #=-56 (107705,320481,212720) : difference with theory (-62) = -6 CORRECTING DEFECT 14 (vertices=3260, convex hull=665, v0=8125) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces After retessellation of defect 14 (v0=8125), euler #=-55 (108260,322473,214158) : difference with theory (-61) = -6 CORRECTING DEFECT 15 (vertices=43, convex hull=35, v0=8591) After retessellation of defect 15 (v0=8591), euler #=-54 (108267,322507,214186) : difference with theory (-60) = -6 CORRECTING DEFECT 16 (vertices=14, convex hull=14, v0=9358) After retessellation of defect 16 (v0=9358), euler #=-53 (108267,322513,214193) : difference with theory (-59) = -6 CORRECTING DEFECT 17 (vertices=24, convex hull=41, v0=9437) After retessellation of defect 17 (v0=9437), euler #=-52 (108269,322533,214212) : difference with theory (-58) = -6 CORRECTING DEFECT 18 (vertices=379, convex hull=166, v0=10081) After retessellation of defect 18 (v0=10081), euler #=-51 (108329,322793,214413) : difference with theory (-57) = -6 CORRECTING DEFECT 19 (vertices=45, convex hull=99, v0=11509) After retessellation of defect 19 (v0=11509), euler #=-50 (108353,322908,214505) : difference with theory (-56) = -6 CORRECTING DEFECT 20 (vertices=226, convex hull=107, v0=12464) After retessellation of defect 20 (v0=12464), euler #=-49 (108390,323066,214627) : difference with theory (-55) = -6 CORRECTING DEFECT 21 (vertices=107, convex hull=48, v0=14977) After retessellation of defect 21 (v0=14977), euler #=-48 (108400,323116,214668) : difference with theory (-54) = -6 CORRECTING DEFECT 22 (vertices=4749, convex hull=862, v0=16341) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 22 (v0=16341), euler #=-51 (108799,324787,215937) : difference with theory (-53) = -2 CORRECTING DEFECT 23 (vertices=196, convex hull=144, v0=17306) After retessellation of defect 23 (v0=17306), euler #=-51 (108823,324937,216063) : difference with theory (-52) = -1 CORRECTING DEFECT 24 (vertices=23, convex hull=49, v0=17534) After retessellation of defect 24 (v0=17534), euler #=-50 (108832,324982,216100) : difference with theory (-51) = -1 CORRECTING DEFECT 25 (vertices=41, convex hull=72, v0=17858) After retessellation of defect 25 (v0=17858), euler #=-49 (108857,325087,216181) : difference with theory (-50) = -1 CORRECTING DEFECT 26 (vertices=21, convex hull=43, v0=19980) After retessellation of defect 26 (v0=19980), euler #=-48 (108867,325135,216220) : difference with theory (-49) = -1 CORRECTING DEFECT 27 (vertices=211, convex hull=108, v0=20074) After retessellation of defect 27 (v0=20074), euler #=-47 (108890,325256,216319) : difference with theory (-48) = -1 CORRECTING DEFECT 28 (vertices=73, convex hull=82, v0=20223) After retessellation of defect 28 (v0=20223), euler #=-46 (108914,325366,216406) : difference with theory (-47) = -1 CORRECTING DEFECT 29 (vertices=47, convex hull=66, v0=28501) After retessellation of defect 29 (v0=28501), euler #=-45 (108941,325474,216488) : difference with theory (-46) = -1 CORRECTING DEFECT 30 (vertices=48, convex hull=91, v0=31242) After retessellation of defect 30 (v0=31242), euler #=-44 (108968,325597,216585) : difference with theory (-45) = -1 CORRECTING DEFECT 31 (vertices=26, convex hull=68, v0=31955) After retessellation of defect 31 (v0=31955), euler #=-43 (108984,325672,216645) : difference with theory (-44) = -1 CORRECTING DEFECT 32 (vertices=15, convex hull=20, v0=37441) After retessellation of defect 32 (v0=37441), euler #=-42 (108986,325685,216657) : difference with theory (-43) = -1 CORRECTING DEFECT 33 (vertices=124, convex hull=73, v0=40050) After retessellation of defect 33 (v0=40050), euler #=-41 (109015,325799,216743) : difference with theory (-42) = -1 CORRECTING DEFECT 34 (vertices=88, convex hull=43, v0=42020) After retessellation of defect 34 (v0=42020), euler #=-40 (109031,325861,216790) : difference with theory (-41) = -1 CORRECTING DEFECT 35 (vertices=30, convex hull=51, v0=43203) After retessellation of defect 35 (v0=43203), euler #=-39 (109044,325918,216835) : difference with theory (-40) = -1 CORRECTING DEFECT 36 (vertices=30, convex hull=22, v0=46015) After retessellation of defect 36 (v0=46015), euler #=-38 (109048,325936,216850) : difference with theory (-39) = -1 CORRECTING DEFECT 37 (vertices=28, convex hull=74, v0=46904) After retessellation of defect 37 (v0=46904), euler #=-37 (109063,326009,216909) : difference with theory (-38) = -1 CORRECTING DEFECT 38 (vertices=20, convex hull=17, v0=48824) After retessellation of defect 38 (v0=48824), euler #=-36 (109066,326022,216920) : difference with theory (-37) = -1 CORRECTING DEFECT 39 (vertices=25, convex hull=37, v0=50013) After retessellation of defect 39 (v0=50013), euler #=-35 (109071,326050,216944) : difference with theory (-36) = -1 CORRECTING DEFECT 40 (vertices=32, convex hull=23, v0=50689) After retessellation of defect 40 (v0=50689), euler #=-34 (109077,326074,216963) : difference with theory (-35) = -1 CORRECTING DEFECT 41 (vertices=617, convex hull=291, v0=52324) After retessellation of defect 41 (v0=52324), euler #=-34 (109204,326606,217368) : difference with theory (-34) = 0 CORRECTING DEFECT 42 (vertices=1971, convex hull=414, v0=56047) A large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview Warning - incorrect dp selected!!!!(-114.419200 >= -114.418800 ) After retessellation of defect 42 (v0=56047), euler #=-33 (109236,326906,217637) : difference with theory (-33) = 0 CORRECTING DEFECT 43 (vertices=37, convex hull=29, v0=56408) After retessellation of defect 43 (v0=56408), euler #=-32 (109239,326924,217653) : difference with theory (-32) = 0 CORRECTING DEFECT 44 (vertices=46, convex hull=29, v0=56458) After retessellation of defect 44 (v0=56458), euler #=-31 (109247,326957,217679) : difference with theory (-31) = 0 CORRECTING DEFECT 45 (vertices=26, convex hull=29, v0=56976) After retessellation of defect 45 (v0=56976), euler #=-30 (109251,326978,217697) : difference with theory (-30) = 0 CORRECTING DEFECT 46 (vertices=187, convex hull=125, v0=64223) After retessellation of defect 46 (v0=64223), euler #=-29 (109307,327207,217871) : difference with theory (-29) = 0 CORRECTING DEFECT 47 (vertices=48, convex hull=67, v0=64550) After retessellation of defect 47 (v0=64550), euler #=-28 (109332,327307,217947) : difference with theory (-28) = 0 CORRECTING DEFECT 48 (vertices=45, convex hull=41, v0=67317) After retessellation of defect 48 (v0=67317), euler #=-27 (109338,327339,217974) : difference with theory (-27) = 0 CORRECTING DEFECT 49 (vertices=36, convex hull=53, v0=67750) After retessellation of defect 49 (v0=67750), euler #=-26 (109347,327387,218014) : difference with theory (-26) = 0 CORRECTING DEFECT 50 (vertices=34, convex hull=42, v0=67839) After retessellation of defect 50 (v0=67839), euler #=-26 (109359,327441,218056) : difference with theory (-25) = 1 CORRECTING DEFECT 51 (vertices=51, convex hull=38, v0=71899) After retessellation of defect 51 (v0=71899), euler #=-25 (109369,327485,218091) : difference with theory (-24) = 1 CORRECTING DEFECT 52 (vertices=75, convex hull=100, v0=75484) After retessellation of defect 52 (v0=75484), euler #=-24 (109409,327644,218211) : difference with theory (-23) = 1 CORRECTING DEFECT 53 (vertices=17, convex hull=58, v0=76350) After retessellation of defect 53 (v0=76350), euler #=-23 (109420,327694,218251) : difference with theory (-22) = 1 CORRECTING DEFECT 54 (vertices=50, convex hull=45, v0=76442) After retessellation of defect 54 (v0=76442), euler #=-22 (109437,327762,218303) : difference with theory (-21) = 1 CORRECTING DEFECT 55 (vertices=270, convex hull=69, v0=76700) After retessellation of defect 55 (v0=76700), euler #=-21 (109454,327842,218367) : difference with theory (-20) = 1 CORRECTING DEFECT 56 (vertices=30, convex hull=72, v0=81189) After retessellation of defect 56 (v0=81189), euler #=-20 (109469,327916,218427) : difference with theory (-19) = 1 CORRECTING DEFECT 57 (vertices=21, convex hull=30, v0=82149) After retessellation of defect 57 (v0=82149), euler #=-19 (109472,327931,218440) : difference with theory (-18) = 1 CORRECTING DEFECT 58 (vertices=18, convex hull=49, v0=82782) After retessellation of defect 58 (v0=82782), euler #=-18 (109481,327975,218476) : difference with theory (-17) = 1 CORRECTING DEFECT 59 (vertices=30, convex hull=34, v0=83311) After retessellation of defect 59 (v0=83311), euler #=-17 (109486,328001,218498) : difference with theory (-16) = 1 CORRECTING DEFECT 60 (vertices=132, convex hull=138, v0=92267) After retessellation of defect 60 (v0=92267), euler #=-16 (109529,328187,218642) : difference with theory (-15) = 1 CORRECTING DEFECT 61 (vertices=40, convex hull=51, v0=92355) After retessellation of defect 61 (v0=92355), euler #=-15 (109547,328262,218700) : difference with theory (-14) = 1 CORRECTING DEFECT 62 (vertices=18, convex hull=25, v0=97495) After retessellation of defect 62 (v0=97495), euler #=-14 (109552,328283,218717) : difference with theory (-13) = 1 CORRECTING DEFECT 63 (vertices=19, convex hull=44, v0=97634) After retessellation of defect 63 (v0=97634), euler #=-13 (109562,328328,218753) : difference with theory (-12) = 1 CORRECTING DEFECT 64 (vertices=101, convex hull=33, v0=97904) After retessellation of defect 64 (v0=97904), euler #=-12 (109570,328362,218780) : difference with theory (-11) = 1 CORRECTING DEFECT 65 (vertices=141, convex hull=171, v0=98776) After retessellation of defect 65 (v0=98776), euler #=-10 (109629,328617,218978) : difference with theory (-10) = 0 CORRECTING DEFECT 66 (vertices=79, convex hull=31, v0=100361) After retessellation of defect 66 (v0=100361), euler #=-9 (109639,328654,219006) : difference with theory (-9) = 0 CORRECTING DEFECT 67 (vertices=9, convex hull=22, v0=101123) After retessellation of defect 67 (v0=101123), euler #=-8 (109639,328660,219013) : difference with theory (-8) = 0 CORRECTING DEFECT 68 (vertices=40, convex hull=49, v0=101187) After retessellation of defect 68 (v0=101187), euler #=-7 (109650,328709,219052) : difference with theory (-7) = 0 CORRECTING DEFECT 69 (vertices=28, convex hull=36, v0=105321) After retessellation of defect 69 (v0=105321), euler #=-7 (109667,328776,219102) : difference with theory (-6) = 1 CORRECTING DEFECT 70 (vertices=249, convex hull=102, v0=108009) After retessellation of defect 70 (v0=108009), euler #=-6 (109687,328885,219192) : difference with theory (-5) = 1 CORRECTING DEFECT 71 (vertices=94, convex hull=54, v0=108653) After retessellation of defect 71 (v0=108653), euler #=-5 (109699,328942,219238) : difference with theory (-4) = 1 CORRECTING DEFECT 72 (vertices=50, convex hull=81, v0=108776) After retessellation of defect 72 (v0=108776), euler #=-4 (109724,329051,219323) : difference with theory (-3) = 1 CORRECTING DEFECT 73 (vertices=77, convex hull=110, v0=108953) After retessellation of defect 73 (v0=108953), euler #=-2 (109741,329152,219409) : difference with theory (-2) = 0 CORRECTING DEFECT 74 (vertices=29, convex hull=53, v0=111646) After retessellation of defect 74 (v0=111646), euler #=-1 (109759,329227,219467) : difference with theory (-1) = 0 CORRECTING DEFECT 75 (vertices=26, convex hull=29, v0=118540) After retessellation of defect 75 (v0=118540), euler #=0 (109764,329253,219489) : difference with theory (0) = 0 CORRECTING DEFECT 76 (vertices=103, convex hull=33, v0=122600) After retessellation of defect 76 (v0=122600), euler #=1 (109775,329300,219526) : difference with theory (1) = 0 CORRECTING DEFECT 77 (vertices=18, convex hull=50, v0=124007) After retessellation of defect 77 (v0=124007), euler #=2 (109783,329343,219562) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.34 (0.03-->21.11) (max @ vno 15149 --> 26597) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.34 (0.03-->21.11) (max @ vno 15149 --> 26597) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 286 mutations (34.5%), 544 crossovers (65.5%), 1168 vertices were eliminated building final representation... 14687 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109783, nf=219562, ne=329343, g=0) writing corrected surface to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig.premesh... defective orientation at vertex 15149(16198) with faces 30081 and 215875 defective orientation at vertex 15149(16199) with faces 30081 and 215878 defective orientation at vertex 16198(15149) with faces 30081 and 215875 defective orientation at vertex 16198(16199) with faces 30081 and 215876 defective orientation at vertex 16199(15149) with faces 30081 and 215878 defective orientation at vertex 16199(16198) with faces 30081 and 215876 0.005 % of the vertices (6 vertices) exhibit an orientation change removing intersecting faces 000: 1654 intersecting 001: 192 intersecting 002: 90 intersecting 003: 44 intersecting 004: 19 intersecting 005: 7 intersecting step 1 with no progress (num=7, old_num=7) 006: 7 intersecting step 2 with no progress (num=7, old_num=7) 007: 7 intersecting step 3 with no progress (num=7, old_num=7) 008: 7 intersecting step 4 with no progress (num=7, old_num=7) 009: 7 intersecting step 5 with no progress (num=7, old_num=7) 010: 7 intersecting step 6 with no progress (num=7, old_num=7) 011: 7 intersecting step 7 with no progress (num=7, old_num=7) 012: 7 intersecting step 8 with no progress (num=7, old_num=7) 013: 7 intersecting step 9 with no progress (num=7, old_num=7) 014: 7 intersecting step 10 with no progress (num=7, old_num=7) 015: 7 intersecting step 11 with no progress (num=7, old_num=7) 016: 7 intersecting step 12 with no progress (num=7, old_num=7) 017: 7 intersecting step 13 with no progress (num=7, old_num=7) 018: 7 intersecting step 14 with no progress (num=7, old_num=7) 019: 7 intersecting step 15 with no progress (num=7, old_num=7) 020: 7 intersecting step 16 with no progress (num=7, old_num=7) terminating search with 7 intersecting topology fixing took 7.1 minutes FSRUNTIME@ mris_fix_topology rh 0.1185 hours 4 threads #VMPC# mris_fix_topology VmPeak 960784 PIDs (737782 737785) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 112263 - 336783 + 224522 = 2 --> 0 holes F =2V-4: 224522 = 224526-4 (0) 2E=3F: 673566 = 673566 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 109783 - 329343 + 219562 = 2 --> 0 holes F =2V-4: 219562 = 219566-4 (0) 2E=3F: 658686 = 658686 (0) total defect index = 0 Tue Jan 10 12:40:23 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/bin/defect2seg --s Test_withT2 --cortex freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 defect2seg 7.3.2 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux pid 737888 mri_label2label --label-cortex /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig.nofix /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/aseg.presurf.mgz 0 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 30 non-cortical segments detected only using segment with 8399 vertices erasing segment 1 (vno[0] = 43946) erasing segment 2 (vno[0] = 44934) erasing segment 3 (vno[0] = 45975) erasing segment 4 (vno[0] = 53028) erasing segment 5 (vno[0] = 56574) erasing segment 6 (vno[0] = 60752) erasing segment 7 (vno[0] = 63085) erasing segment 8 (vno[0] = 64636) erasing segment 9 (vno[0] = 70431) erasing segment 10 (vno[0] = 70452) erasing segment 11 (vno[0] = 73193) erasing segment 12 (vno[0] = 75634) erasing segment 13 (vno[0] = 77160) erasing segment 14 (vno[0] = 79142) erasing segment 15 (vno[0] = 83926) erasing segment 16 (vno[0] = 88062) erasing segment 17 (vno[0] = 92705) erasing segment 18 (vno[0] = 92747) erasing segment 19 (vno[0] = 93624) erasing segment 20 (vno[0] = 93645) erasing segment 21 (vno[0] = 93754) erasing segment 22 (vno[0] = 94507) erasing segment 23 (vno[0] = 95407) erasing segment 24 (vno[0] = 95555) erasing segment 25 (vno[0] = 96261) erasing segment 26 (vno[0] = 96343) erasing segment 27 (vno[0] = 96372) erasing segment 28 (vno[0] = 98772) erasing segment 29 (vno[0] = 99682) mri_label2vol --defects /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig.nofix /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.defect_labels /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz 1000 0 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/surface.defects.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/surface.defects.mgz mris_defects_pointset -s /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig.nofix -d /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.defect_labels -o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.defects.pointset --label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/lh.nofix.cortex.label Reading in surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig.nofix Reading in defect segmentation /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.defect_labels Reading in label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 536272 mris_defects_pointset done mri_label2label --label-cortex /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig.nofix /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/aseg.presurf.mgz 0 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 30 non-cortical segments detected only using segment with 7861 vertices erasing segment 1 (vno[0] = 43580) erasing segment 2 (vno[0] = 44923) erasing segment 3 (vno[0] = 48406) erasing segment 4 (vno[0] = 51842) erasing segment 5 (vno[0] = 57083) erasing segment 6 (vno[0] = 60850) erasing segment 7 (vno[0] = 62376) erasing segment 8 (vno[0] = 66972) erasing segment 9 (vno[0] = 75076) erasing segment 10 (vno[0] = 75873) erasing segment 11 (vno[0] = 77848) erasing segment 12 (vno[0] = 85777) erasing segment 13 (vno[0] = 87533) erasing segment 14 (vno[0] = 93157) erasing segment 15 (vno[0] = 94901) erasing segment 16 (vno[0] = 95881) erasing segment 17 (vno[0] = 96780) erasing segment 18 (vno[0] = 97730) erasing segment 19 (vno[0] = 97870) erasing segment 20 (vno[0] = 97898) erasing segment 21 (vno[0] = 97901) erasing segment 22 (vno[0] = 98335) erasing segment 23 (vno[0] = 98655) erasing segment 24 (vno[0] = 99549) erasing segment 25 (vno[0] = 100324) erasing segment 26 (vno[0] = 107733) erasing segment 27 (vno[0] = 109245) erasing segment 28 (vno[0] = 110589) erasing segment 29 (vno[0] = 112051) mri_label2vol --defects /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig.nofix /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.defect_labels /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/surface.defects.mgz 2000 1 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/surface.defects.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/surface.defects.mgz mris_defects_pointset -s /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig.nofix -d /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.defect_labels -o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.defects.pointset --label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/rh.nofix.cortex.label Reading in surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig.nofix Reading in defect segmentation /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.defect_labels Reading in label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 473696 mris_defects_pointset done Started at Tue Jan 10 12:40:23 CET 2023 Ended at Tue Jan 10 12:40:51 CET 2023 Defect2seg-Run-Time-Sec 28 Defect2seg-Run-Time-Min 0.56 Defect2seg-Run-Time-Hours 0.01 tkmeditfv Test_withT2 brain.finalsurfs.mgz -defect defect2seg Done mris_remesh --remesh --iters 3 --input /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig.premesh --output /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.717484 remeshing to edge length 0.717484 with 3 iterations avg qual before : 0.883059 after: 0.971317 Removing intersections removing intersecting faces 000: 148 intersecting 001: 115 intersecting 002: 100 intersecting 003: 93 intersecting 004: 83 intersecting 005: 72 intersecting 006: 62 intersecting step 1 with no progress (num=62, old_num=62) 007: 62 intersecting step 2 with no progress (num=62, old_num=62) 008: 62 intersecting step 3 with no progress (num=62, old_num=62) 009: 62 intersecting step 4 with no progress (num=62, old_num=62) 010: 62 intersecting step 5 with no progress (num=62, old_num=62) 011: 62 intersecting step 6 with no progress (num=62, old_num=62) 012: 62 intersecting step 7 with no progress (num=62, old_num=62) 013: 62 intersecting step 8 with no progress (num=62, old_num=62) 014: 62 intersecting step 9 with no progress (num=62, old_num=62) 015: 62 intersecting step 10 with no progress (num=62, old_num=62) 016: 62 intersecting step 11 with no progress (num=62, old_num=62) 017: 62 intersecting step 12 with no progress (num=62, old_num=62) 018: 62 intersecting step 13 with no progress (num=62, old_num=62) 019: 62 intersecting step 14 with no progress (num=62, old_num=62) 020: 62 intersecting step 15 with no progress (num=62, old_num=62) 021: 62 intersecting step 16 with no progress (num=62, old_num=62) terminating search with 62 intersecting Remeshed surface quality stats nv0 = 112263 nv = 115656 1.03022 Area 231308 0.30728 0.03434 0.021150 0.4921 Corner 693924 60.00000 8.78124 5.652080 152.5449 Edge 346962 0.85038 0.08319 0.074343 1.4832 Hinge 346962 10.83366 11.84977 0.000016 179.3596 mris_remesh done mris_remesh --remesh --iters 3 --input /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig.premesh --output /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.718214 remeshing to edge length 0.718214 with 3 iterations avg qual before : 0.881785 after: 0.970632 Removing intersections removing intersecting faces 000: 286 intersecting 001: 135 intersecting 002: 97 intersecting step 1 with no progress (num=97, old_num=97) 003: 97 intersecting step 2 with no progress (num=97, old_num=97) 004: 97 intersecting step 3 with no progress (num=97, old_num=97) 005: 97 intersecting step 4 with no progress (num=97, old_num=97) 006: 97 intersecting step 5 with no progress (num=97, old_num=97) 007: 97 intersecting step 6 with no progress (num=97, old_num=97) 008: 97 intersecting step 7 with no progress (num=97, old_num=97) 009: 97 intersecting step 8 with no progress (num=97, old_num=97) 010: 97 intersecting step 9 with no progress (num=97, old_num=97) 011: 97 intersecting step 10 with no progress (num=97, old_num=97) 012: 97 intersecting step 11 with no progress (num=97, old_num=97) 013: 97 intersecting step 12 with no progress (num=97, old_num=97) 014: 97 intersecting step 13 with no progress (num=97, old_num=97) 015: 97 intersecting step 14 with no progress (num=97, old_num=97) 016: 97 intersecting step 15 with no progress (num=97, old_num=97) 017: 97 intersecting step 16 with no progress (num=97, old_num=97) terminating search with 97 intersecting Remeshed surface quality stats nv0 = 109783 nv = 112409 1.02392 Area 224814 0.30750 0.03641 0.000412 0.5747 Corner 674442 60.00000 9.09611 0.081422 179.1478 Edge 337221 0.85084 0.08559 0.017367 1.5688 Hinge 337221 10.84511 12.09703 0.000008 176.3987 mris_remesh done /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 62 intersecting step 1 with no progress (num=62, old_num=62) 001: 62 intersecting step 2 with no progress (num=62, old_num=62) 002: 62 intersecting step 3 with no progress (num=62, old_num=62) 003: 62 intersecting step 4 with no progress (num=62, old_num=62) 004: 62 intersecting step 5 with no progress (num=62, old_num=62) 005: 62 intersecting step 6 with no progress (num=62, old_num=62) 006: 62 intersecting step 7 with no progress (num=62, old_num=62) 007: 62 intersecting step 8 with no progress (num=62, old_num=62) 008: 62 intersecting step 9 with no progress (num=62, old_num=62) 009: 62 intersecting step 10 with no progress (num=62, old_num=62) 010: 62 intersecting step 11 with no progress (num=62, old_num=62) 011: 62 intersecting step 12 with no progress (num=62, old_num=62) 012: 62 intersecting step 13 with no progress (num=62, old_num=62) 013: 62 intersecting step 14 with no progress (num=62, old_num=62) 014: 62 intersecting step 15 with no progress (num=62, old_num=62) 015: 62 intersecting step 16 with no progress (num=62, old_num=62) terminating search with 62 intersecting writing corrected surface to ../surf/lh.orig rm -f ../surf/lh.inflated /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.01 hours removing intersecting faces 000: 97 intersecting step 1 with no progress (num=97, old_num=97) 001: 97 intersecting step 2 with no progress (num=97, old_num=97) 002: 97 intersecting step 3 with no progress (num=97, old_num=97) 003: 97 intersecting step 4 with no progress (num=97, old_num=97) 004: 97 intersecting step 5 with no progress (num=97, old_num=97) 005: 97 intersecting step 6 with no progress (num=97, old_num=97) 006: 97 intersecting step 7 with no progress (num=97, old_num=97) 007: 97 intersecting step 8 with no progress (num=97, old_num=97) 008: 97 intersecting step 9 with no progress (num=97, old_num=97) 009: 97 intersecting step 10 with no progress (num=97, old_num=97) 010: 97 intersecting step 11 with no progress (num=97, old_num=97) 011: 97 intersecting step 12 with no progress (num=97, old_num=97) 012: 97 intersecting step 13 with no progress (num=97, old_num=97) 013: 97 intersecting step 14 with no progress (num=97, old_num=97) 014: 97 intersecting step 15 with no progress (num=97, old_num=97) 015: 97 intersecting step 16 with no progress (num=97, old_num=97) terminating search with 97 intersecting writing corrected surface to ../surf/rh.orig rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Tue Jan 10 12:43:14 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 234700 voxels (1.40%) border gray 297479 voxels (1.77%) 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=28065, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 81.7 +- 11.2 [30.0 --> 110.0] white_mean = 101.547 +/- 6.7521, gray_mean = 81.6967 +/- 11.2327 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=105+-5.2, GM=82+-7.0 white_mode = 105, gray_mode = 82 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 70.8 (was 70.000000) setting MAX_BORDER_WHITE to 111.8 (was 105.000000) setting MIN_BORDER_WHITE to 82.0 (was 85.000000) setting MAX_CSF to 59.5 (was 40.000000) setting MAX_GRAY to 98.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 70.8 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 48.3 (was 40.000000) When placing the white surface white_border_hi = 111.752; white_border_low = 82; white_outside_low = 70.7673; white_inside_hi = 120; white_outside_hi = 111.752; When placing the pial surface pial_border_hi = 70.7673; pial_border_low = 48.3018; pial_outside_low = 10; pial_inside_hi = 98.2479; pial_outside_hi = 65.1509; #VMPC# mris_autodet_gwstats VmPeak 563760 mris_autodet_gwstats done #-------------------------------------------- #@# AutoDetGWStats rh Tue Jan 10 12:43:17 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 234700 voxels (1.40%) border gray 297479 voxels (1.77%) 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=28065, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 81.7 +- 11.2 [30.0 --> 110.0] white_mean = 101.547 +/- 6.7521, gray_mean = 81.6967 +/- 11.2327 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=105+-5.2, GM=83+-7.8 white_mode = 105, gray_mode = 83 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 71.8 (was 70.000000) setting MAX_BORDER_WHITE to 111.8 (was 105.000000) setting MIN_BORDER_WHITE to 83.0 (was 85.000000) setting MAX_CSF to 60.5 (was 40.000000) setting MAX_GRAY to 98.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 71.8 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 49.3 (was 40.000000) When placing the white surface white_border_hi = 111.752; white_border_low = 83; white_outside_low = 71.7673; white_inside_hi = 120; white_outside_hi = 111.752; When placing the pial surface pial_border_hi = 71.7673; pial_border_low = 49.3018; pial_outside_low = 10; pial_inside_hi = 98.2479; pial_outside_hi = 66.1509; #VMPC# mris_autodet_gwstats VmPeak 561876 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Tue Jan 10 12:43:20 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --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 before ripping with 5 iterations removing intersecting faces 000: 55 intersecting 001: 49 intersecting 002: 36 intersecting step 1 with no progress (num=36, old_num=36) 003: 36 intersecting step 2 with no progress (num=36, old_num=36) 004: 36 intersecting step 3 with no progress (num=36, old_num=36) 005: 36 intersecting step 4 with no progress (num=36, old_num=36) 006: 36 intersecting step 5 with no progress (num=36, old_num=36) 007: 36 intersecting step 6 with no progress (num=36, old_num=36) 008: 36 intersecting step 7 with no progress (num=36, old_num=36) 009: 36 intersecting step 8 with no progress (num=36, old_num=36) 010: 36 intersecting step 9 with no progress (num=36, old_num=36) 011: 36 intersecting step 10 with no progress (num=36, old_num=36) 012: 36 intersecting step 11 with no progress (num=36, old_num=36) 013: 36 intersecting step 12 with no progress (num=36, old_num=36) 014: 36 intersecting step 13 with no progress (num=36, old_num=36) 015: 36 intersecting step 14 with no progress (num=36, old_num=36) 016: 36 intersecting step 15 with no progress (num=36, old_num=36) 017: 36 intersecting step 16 with no progress (num=36, old_num=36) terminating search with 36 intersecting Area 231308 0.26709 0.06714 0.000508 0.5676 Corner 693924 60.00000 9.85694 1.737635 170.8789 Edge 346962 0.78866 0.12184 0.008151 1.4321 Hinge 346962 6.82518 7.10687 0.000010 174.3819 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 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 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6584, nmarked2=0, nripped=6584 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (0,0,0) CBVO Creating mask 115656 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=6584 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6584, nmarked2=0, nripped=6584 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=2 had to be increased for 677 vertices, nripped=6584 mean border=90.4, 418 (418) missing vertices, mean dist 0.1 [0.9 (%43.4)->0.8 (%56.6))] %62 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0421 min Finding expansion regions mean absolute distance = 0.87 +- 1.13 3419 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=shark, 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=2528325.0, rms=10.486 001: dt: 0.5000, sse=1693316.8, rms=8.457 (19.344%) 002: dt: 0.5000, sse=1217312.6, rms=7.015 (17.053%) 003: dt: 0.5000, sse=936570.4, rms=6.037 (13.941%) 004: dt: 0.5000, sse=754438.1, rms=5.283 (12.489%) 005: dt: 0.5000, sse=624492.1, rms=4.647 (12.049%) 006: dt: 0.5000, sse=549059.0, rms=4.221 (9.151%) 007: dt: 0.5000, sse=499075.8, rms=3.941 (6.645%) 008: dt: 0.5000, sse=468261.2, rms=3.730 (5.360%) 009: dt: 0.5000, sse=456726.0, rms=3.596 (3.581%) 010: dt: 0.5000, sse=440985.1, rms=3.491 (2.934%) rms = 3.4497/3.4907, sse=444922.6/440985.1, time step reduction 1 of 3 to 0.250 0 1 1 011: dt: 0.5000, sse=444922.6, rms=3.450 (1.175%) 012: dt: 0.2500, sse=368516.5, rms=2.976 (13.717%) 013: dt: 0.2500, sse=345242.9, rms=2.869 (3.617%) rms = 2.8241/2.8688, sse=352332.0/345242.9, time step reduction 2 of 3 to 0.125 0 1 1 014: dt: 0.2500, sse=352332.0, rms=2.824 (1.558%) rms = 2.7922/2.8241, sse=360158.3/352332.0, time step reduction 3 of 3 to 0.062 0 1 1 015: dt: 0.1250, sse=360158.3, rms=2.792 (1.130%) maximum number of reductions reached, breaking from loop positioning took 0.8 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=6584 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7075, nmarked2=0, nripped=7075 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=1 had to be increased for 502 vertices, nripped=7075 mean border=92.1, 578 (181) missing vertices, mean dist -0.2 [0.5 (%65.3)->0.3 (%34.7))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0339 min Finding expansion regions mean absolute distance = 0.41 +- 0.70 3523 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=shark, 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=573027.4, rms=3.986 016: dt: 0.5000, sse=426386.6, rms=3.102 (22.173%) 017: dt: 0.5000, sse=394582.6, rms=2.810 (9.432%) rms = 2.7436/2.8096, sse=395322.5/394582.6, time step reduction 1 of 3 to 0.250 0 1 0 018: dt: 0.5000, sse=395322.5, rms=2.744 (2.350%) 019: dt: 0.2500, sse=361048.4, rms=2.452 (10.626%) 020: dt: 0.2500, sse=352249.1, rms=2.371 (3.286%) rms = 2.3524/2.3715, sse=352178.9/352249.1, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=352178.9, rms=2.352 (0.803%) rms = 2.3084/2.3524, sse=352116.0/352178.9, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=352116.0, rms=2.308 (1.872%) maximum number of reductions reached, breaking from loop positioning took 0.3 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=7075 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7132, nmarked2=0, nripped=7132 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; 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=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 546 vertices, nripped=7132 mean border=92.9, 637 (144) missing vertices, mean dist -0.1 [0.3 (%58.7)->0.2 (%41.3))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0154 min Finding expansion regions mean absolute distance = 0.29 +- 0.46 3217 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=shark, 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=400315.2, rms=2.756 023: dt: 0.5000, sse=379880.2, rms=2.438 (11.530%) 024: dt: 0.5000, sse=346875.2, rms=2.313 (5.147%) rms = 2.3770/2.3127, sse=367942.1/346875.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=325449.2, rms=2.149 (7.075%) rms = 2.0887/2.1491, sse=326212.0/325449.2, time step reduction 2 of 3 to 0.125 0 1 0 026: dt: 0.2500, sse=326212.0, rms=2.089 (2.808%) 027: dt: 0.1250, sse=320424.2, rms=2.037 (2.461%) rms = 2.0157/2.0373, sse=318933.4/320424.2, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=318933.4, rms=2.016 (1.064%) maximum number of reductions reached, breaking from loop positioning took 0.3 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=7132 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7184, nmarked2=0, nripped=7184 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; 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=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 517 vertices, nripped=7184 mean border=93.2, 648 (123) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.2 (%47.7))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0117 min Finding expansion regions mean absolute distance = 0.26 +- 0.39 3157 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=shark, 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=325650.7, rms=2.110 rms = 2.1141/2.1101, sse=320812.6/325650.7, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 029: dt: 0.2500, sse=299174.1, rms=1.955 (7.375%) 030: dt: 0.2500, sse=295661.8, rms=1.903 (2.654%) rms = 1.9392/1.9027, sse=300753.5/295661.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.8738/1.9027, sse=292140.1/295661.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=292140.2, rms=1.874 (1.517%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 36 intersecting step 1 with no progress (num=37, old_num=36) 001: 37 intersecting step 2 with no progress (num=39, old_num=37) 002: 39 intersecting 003: 29 intersecting step 1 with no progress (num=31, old_num=29) 004: 31 intersecting step 2 with no progress (num=31, old_num=31) 005: 31 intersecting step 3 with no progress (num=31, old_num=31) 006: 31 intersecting step 4 with no progress (num=31, old_num=31) 007: 31 intersecting step 5 with no progress (num=31, old_num=31) 008: 31 intersecting step 6 with no progress (num=31, old_num=31) 009: 31 intersecting step 7 with no progress (num=31, old_num=31) 010: 31 intersecting step 8 with no progress (num=31, old_num=31) 011: 31 intersecting step 9 with no progress (num=31, old_num=31) 012: 31 intersecting step 10 with no progress (num=31, old_num=31) 013: 31 intersecting step 11 with no progress (num=31, old_num=31) 014: 31 intersecting step 12 with no progress (num=31, old_num=31) 015: 31 intersecting step 13 with no progress (num=31, old_num=31) 016: 31 intersecting step 14 with no progress (num=31, old_num=31) 017: 31 intersecting step 15 with no progress (num=31, old_num=31) 018: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 29 intersecting Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.22 minutes #VMPC# mris_place_surfaces VmPeak 2093912 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Tue Jan 10 12:46:02 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --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 before ripping with 5 iterations removing intersecting faces 000: 156 intersecting 001: 144 intersecting step 1 with no progress (num=167, old_num=144) 002: 167 intersecting 003: 157 intersecting step 1 with no progress (num=167, old_num=157) 004: 167 intersecting 005: 156 intersecting 006: 152 intersecting 007: 140 intersecting step 1 with no progress (num=148, old_num=140) 008: 148 intersecting 009: 139 intersecting 010: 135 intersecting step 1 with no progress (num=150, old_num=135) 011: 150 intersecting 012: 139 intersecting 013: 136 intersecting step 1 with no progress (num=150, old_num=136) 014: 150 intersecting step 2 with no progress (num=150, old_num=150) 015: 150 intersecting 016: 143 intersecting step 1 with no progress (num=149, old_num=143) 017: 149 intersecting step 2 with no progress (num=152, old_num=149) 018: 152 intersecting 019: 148 intersecting step 1 with no progress (num=158, old_num=148) 020: 158 intersecting step 2 with no progress (num=167, old_num=158) 021: 167 intersecting 022: 152 intersecting step 1 with no progress (num=169, old_num=152) 023: 169 intersecting 024: 157 intersecting step 1 with no progress (num=157, old_num=157) 025: 157 intersecting step 2 with no progress (num=166, old_num=157) 026: 166 intersecting step 3 with no progress (num=166, old_num=166) 027: 166 intersecting 028: 153 intersecting step 1 with no progress (num=168, old_num=153) 029: 168 intersecting 030: 162 intersecting step 1 with no progress (num=165, old_num=162) 031: 165 intersecting 032: 155 intersecting step 1 with no progress (num=162, old_num=155) 033: 162 intersecting step 2 with no progress (num=173, old_num=162) 034: 173 intersecting 035: 170 intersecting step 1 with no progress (num=175, old_num=170) 036: 175 intersecting 037: 164 intersecting 038: 160 intersecting step 1 with no progress (num=160, old_num=160) 039: 160 intersecting step 2 with no progress (num=168, old_num=160) 040: 168 intersecting 041: 155 intersecting step 1 with no progress (num=177, old_num=155) 042: 177 intersecting 043: 160 intersecting step 1 with no progress (num=163, old_num=160) 044: 163 intersecting 045: 156 intersecting step 1 with no progress (num=158, old_num=156) 046: 158 intersecting step 2 with no progress (num=162, old_num=158) 047: 162 intersecting step 3 with no progress (num=162, old_num=162) 048: 162 intersecting step 4 with no progress (num=168, old_num=162) 049: 168 intersecting step 5 with no progress (num=175, old_num=168) 050: 175 intersecting 051: 165 intersecting step 1 with no progress (num=165, old_num=165) 052: 165 intersecting 053: 158 intersecting 054: 154 intersecting step 1 with no progress (num=165, old_num=154) 055: 165 intersecting 056: 163 intersecting step 1 with no progress (num=171, old_num=163) 057: 171 intersecting 058: 166 intersecting 059: 157 intersecting step 1 with no progress (num=167, old_num=157) 060: 167 intersecting step 2 with no progress (num=180, old_num=167) 061: 180 intersecting 062: 171 intersecting 063: 165 intersecting step 1 with no progress (num=167, old_num=165) 064: 167 intersecting step 2 with no progress (num=167, old_num=167) 065: 167 intersecting step 3 with no progress (num=168, old_num=167) 066: 168 intersecting 067: 166 intersecting 068: 164 intersecting step 1 with no progress (num=179, old_num=164) 069: 179 intersecting 070: 167 intersecting step 1 with no progress (num=169, old_num=167) 071: 169 intersecting step 2 with no progress (num=173, old_num=169) 072: 173 intersecting 073: 172 intersecting step 1 with no progress (num=173, old_num=172) 074: 173 intersecting 075: 166 intersecting 076: 165 intersecting step 1 with no progress (num=166, old_num=165) 077: 166 intersecting step 2 with no progress (num=173, old_num=166) 078: 173 intersecting step 3 with no progress (num=174, old_num=173) 079: 174 intersecting step 4 with no progress (num=174, old_num=174) 080: 174 intersecting 081: 167 intersecting step 1 with no progress (num=183, old_num=167) 082: 183 intersecting 083: 168 intersecting step 1 with no progress (num=168, old_num=168) 084: 168 intersecting step 2 with no progress (num=174, old_num=168) 085: 174 intersecting step 3 with no progress (num=176, old_num=174) 086: 176 intersecting 087: 173 intersecting step 1 with no progress (num=186, old_num=173) 088: 186 intersecting 089: 182 intersecting 090: 173 intersecting 091: 171 intersecting step 1 with no progress (num=185, old_num=171) 092: 185 intersecting step 2 with no progress (num=185, old_num=185) 093: 185 intersecting step 3 with no progress (num=187, old_num=185) 094: 187 intersecting 095: 183 intersecting 096: 177 intersecting step 1 with no progress (num=180, old_num=177) 097: 180 intersecting step 2 with no progress (num=180, old_num=180) 098: 180 intersecting step 3 with no progress (num=183, old_num=180) 099: 183 intersecting step 4 with no progress (num=188, old_num=183) 100: 188 intersecting step 5 with no progress (num=188, old_num=188) 101: 188 intersecting terminating search with 135 intersecting Area 224814 0.26782 0.06852 0.000000 0.7364 Corner 674442 60.00000 10.64036 0.000135 179.9997 Edge 337221 0.78952 0.12551 0.000071 1.7606 Hinge 337221 6.83215 7.85956 0.000031 179.7261 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 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 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 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6593, nmarked2=5, nripped=6593 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56205: xyz = (-0.213273,-15.8915,75.9194) oxyz = (-0.213273,-15.8915,75.9194) wxzy = (-0.213273,-15.8915,75.9194) pxyz = (0,0,0) CBVO Creating mask 112409 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=6593 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 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6593, nmarked2=5, nripped=6593 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=2 had to be increased for 536 vertices, nripped=6593 mean border=91.0, 358 (358) missing vertices, mean dist 0.0 [0.9 (%44.6)->0.8 (%55.4))] %59 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0403 min Finding expansion regions mean absolute distance = 0.87 +- 1.14 3256 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=shark, 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=3909730.2, rms=10.432 001: dt: 0.5000, sse=3403003.8, rms=8.172 (21.663%) 002: dt: 0.5000, sse=2607794.0, rms=6.499 (20.477%) 003: dt: 0.5000, sse=2215238.2, rms=5.196 (20.046%) 004: dt: 0.5000, sse=2012198.1, rms=4.176 (19.635%) 005: dt: 0.5000, sse=1487258.9, rms=3.430 (17.862%) 006: dt: 0.5000, sse=1445987.0, rms=3.025 (11.816%) 007: dt: 0.5000, sse=1430222.2, rms=2.820 (6.761%) 008: dt: 0.5000, sse=1427830.2, rms=2.725 (3.391%) 009: dt: 0.5000, sse=1410493.4, rms=2.626 (3.634%) 010: dt: 0.5000, sse=1385976.6, rms=2.567 (2.214%) rms = 2.5379/2.5674, sse=1393725.3/1385976.6, time step reduction 1 of 3 to 0.250 0 1 1 011: dt: 0.5000, sse=1393725.4, rms=2.538 (1.150%) 012: dt: 0.2500, sse=1340966.5, rms=1.919 (24.377%) 013: dt: 0.2500, sse=601853.8, rms=1.810 (5.708%) rms = 1.7764/1.8097, sse=992367.4/601853.7, time step reduction 2 of 3 to 0.125 0 1 1 014: dt: 0.2500, sse=992367.4, rms=1.776 (1.837%) rms = 1.7377/1.7764, sse=1311573.3/992367.4, time step reduction 3 of 3 to 0.062 0 1 1 015: dt: 0.1250, sse=1311573.2, rms=1.738 (2.181%) maximum number of reductions reached, breaking from loop positioning took 0.7 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=6593 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 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 #FML# MRISripMidline(): nmarked=7140, nmarked2=24, nripped=7140 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=1 had to be increased for 487 vertices, nripped=7140 mean border=92.5, 511 (170) missing vertices, mean dist -0.2 [0.5 (%63.6)->0.3 (%36.4))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0237 min Finding expansion regions mean absolute distance = 0.42 +- 0.74 3395 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=shark, 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=1422410.4, rms=3.334 016: dt: 0.5000, sse=1406118.0, rms=2.343 (29.708%) rms = 2.0661/2.3434, sse=1406375.8/1406118.0, time step reduction 1 of 3 to 0.250 0 1 0 017: dt: 0.5000, sse=1406375.8, rms=2.066 (11.832%) 018: dt: 0.2500, sse=1181145.4, rms=1.761 (14.750%) 019: dt: 0.2500, sse=1178874.2, rms=1.669 (5.259%) rms = 1.6345/1.6687, sse=1186893.1/1178874.2, time step reduction 2 of 3 to 0.125 0 1 1 020: dt: 0.2500, sse=1186893.1, rms=1.634 (2.053%) rms = 1.5994/1.6345, sse=1169148.7/1186893.1, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=1169148.6, rms=1.599 (2.143%) maximum number of reductions reached, breaking from loop positioning took 0.3 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=7140 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 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 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7163, nmarked2=24, nripped=7163 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; 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=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 544 vertices, nripped=7163 mean border=93.3, 524 (136) missing vertices, mean dist -0.1 [0.4 (%57.3)->0.2 (%42.7))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0127 min Finding expansion regions mean absolute distance = 0.31 +- 0.51 3305 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=shark, 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=1223019.6, rms=2.271 022: dt: 0.5000, sse=1211771.9, rms=1.853 (18.391%) 023: dt: 0.5000, sse=1207634.2, rms=1.755 (5.295%) rms = 1.8156/1.7550, sse=1203872.5/1207634.2, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 024: dt: 0.2500, sse=1188254.0, rms=1.573 (10.344%) 025: dt: 0.2500, sse=1183450.1, rms=1.508 (4.140%) rms = 1.4948/1.5083, sse=1187724.0/1183450.2, time step reduction 2 of 3 to 0.125 0 1 1 026: dt: 0.2500, sse=1187724.0, rms=1.495 (0.894%) rms = 1.4711/1.4948, sse=1176733.5/1187724.0, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=1176733.5, rms=1.471 (1.590%) maximum number of reductions reached, breaking from loop positioning took 0.3 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=7163 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 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=7182, nmarked2=24, nripped=7182 Ripping segs (eg, WMSA, BG, frozen) 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 = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; 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=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 510 vertices, nripped=7182 mean border=93.5, 583 (120) missing vertices, mean dist -0.0 [0.3 (%51.7)->0.2 (%48.3))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0081 min Finding expansion regions mean absolute distance = 0.27 +- 0.41 2753 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=shark, 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=1187895.2, rms=1.665 rms = 1.5996/1.6655, sse=1200971.5/1187895.3, time step reduction 1 of 3 to 0.250 0 1 0 028: dt: 0.5000, sse=1200971.5, rms=1.600 (3.958%) 029: dt: 0.2500, sse=1200608.0, rms=1.419 (11.261%) rms = 1.4013/1.4194, sse=1193068.2/1200608.0, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=1193068.2, rms=1.401 (1.276%) 031: dt: 0.1250, sse=1156053.6, rms=1.322 (5.683%) rms = 1.3006/1.3217, sse=1160696.5/1156053.6, time step reduction 3 of 3 to 0.062 0 1 1 032: dt: 0.1250, sse=1160696.5, rms=1.301 (1.593%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 122 intersecting step 1 with no progress (num=123, old_num=122) 001: 123 intersecting 002: 109 intersecting 003: 104 intersecting 004: 98 intersecting step 1 with no progress (num=98, old_num=98) 005: 98 intersecting 006: 92 intersecting 007: 90 intersecting step 1 with no progress (num=93, old_num=90) 008: 93 intersecting step 2 with no progress (num=94, old_num=93) 009: 94 intersecting step 3 with no progress (num=108, old_num=94) 010: 108 intersecting 011: 101 intersecting 012: 98 intersecting step 1 with no progress (num=98, old_num=98) 013: 98 intersecting 014: 92 intersecting step 1 with no progress (num=95, old_num=92) 015: 95 intersecting 016: 93 intersecting step 1 with no progress (num=96, old_num=93) 017: 96 intersecting 018: 94 intersecting 019: 91 intersecting step 1 with no progress (num=96, old_num=91) 020: 96 intersecting step 2 with no progress (num=103, old_num=96) 021: 103 intersecting 022: 90 intersecting step 1 with no progress (num=99, old_num=90) 023: 99 intersecting 024: 98 intersecting step 1 with no progress (num=103, old_num=98) 025: 103 intersecting 026: 100 intersecting step 1 with no progress (num=119, old_num=100) 027: 119 intersecting 028: 118 intersecting 029: 116 intersecting 030: 111 intersecting step 1 with no progress (num=113, old_num=111) 031: 113 intersecting step 2 with no progress (num=113, old_num=113) 032: 113 intersecting step 3 with no progress (num=114, old_num=113) 033: 114 intersecting step 4 with no progress (num=114, old_num=114) 034: 114 intersecting step 5 with no progress (num=114, old_num=114) 035: 114 intersecting step 6 with no progress (num=114, old_num=114) 036: 114 intersecting step 7 with no progress (num=114, old_num=114) 037: 114 intersecting step 8 with no progress (num=114, old_num=114) 038: 114 intersecting step 9 with no progress (num=114, old_num=114) 039: 114 intersecting step 10 with no progress (num=114, old_num=114) 040: 114 intersecting step 11 with no progress (num=114, old_num=114) 041: 114 intersecting step 12 with no progress (num=114, old_num=114) 042: 114 intersecting step 13 with no progress (num=114, old_num=114) 043: 114 intersecting step 14 with no progress (num=114, old_num=114) 044: 114 intersecting step 15 with no progress (num=114, old_num=114) 045: 114 intersecting step 16 with no progress (num=114, old_num=114) terminating search with 90 intersecting Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.37 minutes #VMPC# mris_place_surfaces VmPeak 2290344 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Tue Jan 10 12:50:15 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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 12 non-cortical segments detected only using segment with 7347 vertices erasing segment 1 (vno[0] = 31623) erasing segment 2 (vno[0] = 32374) erasing segment 3 (vno[0] = 37769) erasing segment 4 (vno[0] = 38012) erasing segment 5 (vno[0] = 42052) erasing segment 6 (vno[0] = 68872) erasing segment 7 (vno[0] = 70987) erasing segment 8 (vno[0] = 71001) erasing segment 9 (vno[0] = 71626) erasing segment 10 (vno[0] = 108629) erasing segment 11 (vno[0] = 111222) #-------------------------------------------- #@# CortexLabel+HipAmyg lh Tue Jan 10 12:50:25 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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 24 non-cortical segments detected only using segment with 5652 vertices erasing segment 1 (vno[0] = 31623) erasing segment 2 (vno[0] = 32374) erasing segment 3 (vno[0] = 37769) erasing segment 4 (vno[0] = 41588) erasing segment 5 (vno[0] = 42052) erasing segment 6 (vno[0] = 44802) erasing segment 7 (vno[0] = 54342) erasing segment 8 (vno[0] = 61150) erasing segment 9 (vno[0] = 68872) erasing segment 10 (vno[0] = 70987) erasing segment 11 (vno[0] = 71001) erasing segment 12 (vno[0] = 71626) erasing segment 13 (vno[0] = 92834) erasing segment 14 (vno[0] = 92923) erasing segment 15 (vno[0] = 92968) erasing segment 16 (vno[0] = 93043) erasing segment 17 (vno[0] = 93739) erasing segment 18 (vno[0] = 94728) erasing segment 19 (vno[0] = 94845) erasing segment 20 (vno[0] = 95197) erasing segment 21 (vno[0] = 108187) erasing segment 22 (vno[0] = 110321) erasing segment 23 (vno[0] = 111222) #-------------------------------------------- #@# CortexLabel rh Tue Jan 10 12:50:35 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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 10 non-cortical segments detected only using segment with 7056 vertices erasing segment 1 (vno[0] = 57126) erasing segment 2 (vno[0] = 58583) erasing segment 3 (vno[0] = 68697) erasing segment 4 (vno[0] = 70082) erasing segment 5 (vno[0] = 72790) erasing segment 6 (vno[0] = 73488) erasing segment 7 (vno[0] = 77919) erasing segment 8 (vno[0] = 91644) erasing segment 9 (vno[0] = 109976) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Tue Jan 10 12:50:45 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/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 10 non-cortical segments detected only using segment with 5972 vertices erasing segment 1 (vno[0] = 57126) erasing segment 2 (vno[0] = 58583) erasing segment 3 (vno[0] = 68697) erasing segment 4 (vno[0] = 70082) erasing segment 5 (vno[0] = 72790) erasing segment 6 (vno[0] = 73488) erasing segment 7 (vno[0] = 77919) erasing segment 8 (vno[0] = 91644) erasing segment 9 (vno[0] = 109976) #-------------------------------------------- #@# Smooth2 lh Tue Jan 10 12:50:56 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Tue Jan 10 12:50:56 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 739087 of (739087 739090) to complete... Waiting for PID 739090 of (739087 739090) to complete... 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... 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... PIDs (739087 739090) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Tue Jan 10 12:50:58 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Tue Jan 10 12:50:58 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 739139 of (739139 739142) to complete... Waiting for PID 739142 of (739139 739142) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.6 mm, total surface area = 70679 mm^2 step 000: RMS=0.177 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (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/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 27.205206 mris_inflate stimesec 0.055862 mris_inflate ru_maxrss 181568 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28627 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9048 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1163 mris_inflate ru_nivcsw 115 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.8 mm, total surface area = 67911 mm^2 step 000: RMS=0.174 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 29.341199 mris_inflate stimesec 0.804304 mris_inflate ru_maxrss 176116 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 429016 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8800 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1097 mris_inflate ru_nivcsw 72 PIDs (739139 739142) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Tue Jan 10 12:51:10 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf mris_curvature -w -seed 1234 lh.white.preaparc 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 #-------------------------------------------- #@# Curv .H and .K rh Tue Jan 10 12:51:10 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf mris_curvature -w -seed 1234 rh.white.preaparc 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 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf reconbatchjobs /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 739356 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739359 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739362 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739365 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739368 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739371 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739374 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739377 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739380 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739383 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739386 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... Waiting for PID 739389 of (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 20.424*4pi (256.653) --> -19 handles ICI = 162.7, FI = 1440.7, variation=23326.234 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. 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 101 vertices thresholded to be in k1 ~ [-0.56 0.44], k2 ~ [-0.23 0.10] total integrated curvature = 0.502*4pi (6.310) --> 0 handles ICI = 1.4, FI = 9.2, variation=154.578 102 vertices thresholded to be in [-0.02 0.06] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 109 vertices thresholded to be in [-0.28 0.21] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.025 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 32.715*4pi (411.107) --> -32 handles ICI = 169.2, FI = 1484.4, variation=23899.315 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. 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 148 vertices thresholded to be in k1 ~ [-1.53 1.39], k2 ~ [-0.26 1.09] total integrated curvature = 0.527*4pi (6.622) --> 0 handles ICI = 1.5, FI = 8.3, variation=147.058 144 vertices thresholded to be in [-0.20 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.005 76 vertices thresholded to be in [-0.31 0.66] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.026 done. PIDs (739356 739359 739362 739365 739368 739371 739374 739377 739380 739383 739386 739389) completed and logs appended. #-------------------------------------------- #@# Sphere lh Tue Jan 10 12:51:42 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Tue Jan 10 12:51:42 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 739535 of (739535 739538) to complete... Waiting for PID 739538 of (739535 739538) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.322... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.10 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.97 removing remaining folds... final distance error %20.00 MRISunfold() return, current seed 1234 -01: dt=0.0000, 39 negative triangles VmPeak 771600 182: dt=0.9900, 39 negative triangles 183: dt=0.9900, 23 negative triangles 184: dt=0.9900, 14 negative triangles 185: dt=0.9900, 13 negative triangles 186: dt=0.9900, 15 negative triangles 187: dt=0.9900, 12 negative triangles 188: dt=0.9900, 10 negative triangles 189: dt=0.9900, 6 negative triangles 190: dt=0.9900, 10 negative triangles 191: dt=0.9900, 7 negative triangles 192: dt=0.9900, 7 negative triangles 193: dt=0.9900, 4 negative triangles 194: dt=0.9900, 9 negative triangles 195: dt=0.9900, 4 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 6 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 2 negative triangles 202: dt=0.9900, 2 negative triangles 203: dt=0.9900, 4 negative triangles 204: dt=0.9900, 2 negative triangles 205: dt=0.9900, 2 negative triangles 206: dt=0.9900, 2 negative triangles 207: dt=0.9900, 3 negative triangles 208: dt=0.9900, 2 negative triangles 209: dt=0.9900, 1 negative triangles 210: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0601 hours FSRUNTIME@ mris_sphere 0.0601 hours 4 threads #VMPC# mris_sphere VmPeak 771600 mris_sphere done mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.329... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=shark, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.52 pass 1: epoch 2 of 3 starting distance error %20.50 unfolding complete - removing small folds... starting distance error %20.37 removing remaining folds... final distance error %20.41 MRISunfold() return, current seed 1234 -01: dt=0.0000, 449 negative triangles VmPeak 713988 203: dt=0.9900, 449 negative triangles 204: dt=0.9900, 422 negative triangles 205: dt=0.9900, 405 negative triangles 206: dt=0.9900, 407 negative triangles 207: dt=0.9900, 414 negative triangles 208: dt=0.9900, 401 negative triangles 209: dt=0.9900, 390 negative triangles 210: dt=0.9900, 387 negative triangles 211: dt=0.9900, 398 negative triangles 212: dt=0.9900, 375 negative triangles 213: dt=0.9900, 388 negative triangles 214: dt=0.9900, 375 negative triangles 215: dt=0.9900, 383 negative triangles 216: dt=0.9900, 376 negative triangles 217: dt=0.9900, 377 negative triangles 218: dt=0.9900, 381 negative triangles 219: dt=0.9900, 369 negative triangles 220: dt=0.9900, 373 negative triangles 221: dt=0.9900, 375 negative triangles 222: dt=0.9900, 375 negative triangles 223: dt=0.9900, 373 negative triangles 224: dt=0.9900, 372 negative triangles 225: dt=0.9900, 378 negative triangles 226: dt=0.9900, 375 negative triangles 227: dt=0.9900, 369 negative triangles 228: dt=0.9900, 371 negative triangles 229: dt=0.9900, 367 negative triangles 230: dt=0.9900, 368 negative triangles 231: dt=0.9900, 364 negative triangles 232: dt=0.9900, 373 negative triangles 233: dt=0.9900, 368 negative triangles 234: dt=0.9900, 372 negative triangles 235: dt=0.9900, 372 negative triangles 236: dt=0.9900, 372 negative triangles 237: dt=0.9900, 361 negative triangles 238: dt=0.9900, 359 negative triangles 239: dt=0.9900, 364 negative triangles 240: dt=0.9900, 366 negative triangles 241: dt=0.9900, 364 negative triangles 242: dt=0.9900, 360 negative triangles 243: dt=0.9900, 360 negative triangles 244: dt=0.9900, 363 negative triangles 245: dt=0.9900, 365 negative triangles 246: dt=0.9900, 364 negative triangles 247: dt=0.9900, 357 negative triangles 248: dt=0.9900, 360 negative triangles 249: dt=0.9900, 351 negative triangles 250: dt=0.9900, 369 negative triangles 251: dt=0.9900, 355 negative triangles 252: dt=0.9900, 358 negative triangles 253: dt=0.9900, 350 negative triangles 254: dt=0.9900, 351 negative triangles 255: dt=0.9900, 353 negative triangles 256: dt=0.9900, 359 negative triangles 257: dt=0.9900, 353 negative triangles 258: dt=0.9900, 354 negative triangles 259: dt=0.9900, 358 negative triangles 260: dt=0.9900, 358 negative triangles 261: dt=0.9900, 362 negative triangles 262: dt=0.9900, 348 negative triangles 263: dt=0.9900, 360 negative triangles 264: dt=0.9900, 356 negative triangles 265: dt=0.9900, 356 negative triangles 266: dt=0.9900, 357 negative triangles 267: dt=0.9900, 353 negative triangles 268: dt=0.9900, 354 negative triangles 269: dt=0.9900, 356 negative triangles 270: dt=0.9900, 354 negative triangles 271: dt=0.9900, 364 negative triangles 272: dt=0.9405, 350 negative triangles 273: dt=0.9405, 360 negative triangles 274: dt=0.9405, 352 negative triangles 275: dt=0.9405, 353 negative triangles 276: dt=0.9405, 351 negative triangles 277: dt=0.9405, 349 negative triangles 278: dt=0.9405, 348 negative triangles 279: dt=0.9405, 356 negative triangles 280: dt=0.9405, 349 negative triangles 281: dt=0.9405, 351 negative triangles 282: dt=0.8935, 351 negative triangles 283: dt=0.8935, 350 negative triangles 284: dt=0.8935, 354 negative triangles 285: dt=0.8935, 353 negative triangles 286: dt=0.8935, 349 negative triangles 287: dt=0.8935, 350 negative triangles 288: dt=0.8935, 356 negative triangles 289: dt=0.8935, 356 negative triangles 290: dt=0.8935, 354 negative triangles 291: dt=0.8935, 349 negative triangles 292: dt=0.8488, 350 negative triangles 293: dt=0.8488, 356 negative triangles 294: dt=0.8488, 351 negative triangles 295: dt=0.8488, 348 negative triangles 296: dt=0.8488, 352 negative triangles 297: dt=0.8488, 354 negative triangles 298: dt=0.8488, 347 negative triangles 299: dt=0.8488, 353 negative triangles 300: dt=0.8488, 353 negative triangles 301: dt=0.8488, 354 negative triangles 302: dt=0.8488, 355 negative triangles 303: dt=0.8488, 360 negative triangles 304: dt=0.8488, 351 negative triangles 305: dt=0.8488, 348 negative triangles 306: dt=0.8488, 349 negative triangles 307: dt=0.8488, 342 negative triangles 308: dt=0.8488, 353 negative triangles 309: dt=0.8488, 352 negative triangles 310: dt=0.8488, 346 negative triangles 311: dt=0.8488, 349 negative triangles 312: dt=0.8488, 355 negative triangles 313: dt=0.8488, 355 negative triangles 314: dt=0.8488, 347 negative triangles 315: dt=0.8488, 358 negative triangles 316: dt=0.8488, 346 negative triangles 317: dt=0.8064, 354 negative triangles 318: dt=0.8064, 352 negative triangles 319: dt=0.8064, 357 negative triangles 320: dt=0.8064, 356 negative triangles 321: dt=0.8064, 350 negative triangles 322: dt=0.8064, 351 negative triangles 323: dt=0.8064, 354 negative triangles 324: dt=0.8064, 357 negative triangles 325: dt=0.8064, 356 negative triangles 326: dt=0.8064, 352 negative triangles 327: dt=0.7660, 352 negative triangles 328: dt=0.7660, 352 negative triangles 329: dt=0.7660, 353 negative triangles 330: dt=0.7660, 345 negative triangles 331: dt=0.7660, 355 negative triangles 332: dt=0.7660, 353 negative triangles 333: dt=0.7660, 356 negative triangles 334: dt=0.7660, 350 negative triangles 335: dt=0.7660, 353 negative triangles 336: dt=0.7660, 353 negative triangles 337: dt=0.7277, 355 negative triangles 338: dt=0.7277, 349 negative triangles 339: dt=0.7277, 350 negative triangles 340: dt=0.7277, 353 negative triangles 341: dt=0.7277, 352 negative triangles 342: dt=0.7277, 346 negative triangles 343: dt=0.7277, 351 negative triangles 344: dt=0.7277, 342 negative triangles 345: dt=0.7277, 345 negative triangles 346: dt=0.7277, 348 negative triangles 347: dt=0.6914, 347 negative triangles 348: dt=0.6914, 346 negative triangles 349: dt=0.6914, 352 negative triangles 350: dt=0.6914, 340 negative triangles 351: dt=0.6914, 348 negative triangles 352: dt=0.6914, 336 negative triangles 353: dt=0.6914, 357 negative triangles 354: dt=0.6914, 349 negative triangles 355: dt=0.6914, 345 negative triangles 356: dt=0.6914, 354 negative triangles 357: dt=0.6914, 354 negative triangles 358: dt=0.6914, 354 negative triangles 359: dt=0.6914, 350 negative triangles 360: dt=0.6914, 350 negative triangles 361: dt=0.6914, 357 negative triangles 362: dt=0.6568, 356 negative triangles 363: dt=0.6568, 352 negative triangles 364: dt=0.6568, 347 negative triangles 365: dt=0.6568, 352 negative triangles 366: dt=0.6568, 341 negative triangles 367: dt=0.6568, 350 negative triangles 368: dt=0.6568, 344 negative triangles 369: dt=0.6568, 348 negative triangles 370: dt=0.6568, 347 negative triangles 371: dt=0.6568, 353 negative triangles 372: dt=0.6239, 350 negative triangles 373: dt=0.6239, 345 negative triangles 374: dt=0.6239, 336 negative triangles 375: dt=0.6239, 346 negative triangles 376: dt=0.6239, 341 negative triangles 377: dt=0.6239, 355 negative triangles 378: dt=0.6239, 349 negative triangles 379: dt=0.6239, 347 negative triangles 380: dt=0.6239, 350 negative triangles 381: dt=0.6239, 346 negative triangles 382: dt=0.5927, 357 negative triangles 383: dt=0.5927, 342 negative triangles 384: dt=0.5927, 338 negative triangles 385: dt=0.5927, 348 negative triangles 386: dt=0.5927, 342 negative triangles 387: dt=0.5927, 354 negative triangles 388: dt=0.5927, 351 negative triangles 389: dt=0.5927, 343 negative triangles 390: dt=0.5927, 344 negative triangles 391: dt=0.5927, 344 negative triangles 392: dt=0.5631, 339 negative triangles 393: dt=0.5631, 342 negative triangles 394: dt=0.5631, 344 negative triangles 395: dt=0.5631, 338 negative triangles 396: dt=0.5631, 348 negative triangles 397: dt=0.5631, 351 negative triangles 398: dt=0.5631, 348 negative triangles 399: dt=0.5631, 344 negative triangles 400: dt=0.5631, 338 negative triangles 401: dt=0.5631, 346 negative triangles 402: dt=0.5350, 346 negative triangles expanding nbhd size to 1 403: dt=0.9900, 343 negative triangles 404: dt=0.9900, 336 negative triangles 405: dt=0.9900, 331 negative triangles 406: dt=0.9900, 346 negative triangles 407: dt=0.9900, 347 negative triangles 408: dt=0.9900, 337 negative triangles 409: dt=0.9900, 335 negative triangles 410: dt=0.9900, 336 negative triangles 411: dt=0.9900, 339 negative triangles 412: dt=0.9900, 332 negative triangles 413: dt=0.9900, 340 negative triangles 414: dt=0.9900, 337 negative triangles 415: dt=0.9405, 335 negative triangles 416: dt=0.9405, 336 negative triangles 417: dt=0.9405, 339 negative triangles 418: dt=0.9405, 342 negative triangles 419: dt=0.9405, 347 negative triangles 420: dt=0.9405, 338 negative triangles 421: dt=0.9405, 337 negative triangles 422: dt=0.9405, 336 negative triangles 423: dt=0.9405, 338 negative triangles 424: dt=0.9405, 336 negative triangles 425: dt=0.8935, 344 negative triangles 426: dt=0.8935, 340 negative triangles 427: dt=0.8935, 343 negative triangles 428: dt=0.8935, 339 negative triangles 429: dt=0.8935, 334 negative triangles 430: dt=0.8935, 339 negative triangles 431: dt=0.8935, 338 negative triangles 432: dt=0.8935, 335 negative triangles 433: dt=0.8935, 338 negative triangles 434: dt=0.8935, 338 negative triangles 435: dt=0.8488, 339 negative triangles 436: dt=0.8488, 331 negative triangles 437: dt=0.8488, 337 negative triangles 438: dt=0.8488, 332 negative triangles 439: dt=0.8488, 330 negative triangles 440: dt=0.8488, 334 negative triangles 441: dt=0.8488, 333 negative triangles 442: dt=0.8488, 333 negative triangles 443: dt=0.8488, 333 negative triangles 444: dt=0.8488, 336 negative triangles 445: dt=0.8488, 337 negative triangles 446: dt=0.8488, 339 negative triangles 447: dt=0.8488, 337 negative triangles 448: dt=0.8488, 333 negative triangles 449: dt=0.8064, 336 negative triangles 450: dt=0.8064, 337 negative triangles 451: dt=0.8064, 336 negative triangles 452: dt=0.8064, 333 negative triangles 453: dt=0.8064, 336 negative triangles 454: dt=0.8064, 338 negative triangles 455: dt=0.8064, 340 negative triangles 456: dt=0.8064, 342 negative triangles 457: dt=0.8064, 337 negative triangles 458: dt=0.8064, 336 negative triangles 459: dt=0.7660, 337 negative triangles 460: dt=0.7660, 339 negative triangles 461: dt=0.7660, 341 negative triangles 462: dt=0.7660, 338 negative triangles 463: dt=0.7660, 338 negative triangles 464: dt=0.7660, 339 negative triangles 465: dt=0.7660, 336 negative triangles 466: dt=0.7660, 335 negative triangles 467: dt=0.7660, 337 negative triangles 468: dt=0.7660, 342 negative triangles 469: dt=0.7277, 338 negative triangles 470: dt=0.7277, 343 negative triangles 471: dt=0.7277, 339 negative triangles 472: dt=0.7277, 339 negative triangles 473: dt=0.7277, 338 negative triangles 474: dt=0.7277, 336 negative triangles 475: dt=0.7277, 332 negative triangles 476: dt=0.7277, 340 negative triangles 477: dt=0.7277, 337 negative triangles 478: dt=0.7277, 331 negative triangles 479: dt=0.6914, 338 negative triangles 480: dt=0.6914, 335 negative triangles 481: dt=0.6914, 342 negative triangles 482: dt=0.6914, 336 negative triangles 483: dt=0.6914, 335 negative triangles 484: dt=0.6914, 337 negative triangles 485: dt=0.6914, 337 negative triangles 486: dt=0.6914, 335 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negative triangles 1024: dt=0.0480, 348 negative triangles 1025: dt=0.0480, 348 negative triangles 1026: dt=0.0456, 350 negative triangles 1027: dt=0.0456, 347 negative triangles 1028: dt=0.0456, 348 negative triangles 1029: dt=0.0456, 344 negative triangles 1030: dt=0.0456, 345 negative triangles 1031: dt=0.0456, 342 negative triangles 1032: dt=0.0456, 338 negative triangles 1033: dt=0.0456, 339 negative triangles 1034: dt=0.0456, 339 negative triangles 1035: dt=0.0456, 340 negative triangles 1036: dt=0.0433, 338 negative triangles 1037: dt=0.0433, 340 negative triangles 1038: dt=0.0433, 338 negative triangles 1039: dt=0.0433, 337 negative triangles 1040: dt=0.0433, 341 negative triangles 1041: dt=0.0433, 340 negative triangles 1042: dt=0.0433, 338 negative triangles 1043: dt=0.0433, 338 negative triangles 1044: dt=0.0433, 340 negative triangles 1045: dt=0.0433, 338 negative triangles 1046: dt=0.0412, 340 negative triangles 1047: dt=0.0412, 337 negative triangles 1048: dt=0.0412, 336 negative triangles 1049: dt=0.0412, 334 negative triangles 1050: dt=0.0412, 340 negative triangles 1051: dt=0.0412, 337 negative triangles 1052: dt=0.0412, 345 negative triangles 1053: dt=0.0412, 342 negative triangles 1054: dt=0.0412, 345 negative triangles 1055: dt=0.0412, 342 negative triangles 1056: dt=0.0391, 341 negative triangles 1057: dt=0.0391, 341 negative triangles 1058: dt=0.0391, 347 negative triangles 1059: dt=0.0391, 343 negative triangles 1060: dt=0.0391, 342 negative triangles 1061: dt=0.0391, 346 negative triangles 1062: dt=0.0391, 345 negative triangles 1063: dt=0.0391, 340 negative triangles 1064: dt=0.0391, 337 negative triangles 1065: dt=0.0391, 336 negative triangles 1066: dt=0.0371, 337 negative triangles 1067: dt=0.0371, 335 negative triangles 1068: dt=0.0371, 340 negative triangles 1069: dt=0.0371, 341 negative triangles 1070: dt=0.0371, 339 negative triangles 1071: dt=0.0371, 337 negative triangles 1072: dt=0.0371, 339 negative triangles 1073: dt=0.0371, 343 negative triangles 1074: dt=0.0371, 343 negative triangles 1075: dt=0.0371, 346 negative triangles 1076: dt=0.0353, 340 negative triangles 1077: dt=0.0353, 336 negative triangles 1078: dt=0.0353, 341 negative triangles 1079: dt=0.0353, 338 negative triangles 1080: dt=0.0353, 338 negative triangles 1081: dt=0.0353, 335 negative triangles 1082: dt=0.0353, 331 negative triangles 1083: dt=0.0353, 329 negative triangles 1084: dt=0.0353, 329 negative triangles 1085: dt=0.0353, 328 negative triangles 1086: dt=0.0335, 330 negative triangles 1087: dt=0.0335, 332 negative triangles 1088: dt=0.0335, 330 negative triangles 1089: dt=0.0335, 332 negative triangles 1090: dt=0.0335, 334 negative triangles 1091: dt=0.0335, 333 negative triangles 1092: dt=0.0335, 330 negative triangles 1093: dt=0.0335, 334 negative triangles 1094: dt=0.0335, 342 negative triangles 1095: dt=0.0335, 334 negative triangles 1096: dt=0.0319, 336 negative triangles 1097: dt=0.0319, 334 negative triangles 1098: dt=0.0319, 334 negative triangles 1099: dt=0.0319, 330 negative triangles 1100: dt=0.0319, 336 negative triangles 1101: dt=0.0319, 333 negative triangles 1102: dt=0.0319, 333 negative triangles 1103: dt=0.0319, 334 negative triangles 1104: dt=0.0319, 334 negative triangles 1105: dt=0.0319, 334 negative triangles 1106: dt=0.0303, 337 negative triangles 1107: dt=0.0303, 335 negative triangles 1108: dt=0.0303, 333 negative triangles 1109: dt=0.0303, 335 negative triangles 1110: dt=0.0303, 336 negative triangles 1111: dt=0.0303, 341 negative triangles 1112: dt=0.0303, 334 negative triangles 1113: dt=0.0303, 334 negative triangles 1114: dt=0.0303, 335 negative triangles 1115: dt=0.0303, 335 negative triangles 1116: dt=0.0287, 337 negative triangles 1117: dt=0.0287, 333 negative triangles 1118: dt=0.0287, 337 negative triangles 1119: dt=0.0287, 334 negative triangles 1120: dt=0.0287, 338 negative triangles 1121: dt=0.0287, 336 negative triangles 1122: dt=0.0287, 333 negative triangles 1123: dt=0.0287, 338 negative triangles 1124: dt=0.0287, 339 negative triangles 1125: dt=0.0287, 340 negative triangles 1126: dt=0.0273, 341 negative triangles 1127: dt=0.0273, 342 negative triangles 1128: dt=0.0273, 343 negative triangles 1129: dt=0.0273, 340 negative triangles 1130: dt=0.0273, 340 negative triangles 1131: dt=0.0273, 344 negative triangles 1132: dt=0.0273, 346 negative triangles 1133: dt=0.0273, 341 negative triangles 1134: dt=0.0273, 339 negative triangles 1135: dt=0.0273, 343 negative triangles 1136: dt=0.0259, 341 negative triangles 1137: dt=0.0259, 337 negative triangles 1138: dt=0.0259, 344 negative triangles 1139: dt=0.0259, 339 negative triangles 1140: dt=0.0259, 342 negative triangles 1141: dt=0.0259, 343 negative triangles 1142: dt=0.0259, 346 negative triangles 1143: dt=0.0259, 344 negative triangles 1144: dt=0.0259, 347 negative triangles 1145: dt=0.0259, 347 negative triangles 1146: dt=0.0246, 339 negative triangles 1147: dt=0.0246, 343 negative triangles 1148: dt=0.0246, 346 negative triangles 1149: dt=0.0246, 346 negative triangles 1150: dt=0.0246, 351 negative triangles 1151: dt=0.0246, 354 negative triangles 1152: dt=0.0246, 352 negative triangles 1153: dt=0.0246, 348 negative triangles 1154: dt=0.0246, 344 negative triangles 1155: dt=0.0246, 345 negative triangles 1156: dt=0.0234, 347 negative triangles 1157: dt=0.0234, 348 negative triangles 1158: dt=0.0234, 348 negative triangles 1159: dt=0.0234, 345 negative triangles 1160: dt=0.0234, 352 negative triangles 1161: dt=0.0234, 344 negative triangles 1162: dt=0.0234, 342 negative triangles 1163: dt=0.0234, 342 negative triangles 1164: dt=0.0234, 343 negative triangles 1165: dt=0.0234, 341 negative triangles 1166: dt=0.0222, 339 negative triangles 1167: dt=0.0222, 339 negative triangles 1168: dt=0.0222, 342 negative triangles 1169: dt=0.0222, 338 negative triangles 1170: dt=0.0222, 337 negative triangles 1171: dt=0.0222, 338 negative triangles 1172: dt=0.0222, 338 negative triangles 1173: dt=0.0222, 333 negative triangles 1174: dt=0.0222, 332 negative triangles 1175: dt=0.0222, 338 negative triangles 1176: dt=0.0211, 341 negative triangles 1177: dt=0.0211, 342 negative triangles 1178: dt=0.0211, 335 negative triangles 1179: dt=0.0211, 336 negative triangles 1180: dt=0.0211, 338 negative triangles 1181: dt=0.0211, 340 negative triangles 1182: dt=0.0211, 345 negative triangles 1183: dt=0.0211, 347 negative triangles 1184: dt=0.0211, 346 negative triangles 1185: dt=0.0211, 347 negative triangles 1186: dt=0.0201, 341 negative triangles 1187: dt=0.0201, 345 negative triangles 1188: dt=0.0201, 344 negative triangles 1189: dt=0.0201, 341 negative triangles 1190: dt=0.0201, 337 negative triangles 1191: dt=0.0201, 338 negative triangles 1192: dt=0.0201, 342 negative triangles 1193: dt=0.0201, 342 negative triangles 1194: dt=0.0201, 344 negative triangles 1195: dt=0.0201, 343 negative triangles 1196: dt=0.0191, 343 negative triangles 1197: dt=0.0191, 339 negative triangles 1198: dt=0.0191, 341 negative triangles 1199: dt=0.0191, 336 negative triangles 1200: dt=0.0191, 338 negative triangles 1201: dt=0.0191, 338 negative triangles 1202: dt=0.0191, 334 negative triangles 1203: dt=0.0191, 335 negative triangles 1204: 330 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1073 hours FSRUNTIME@ mris_sphere 0.1073 hours 4 threads #VMPC# mris_sphere VmPeak 713988 mris_sphere done PIDs (739535 739538) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Tue Jan 10 12:58:08 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_register -curv ../surf/lh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Tue Jan 10 12:58:08 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_register -curv ../surf/rh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 739648 of (739648 739651) to complete... Waiting for PID 739651 of (739648 739651) to complete... mris_register -curv ../surf/lh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts cmdline mris_register -curv ../surf/lh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/lh.sphere... reading template parameterization from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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=shark, 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=shark, 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=shark, 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 = 5.333 curvature mean = 0.037, std = 0.819 curvature mean = 0.013, std = 0.877 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (3.00, -11.00, -11.50) sse = 198827.1, elapsed since starting=0.0829 min MRISrigidBodyAlignGlobal() done 0.08 min curvature mean = 0.013, std = 0.845 curvature mean = 0.005, std = 0.954 curvature mean = 0.009, std = 0.854 curvature mean = 0.002, std = 0.982 curvature mean = 0.009, std = 0.858 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.024, std = 0.284 curvature mean = 0.045, std = 0.250 curvature mean = 0.055, std = 0.370 curvature mean = 0.037, std = 0.312 curvature mean = 0.032, std = 0.560 curvature mean = 0.036, std = 0.340 curvature mean = 0.017, std = 0.697 curvature mean = 0.036, std = 0.351 curvature mean = 0.006, std = 0.803 MRISregister() return, current seed 0 -01: dt=0.0000, 24 negative triangles VmPeak 771632 108: dt=0.9900, 24 negative triangles expanding nbhd size to 1 109: dt=0.9900, 27 negative triangles 110: dt=0.9900, 23 negative triangles 111: dt=0.9900, 20 negative triangles 112: dt=0.9900, 21 negative triangles 113: dt=0.9900, 22 negative triangles 114: dt=0.9900, 22 negative triangles 115: dt=0.9900, 21 negative triangles 116: dt=0.9900, 21 negative triangles 117: dt=0.9900, 21 negative triangles 118: dt=0.9900, 20 negative triangles 119: dt=0.9900, 20 negative triangles 120: dt=0.9900, 20 negative triangles 121: dt=0.9900, 19 negative triangles 122: dt=0.9900, 18 negative triangles 123: dt=0.9900, 18 negative triangles 124: dt=0.9900, 18 negative triangles 125: dt=0.9900, 18 negative triangles 126: dt=0.9900, 18 negative triangles 127: dt=0.9900, 18 negative triangles 128: dt=0.9900, 17 negative triangles 129: dt=0.9900, 18 negative triangles 130: dt=0.9900, 17 negative triangles 131: dt=0.9900, 17 negative triangles 132: dt=0.9900, 17 negative triangles 133: dt=0.9900, 17 negative triangles 134: dt=0.9900, 16 negative triangles 135: dt=0.9900, 14 negative triangles 136: dt=0.9900, 13 negative triangles 137: dt=0.9900, 13 negative triangles 138: dt=0.9900, 12 negative triangles 139: dt=0.9900, 11 negative triangles 140: dt=0.9900, 11 negative triangles 141: dt=0.9900, 11 negative triangles 142: dt=0.9900, 11 negative triangles 143: dt=0.9900, 11 negative triangles 144: dt=0.9900, 11 negative triangles 145: dt=0.9900, 11 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 11 negative triangles 148: dt=0.9900, 10 negative triangles 149: dt=0.9900, 9 negative triangles 150: dt=0.9900, 10 negative triangles 151: dt=0.9900, 9 negative triangles 152: dt=0.9900, 9 negative triangles 153: dt=0.9900, 7 negative triangles 154: dt=0.9900, 7 negative triangles 155: dt=0.9900, 7 negative triangles 156: dt=0.9900, 7 negative triangles 157: dt=0.9900, 7 negative triangles 158: dt=0.9900, 7 negative triangles 159: dt=0.9900, 6 negative triangles 160: dt=0.9900, 6 negative triangles 161: dt=0.9900, 6 negative triangles 162: dt=0.9900, 5 negative triangles 163: dt=0.9900, 5 negative triangles 164: dt=0.9900, 4 negative triangles 165: dt=0.9900, 4 negative triangles 166: dt=0.9900, 4 negative triangles 167: dt=0.9900, 4 negative triangles 168: dt=0.9900, 3 negative triangles 169: dt=0.9900, 3 negative triangles 170: dt=0.9900, 3 negative triangles 171: dt=0.9900, 3 negative triangles 172: dt=0.9900, 3 negative triangles 173: dt=0.9900, 2 negative triangles 174: dt=0.9900, 2 negative triangles 175: dt=0.9900, 2 negative triangles 176: dt=0.9900, 2 negative triangles 177: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.05 hours #VMPC# mris_register VmPeak 771632 FSRUNTIME@ mris_register 0.0542 hours 4 threads mris_register -curv ../surf/rh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts cmdline mris_register -curv ../surf/rh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/rh.sphere... reading template parameterization from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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=shark, 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=shark, 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=shark, 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 = 5.437 curvature mean = 0.035, std = 0.809 curvature mean = 0.013, std = 0.882 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (9.50, -14.50, -7.00) sse = 196128.6, elapsed since starting=0.0748 min MRISrigidBodyAlignGlobal() done 0.07 min curvature mean = 0.016, std = 0.834 curvature mean = 0.005, std = 0.957 curvature mean = 0.015, std = 0.845 curvature mean = 0.002, std = 0.983 curvature mean = 0.014, std = 0.848 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.029, std = 1.264 curvature mean = 0.041, std = 0.239 curvature mean = 0.016, std = 0.084 curvature mean = 0.034, std = 0.300 curvature mean = 0.009, std = 0.130 curvature mean = 0.034, std = 0.327 curvature mean = 0.005, std = 0.166 curvature mean = 0.034, std = 0.338 curvature mean = 0.002, std = 0.211 MRISregister() return, current seed 0 -01: dt=0.0000, 422 negative triangles VmPeak 768948 111: dt=0.9900, 422 negative triangles expanding nbhd size to 1 112: dt=0.9900, 437 negative triangles 113: dt=0.9900, 420 negative triangles 114: dt=0.9900, 415 negative triangles 115: dt=0.9900, 417 negative triangles 116: dt=0.9900, 414 negative triangles 117: dt=0.9900, 423 negative triangles 118: dt=0.9900, 421 negative triangles 119: dt=0.9900, 416 negative triangles 120: dt=0.9900, 416 negative triangles 121: dt=0.9900, 415 negative triangles 122: dt=0.9900, 416 negative triangles 123: dt=0.9900, 413 negative triangles 124: dt=0.9900, 411 negative triangles 125: dt=0.9900, 409 negative triangles 126: dt=0.9900, 405 negative triangles 127: dt=0.9900, 404 negative triangles 128: dt=0.9900, 400 negative triangles 129: dt=0.9900, 397 negative triangles 130: dt=0.9900, 396 negative triangles 131: dt=0.9900, 391 negative triangles 132: dt=0.9900, 391 negative triangles 133: dt=0.9900, 392 negative triangles 134: dt=0.9900, 393 negative triangles 135: dt=0.9900, 394 negative triangles 136: dt=0.9900, 395 negative triangles 137: dt=0.9900, 396 negative triangles 138: dt=0.9900, 394 negative triangles 139: dt=0.9900, 393 negative triangles 140: dt=0.9900, 396 negative triangles 141: dt=0.9405, 394 negative triangles 142: dt=0.9405, 394 negative triangles 143: dt=0.9405, 397 negative triangles 144: dt=0.9405, 396 negative triangles 145: dt=0.9405, 394 negative triangles 146: dt=0.9405, 396 negative triangles 147: dt=0.9405, 393 negative triangles 148: dt=0.9405, 391 negative triangles 149: dt=0.9405, 392 negative triangles 150: dt=0.9405, 393 negative triangles 151: dt=0.8935, 394 negative triangles 152: dt=0.8935, 396 negative triangles 153: dt=0.8935, 394 negative triangles 154: dt=0.8935, 394 negative triangles 155: dt=0.8935, 396 negative triangles 156: dt=0.8935, 393 negative triangles 157: dt=0.8935, 391 negative triangles 158: dt=0.8935, 390 negative triangles 159: dt=0.8935, 387 negative triangles 160: dt=0.8935, 391 negative triangles 161: dt=0.8935, 390 negative triangles 162: dt=0.8935, 391 negative triangles 163: dt=0.8935, 390 negative triangles 164: dt=0.8935, 393 negative triangles 165: dt=0.8935, 396 negative triangles 166: dt=0.8935, 392 negative triangles 167: dt=0.8935, 392 negative triangles 168: dt=0.8935, 391 negative triangles 169: dt=0.8488, 390 negative triangles 170: dt=0.8488, 386 negative triangles 171: dt=0.8488, 386 negative triangles 172: dt=0.8488, 387 negative triangles 173: dt=0.8488, 390 negative triangles 174: dt=0.8488, 385 negative triangles 175: dt=0.8488, 390 negative triangles 176: dt=0.8488, 385 negative triangles 177: dt=0.8488, 387 negative triangles 178: dt=0.8488, 389 negative triangles 179: dt=0.8488, 385 negative triangles 180: dt=0.8488, 387 negative triangles 181: dt=0.8488, 385 negative triangles 182: dt=0.8488, 383 negative triangles 183: dt=0.8488, 384 negative triangles 184: dt=0.8488, 388 negative triangles 185: dt=0.8488, 387 negative triangles 186: dt=0.8488, 389 negative triangles 187: dt=0.8488, 381 negative triangles 188: dt=0.8488, 391 negative triangles 189: dt=0.8488, 389 negative triangles 190: dt=0.8488, 390 negative triangles 191: dt=0.8488, 390 negative triangles 192: dt=0.8488, 394 negative triangles 193: dt=0.8488, 397 negative triangles 194: dt=0.8488, 390 negative triangles 195: dt=0.8488, 389 negative triangles 196: dt=0.8488, 392 negative triangles 197: dt=0.8064, 383 negative triangles 198: dt=0.8064, 386 negative triangles 199: dt=0.8064, 390 negative triangles 200: dt=0.8064, 391 negative triangles 201: dt=0.8064, 394 negative triangles 202: dt=0.8064, 394 negative triangles 203: dt=0.8064, 391 negative triangles 204: dt=0.8064, 393 negative triangles 205: dt=0.8064, 387 negative triangles 206: dt=0.8064, 386 negative triangles 207: dt=0.7660, 387 negative triangles 208: dt=0.7660, 388 negative triangles 209: dt=0.7660, 391 negative triangles 210: dt=0.7660, 385 negative triangles 211: dt=0.7660, 390 negative triangles 212: dt=0.7660, 385 negative triangles 213: dt=0.7660, 385 negative triangles 214: dt=0.7660, 386 negative triangles 215: dt=0.7660, 386 negative triangles 216: dt=0.7660, 384 negative triangles 217: dt=0.7277, 385 negative triangles 218: dt=0.7277, 387 negative triangles 219: dt=0.7277, 387 negative triangles 220: dt=0.7277, 385 negative triangles 221: dt=0.7277, 391 negative triangles 222: dt=0.7277, 385 negative triangles 223: dt=0.7277, 390 negative triangles 224: dt=0.7277, 385 negative triangles 225: dt=0.7277, 385 negative triangles 226: dt=0.7277, 378 negative triangles 227: dt=0.7277, 379 negative triangles 228: dt=0.7277, 381 negative triangles 229: dt=0.7277, 386 negative triangles 230: dt=0.7277, 387 negative triangles 231: dt=0.7277, 386 negative triangles 232: dt=0.7277, 386 negative triangles 233: dt=0.7277, 386 negative triangles 234: dt=0.7277, 388 negative triangles 235: dt=0.7277, 384 negative triangles 236: dt=0.6914, 382 negative triangles 237: dt=0.6914, 382 negative triangles 238: dt=0.6914, 384 negative triangles 239: dt=0.6914, 383 negative triangles 240: dt=0.6914, 390 negative triangles 241: dt=0.6914, 387 negative triangles 242: dt=0.6914, 380 negative triangles 243: dt=0.6914, 383 negative triangles 244: dt=0.6914, 383 negative triangles 245: dt=0.6914, 383 negative triangles 246: dt=0.6568, 386 negative triangles 247: dt=0.6568, 382 negative triangles 248: dt=0.6568, 387 negative triangles 249: dt=0.6568, 383 negative triangles 250: dt=0.6568, 382 negative triangles 251: dt=0.6568, 383 negative triangles 252: dt=0.6568, 382 negative triangles 253: dt=0.6568, 380 negative triangles 254: dt=0.6568, 383 negative triangles 255: dt=0.6568, 384 negative triangles 256: dt=0.6239, 379 negative triangles 257: dt=0.6239, 389 negative triangles 258: dt=0.6239, 386 negative triangles 259: dt=0.6239, 392 negative triangles 260: dt=0.6239, 392 negative triangles 261: dt=0.6239, 388 negative triangles 262: dt=0.6239, 384 negative triangles 263: dt=0.6239, 386 negative triangles 264: dt=0.6239, 385 negative triangles 265: dt=0.6239, 387 negative triangles 266: dt=0.5927, 384 negative triangles 267: dt=0.5927, 383 negative triangles 268: dt=0.5927, 387 negative triangles 269: dt=0.5927, 385 negative triangles 270: dt=0.5927, 381 negative triangles 271: dt=0.5927, 389 negative triangles 272: dt=0.5927, 390 negative triangles 273: dt=0.5927, 383 negative triangles 274: dt=0.5927, 384 negative triangles 275: dt=0.5927, 385 negative triangles 276: dt=0.5631, 384 negative triangles 277: dt=0.5631, 387 negative triangles 278: dt=0.5631, 385 negative triangles 279: dt=0.5631, 388 negative triangles 280: dt=0.5631, 382 negative triangles 281: dt=0.5631, 384 negative triangles 282: dt=0.5631, 383 negative triangles 283: dt=0.5631, 381 negative triangles 284: dt=0.5631, 387 negative triangles 285: dt=0.5631, 388 negative triangles 286: dt=0.5350, 384 negative triangles 287: dt=0.5350, 383 negative triangles 288: dt=0.5350, 380 negative triangles 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dt=0.2609, 374 negative triangles 469: dt=0.2609, 376 negative triangles 470: dt=0.2609, 379 negative triangles 471: dt=0.2609, 371 negative triangles 472: dt=0.2609, 377 negative triangles 473: dt=0.2609, 375 negative triangles 474: dt=0.2478, 371 negative triangles 475: dt=0.2478, 374 negative triangles 476: dt=0.2478, 372 negative triangles 477: dt=0.2478, 374 negative triangles 478: dt=0.2478, 374 negative triangles 479: dt=0.2478, 376 negative triangles 480: dt=0.2478, 373 negative triangles 481: dt=0.2478, 373 negative triangles 482: dt=0.2478, 369 negative triangles 483: dt=0.2478, 370 negative triangles 484: dt=0.2354, 370 negative triangles 485: dt=0.2354, 370 negative triangles 486: dt=0.2354, 373 negative triangles 487: dt=0.2354, 369 negative triangles 488: dt=0.2354, 365 negative triangles 489: dt=0.2354, 358 negative triangles 490: dt=0.2354, 369 negative triangles 491: dt=0.2354, 363 negative triangles 492: dt=0.2354, 369 negative triangles 493: dt=0.2354, 369 negative 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366 negative triangles 520: dt=0.2019, 372 negative triangles 521: dt=0.2019, 373 negative triangles 522: dt=0.2019, 368 negative triangles 523: dt=0.2019, 367 negative triangles 524: dt=0.2019, 361 negative triangles 525: dt=0.2019, 358 negative triangles 526: dt=0.2019, 367 negative triangles 527: dt=0.2019, 372 negative triangles 528: dt=0.2019, 369 negative triangles 529: dt=0.1918, 372 negative triangles 530: dt=0.1918, 368 negative triangles 531: dt=0.1918, 368 negative triangles 532: dt=0.1918, 364 negative triangles 533: dt=0.1918, 374 negative triangles 534: dt=0.1918, 371 negative triangles 535: dt=0.1918, 375 negative triangles 536: dt=0.1918, 376 negative triangles 537: dt=0.1918, 380 negative triangles 538: dt=0.1918, 376 negative triangles 539: dt=0.1822, 384 negative triangles 540: dt=0.1822, 382 negative triangles 541: dt=0.1822, 386 negative triangles 542: dt=0.1822, 381 negative triangles 543: dt=0.1822, 371 negative triangles 544: dt=0.1822, 374 negative triangles 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dt=0.1410, 367 negative triangles 597: dt=0.1410, 365 negative triangles 598: dt=0.1410, 367 negative triangles 599: dt=0.1339, 366 negative triangles 600: dt=0.1339, 367 negative triangles 601: dt=0.1339, 370 negative triangles 602: dt=0.1339, 368 negative triangles 603: dt=0.1339, 374 negative triangles 604: dt=0.1339, 373 negative triangles 605: dt=0.1339, 373 negative triangles 606: dt=0.1339, 377 negative triangles 607: dt=0.1339, 365 negative triangles 608: dt=0.1339, 368 negative triangles 609: dt=0.1272, 374 negative triangles 610: dt=0.1272, 368 negative triangles 611: dt=0.1272, 368 negative triangles 612: dt=0.1272, 370 negative triangles 613: dt=0.1272, 367 negative triangles 614: dt=0.1272, 368 negative triangles 615: dt=0.1272, 368 negative triangles 616: dt=0.1272, 363 negative triangles 617: dt=0.1272, 365 negative triangles 618: dt=0.1272, 362 negative triangles 619: dt=0.1209, 361 negative triangles 620: dt=0.1209, 355 negative triangles 621: dt=0.1209, 359 negative 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371 negative triangles 648: dt=0.1091, 368 negative triangles 649: dt=0.1091, 367 negative triangles 650: dt=0.1036, 372 negative triangles 651: dt=0.1036, 367 negative triangles 652: dt=0.1036, 361 negative triangles 653: dt=0.1036, 366 negative triangles 654: dt=0.1036, 363 negative triangles 655: dt=0.1036, 373 negative triangles 656: dt=0.1036, 367 negative triangles 657: dt=0.1036, 367 negative triangles 658: dt=0.1036, 373 negative triangles 659: dt=0.1036, 379 negative triangles 660: dt=0.0984, 372 negative triangles 661: dt=0.0984, 371 negative triangles 662: dt=0.0984, 380 negative triangles 663: dt=0.0984, 375 negative triangles 664: dt=0.0984, 372 negative triangles 665: dt=0.0984, 369 negative triangles 666: dt=0.0984, 369 negative triangles 667: dt=0.0984, 371 negative triangles 668: dt=0.0984, 373 negative triangles 669: dt=0.0984, 378 negative triangles 670: dt=0.0935, 373 negative triangles 671: dt=0.0935, 366 negative triangles 672: dt=0.0935, 361 negative triangles 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negative triangles 827: dt=0.0433, 391 negative triangles 828: dt=0.0433, 393 negative triangles 829: dt=0.0433, 392 negative triangles 830: dt=0.0412, 395 negative triangles 831: dt=0.0412, 391 negative triangles 832: dt=0.0412, 389 negative triangles 833: dt=0.0412, 388 negative triangles 834: dt=0.0412, 385 negative triangles 835: dt=0.0412, 385 negative triangles 836: dt=0.0412, 382 negative triangles 837: dt=0.0412, 390 negative triangles 838: dt=0.0412, 383 negative triangles 839: dt=0.0412, 384 negative triangles 840: dt=0.0391, 386 negative triangles 841: dt=0.0391, 387 negative triangles 842: dt=0.0391, 384 negative triangles 843: dt=0.0391, 385 negative triangles 844: dt=0.0391, 380 negative triangles 845: dt=0.0391, 380 negative triangles 846: dt=0.0391, 376 negative triangles 847: dt=0.0391, 382 negative triangles 848: dt=0.0391, 385 negative triangles 849: dt=0.0391, 383 negative triangles 850: dt=0.0371, 384 negative triangles 851: dt=0.0371, 382 negative triangles 852: dt=0.0371, 383 negative triangles 853: dt=0.0371, 383 negative triangles 854: dt=0.0371, 378 negative triangles 855: dt=0.0371, 375 negative triangles 856: dt=0.0371, 377 negative triangles 857: dt=0.0371, 376 negative triangles 858: dt=0.0371, 381 negative triangles 859: dt=0.0371, 379 negative triangles 860: dt=0.0353, 375 negative triangles 861: dt=0.0353, 382 negative triangles 862: dt=0.0353, 379 negative triangles 863: dt=0.0353, 378 negative triangles 864: dt=0.0353, 370 negative triangles 865: dt=0.0353, 371 negative triangles 866: dt=0.0353, 372 negative triangles 867: dt=0.0353, 374 negative triangles 868: dt=0.0353, 371 negative triangles 869: dt=0.0353, 370 negative triangles 870: dt=0.0335, 368 negative triangles 871: dt=0.0335, 369 negative triangles 872: dt=0.0335, 370 negative triangles 873: dt=0.0335, 367 negative triangles 874: dt=0.0335, 373 negative triangles 875: dt=0.0335, 375 negative triangles 876: dt=0.0335, 377 negative triangles 877: dt=0.0335, 377 negative triangles 878: dt=0.0335, 370 negative triangles 879: dt=0.0335, 366 negative triangles 880: dt=0.0319, 371 negative triangles 881: dt=0.0319, 365 negative triangles 882: dt=0.0319, 360 negative triangles 883: dt=0.0319, 364 negative triangles 884: dt=0.0319, 363 negative triangles 885: dt=0.0319, 365 negative triangles 886: dt=0.0319, 368 negative triangles 887: dt=0.0319, 365 negative triangles 888: dt=0.0319, 371 negative triangles 889: dt=0.0319, 374 negative triangles 890: dt=0.0303, 376 negative triangles 891: dt=0.0303, 380 negative triangles 892: dt=0.0303, 382 negative triangles 893: dt=0.0303, 383 negative triangles 894: dt=0.0303, 381 negative triangles 895: dt=0.0303, 384 negative triangles 896: dt=0.0303, 377 negative triangles 897: dt=0.0303, 378 negative triangles 898: dt=0.0303, 375 negative triangles 899: dt=0.0303, 378 negative triangles 900: dt=0.0287, 373 negative triangles 901: dt=0.0287, 379 negative triangles 902: dt=0.0287, 380 negative triangles 903: dt=0.0287, 373 negative triangles 904: dt=0.0287, 380 negative triangles 905: dt=0.0287, 372 negative triangles 906: dt=0.0287, 375 negative triangles 907: dt=0.0287, 371 negative triangles 908: dt=0.0287, 370 negative triangles 909: dt=0.0287, 367 negative triangles 910: dt=0.0273, 366 negative triangles 911: dt=0.0273, 367 negative triangles 912: dt=0.0273, 364 negative triangles 913: dt=0.0273, 365 negative triangles 914: dt=0.0273, 365 negative triangles 915: dt=0.0273, 370 negative triangles 916: dt=0.0273, 367 negative triangles 917: dt=0.0273, 365 negative triangles 918: dt=0.0273, 370 negative triangles 919: dt=0.0273, 370 negative triangles 920: dt=0.0259, 367 negative triangles 921: dt=0.0259, 365 negative triangles 922: dt=0.0259, 367 negative triangles 923: dt=0.0259, 367 negative triangles 924: dt=0.0259, 364 negative triangles 925: dt=0.0259, 363 negative triangles 926: dt=0.0259, 365 negative triangles 927: dt=0.0259, 366 negative triangles 928: dt=0.0259, 365 negative triangles 929: dt=0.0259, 366 negative triangles 930: dt=0.0246, 365 negative triangles 931: dt=0.0246, 367 negative triangles 932: dt=0.0246, 369 negative triangles 933: dt=0.0246, 368 negative triangles 934: dt=0.0246, 369 negative triangles 935: dt=0.0246, 365 negative triangles 936: dt=0.0246, 361 negative triangles 937: dt=0.0246, 363 negative triangles 938: dt=0.0246, 364 negative triangles 939: dt=0.0246, 360 negative triangles 940: dt=0.0234, 363 negative triangles 941: dt=0.0234, 368 negative triangles 942: dt=0.0234, 367 negative triangles 943: dt=0.0234, 371 negative triangles 944: dt=0.0234, 372 negative triangles 945: dt=0.0234, 376 negative triangles 946: dt=0.0234, 375 negative triangles 947: dt=0.0234, 374 negative triangles 948: dt=0.0234, 375 negative triangles 949: dt=0.0234, 376 negative triangles 950: dt=0.0222, 374 negative triangles 951: dt=0.0222, 373 negative triangles 952: dt=0.0222, 374 negative triangles 953: dt=0.0222, 369 negative triangles 954: dt=0.0222, 370 negative triangles 955: dt=0.0222, 372 negative triangles 956: dt=0.0222, 371 negative triangles 957: dt=0.0222, 371 negative triangles 958: dt=0.0222, 366 negative triangles 959: dt=0.0222, 369 negative triangles 960: dt=0.0211, 372 negative triangles 961: dt=0.0211, 377 negative triangles 962: dt=0.0211, 370 negative triangles 963: dt=0.0211, 373 negative triangles 964: dt=0.0211, 377 negative triangles 965: dt=0.0211, 376 negative triangles 966: dt=0.0211, 365 negative triangles 967: dt=0.0211, 367 negative triangles 968: dt=0.0211, 370 negative triangles 969: dt=0.0211, 366 negative triangles 970: dt=0.0201, 369 negative triangles 971: dt=0.0201, 377 negative triangles 972: dt=0.0201, 372 negative triangles 973: dt=0.0201, 370 negative triangles 974: dt=0.0201, 370 negative triangles 975: dt=0.0201, 369 negative triangles 976: dt=0.0201, 369 negative triangles 977: dt=0.0201, 367 negative triangles 978: dt=0.0201, 370 negative triangles 979: dt=0.0201, 374 negative triangles 980: dt=0.0191, 372 negative triangles 981: dt=0.0191, 375 negative triangles 982: dt=0.0191, 371 negative triangles 983: dt=0.0191, 377 negative triangles 984: dt=0.0191, 375 negative triangles 985: dt=0.0191, 377 negative triangles 986: dt=0.0191, 372 negative triangles 987: dt=0.0191, 376 negative triangles 988: dt=0.0191, 371 negative triangles 989: dt=0.0191, 374 negative triangles 990: dt=0.0181, 376 negative triangles 991: dt=0.0181, 379 negative triangles 992: dt=0.0181, 378 negative triangles 993: dt=0.0181, 379 negative triangles 994: dt=0.0181, 378 negative triangles 995: dt=0.0181, 381 negative triangles 996: dt=0.0181, 383 negative triangles 997: dt=0.0181, 385 negative triangles 998: dt=0.0181, 389 negative triangles 999: dt=0.0181, 392 negative triangles 1000: dt=0.0172, 392 negative triangles 1001: dt=0.0172, 388 negative triangles 1002: dt=0.0172, 384 negative triangles 1003: dt=0.0172, 383 negative triangles 1004: dt=0.0172, 385 negative triangles 1005: dt=0.0172, 385 negative triangles 1006: dt=0.0172, 382 negative triangles 1007: dt=0.0172, 382 negative triangles 1008: dt=0.0172, 382 negative triangles 1009: dt=0.0172, 381 negative triangles 1010: dt=0.0164, 380 negative triangles 1011: dt=0.0164, 382 negative triangles 1012: dt=0.0164, 382 negative triangles 1013: dt=0.0164, 386 negative triangles 1014: dt=0.0164, 383 negative triangles 1015: dt=0.0164, 384 negative triangles 1016: dt=0.0164, 383 negative triangles 1017: dt=0.0164, 378 negative triangles 1018: dt=0.0164, 384 negative triangles 1019: dt=0.0164, 383 negative triangles 1020: dt=0.0155, 386 negative triangles 1021: dt=0.0155, 379 negative triangles 1022: dt=0.0155, 378 negative triangles 1023: dt=0.0155, 379 negative triangles 1024: dt=0.0155, 378 negative triangles 1025: dt=0.0155, 375 negative triangles 1026: dt=0.0155, 374 negative triangles 1027: dt=0.0155, 375 negative triangles 1028: dt=0.0155, 379 negative triangles 1029: dt=0.0155, 374 negative triangles 1030: dt=0.0148, 372 negative triangles 1031: dt=0.0148, 370 negative triangles 1032: dt=0.0148, 377 negative triangles 1033: dt=0.0148, 377 negative triangles 1034: dt=0.0148, 377 negative triangles 1035: dt=0.0148, 377 negative triangles 1036: dt=0.0148, 378 negative triangles 1037: dt=0.0148, 380 negative triangles 1038: dt=0.0148, 375 negative triangles 1039: dt=0.0148, 371 negative triangles 1040: dt=0.0140, 372 negative triangles 1041: dt=0.0140, 375 negative triangles 1042: dt=0.0140, 379 negative triangles 1043: dt=0.0140, 379 negative triangles 1044: dt=0.0140, 378 negative triangles 1045: dt=0.0140, 377 negative triangles 1046: dt=0.0140, 379 negative triangles 1047: dt=0.0140, 378 negative triangles 1048: dt=0.0140, 372 negative triangles 1049: dt=0.0140, 377 negative triangles 1050: dt=0.0133, 371 negative triangles 1051: dt=0.0133, 375 negative triangles 1052: dt=0.0133, 377 negative triangles 1053: dt=0.0133, 372 negative triangles 1054: dt=0.0133, 375 negative triangles 1055: dt=0.0133, 377 negative triangles 1056: dt=0.0133, 378 negative triangles 1057: dt=0.0133, 376 negative triangles 1058: dt=0.0133, 377 negative triangles 1059: dt=0.0133, 380 negative triangles 1060: dt=0.0127, 380 negative triangles 1061: dt=0.0127, 381 negative triangles 1062: dt=0.0127, 381 negative triangles 1063: dt=0.0127, 379 negative triangles 1064: dt=0.0127, 377 negative triangles 1065: dt=0.0127, 382 negative triangles 1066: dt=0.0127, 379 negative triangles 1067: dt=0.0127, 380 negative triangles 1068: dt=0.0127, 378 negative triangles 1069: dt=0.0127, 374 negative triangles 1070: dt=0.0120, 377 negative triangles 1071: dt=0.0120, 375 negative triangles 1072: dt=0.0120, 376 negative triangles 1073: dt=0.0120, 375 negative triangles 1074: dt=0.0120, 387 negative triangles 1075: dt=0.0120, 382 negative triangles 1076: dt=0.0120, 383 negative triangles 1077: dt=0.0120, 382 negative triangles 1078: dt=0.0120, 379 negative triangles 1079: dt=0.0120, 381 negative triangles 1080: dt=0.0114, 381 negative triangles 1081: dt=0.0114, 384 negative triangles 1082: dt=0.0114, 382 negative triangles 1083: dt=0.0114, 382 negative triangles 1084: dt=0.0114, 385 negative triangles 1085: dt=0.0114, 384 negative triangles 1086: dt=0.0114, 384 negative triangles 1087: dt=0.0114, 386 negative triangles 1088: dt=0.0114, 389 negative triangles 1089: dt=0.0114, 384 negative triangles 1090: dt=0.0108, 383 negative triangles 1091: dt=0.0108, 383 negative triangles 1092: dt=0.0108, 382 negative triangles 1093: dt=0.0108, 386 negative triangles 1094: dt=0.0108, 386 negative triangles 1095: dt=0.0108, 386 negative triangles 1096: dt=0.0108, 385 negative triangles 1097: dt=0.0108, 381 negative triangles 1098: dt=0.0108, 383 negative triangles 1099: dt=0.0108, 382 negative triangles 1100: dt=0.0103, 382 negative triangles 1101: dt=0.0103, 383 negative triangles 1102: dt=0.0103, 381 negative triangles 1103: dt=0.0103, 382 negative triangles 1104: dt=0.0103, 383 negative triangles 1105: dt=0.0103, 382 negative triangles 1106: dt=0.0103, 377 negative triangles 1107: dt=0.0103, 382 negative triangles 1108: dt=0.0103, 379 negative triangles 1109: dt=0.0103, 377 negative triangles 1110: dt=0.0098, 374 negative triangles writing registered surface to ../surf/rh.sphere.reg... 1111: dt=0.0098, 376 negative triangles 1112: 376 negative triangles registration took 0.09 hours #VMPC# mris_register VmPeak 768948 FSRUNTIME@ mris_register 0.0889 hours 4 threads PIDs (739648 739651) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Tue Jan 10 13:03:28 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Tue Jan 10 13:03:28 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 739707 of (739707 739710) to complete... Waiting for PID 739710 of (739707 739710) to complete... 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 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 PIDs (739707 739710) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Tue Jan 10 13:03:28 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Tue Jan 10 13:03:28 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 739759 of (739759 739762) to complete... Waiting for PID 739762 of (739759 739762) to complete... mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (739759 739762) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Tue Jan 10 13:03:29 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test_withT2 lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Tue Jan 10 13:03:29 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test_withT2 rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 739811 of (739811 739814) to complete... Waiting for PID 739814 of (739811 739814) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test_withT2 lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 7.3.2 7.3.2 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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... 1092 labels changed using aseg relabeling using gibbs priors... 000: 2877 changed, 115656 examined... 001: 724 changed, 12018 examined... 002: 159 changed, 4005 examined... 003: 47 changed, 967 examined... 004: 20 changed, 291 examined... 005: 12 changed, 127 examined... 006: 4 changed, 60 examined... 007: 1 changed, 22 examined... 008: 1 changed, 7 examined... 009: 0 changed, 7 examined... 267 labels changed using aseg 000: 106 total segments, 64 labels (296 vertices) changed 001: 49 total segments, 5 labels (11 vertices) changed 002: 43 total segments, 1 labels (6 vertices) changed 003: 42 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... 1339 vertices marked for relabeling... 1339 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 7 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test_withT2 rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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 7.3.2 7.3.2 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/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... 905 labels changed using aseg relabeling using gibbs priors... 000: 2426 changed, 112409 examined... 001: 547 changed, 10517 examined... 002: 133 changed, 3129 examined... 003: 27 changed, 792 examined... 004: 8 changed, 184 examined... 005: 2 changed, 53 examined... 006: 0 changed, 13 examined... 195 labels changed using aseg 000: 75 total segments, 32 labels (180 vertices) changed 001: 44 total segments, 1 labels (39 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1572 vertices marked for relabeling... 1572 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 6 seconds. PIDs (739811 739814) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Tue Jan 10 13:03:36 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --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 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --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 removing intersecting faces 000: 29 intersecting step 1 with no progress (num=31, old_num=29) 001: 31 intersecting step 2 with no progress (num=31, old_num=31) 002: 31 intersecting step 3 with no progress (num=31, old_num=31) 003: 31 intersecting step 4 with no progress (num=31, old_num=31) 004: 31 intersecting step 5 with no progress (num=31, old_num=31) 005: 31 intersecting step 6 with no progress (num=31, old_num=31) 006: 31 intersecting step 7 with no progress (num=31, old_num=31) 007: 31 intersecting step 8 with no progress (num=31, old_num=31) 008: 31 intersecting step 9 with no progress (num=31, old_num=31) 009: 31 intersecting step 10 with no progress (num=31, old_num=31) 010: 31 intersecting step 11 with no progress (num=31, old_num=31) 011: 31 intersecting step 12 with no progress (num=31, old_num=31) 012: 31 intersecting step 13 with no progress (num=31, old_num=31) 013: 31 intersecting step 14 with no progress (num=31, old_num=31) 014: 31 intersecting step 15 with no progress (num=31, old_num=31) 015: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 29 intersecting Area 231308 0.34111 0.13701 0.000541 2.5012 Corner 693924 60.00000 15.90601 0.234239 179.5104 Edge 346962 0.90160 0.22626 0.014203 4.0142 Hinge 346962 12.06279 14.65518 0.000020 179.9677 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 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 MRISripNotLabel() ripped 8191/115656 vertices (107465 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 457 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (0,0,0) CBVO Creating mask 115656 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=2 had to be increased for 416 vertices, nripped=8648 mean border=90.4, 465 (465) missing vertices, mean dist 0.2 [0.9 (%27.9)->0.6 (%72.1))] %58 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0347 min Finding expansion regions mean absolute distance = 0.68 +- 1.10 3216 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=shark, 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=679868.6, rms=4.719 001: dt: 0.5000, sse=400982.0, rms=3.073 (34.890%) 002: dt: 0.5000, sse=307496.7, rms=2.383 (22.447%) 003: dt: 0.5000, sse=287128.4, rms=2.157 (9.467%) 004: dt: 0.5000, sse=284009.3, rms=2.076 (3.783%) rms = 2.0924/2.0759, sse=282684.6/284009.3, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 005: dt: 0.2500, sse=260239.1, rms=1.802 (13.203%) 006: dt: 0.2500, sse=256415.3, rms=1.686 (6.451%) rms = 1.6510/1.6856, sse=255314.1/256415.3, time step reduction 2 of 3 to 0.125 0 0 1 007: dt: 0.2500, sse=255314.1, rms=1.651 (2.051%) rms = 1.6033/1.6510, sse=257526.9/255314.1, time step reduction 3 of 3 to 0.062 0 1 1 008: dt: 0.1250, sse=257526.9, rms=1.603 (2.888%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=1 had to be increased for 344 vertices, nripped=8648 mean border=92.1, 341 (158) missing vertices, mean dist -0.2 [0.5 (%64.7)->0.3 (%35.3))] %75 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0235 min Finding expansion regions mean absolute distance = 0.39 +- 0.68 2817 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=shark, 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=412405.7, rms=3.089 009: dt: 0.5000, sse=296621.8, rms=2.144 (30.600%) 010: dt: 0.5000, sse=285711.5, rms=1.904 (11.165%) rms = 1.8565/1.9043, sse=279620.5/285711.5, time step reduction 1 of 3 to 0.250 0 0 1 011: dt: 0.5000, sse=279620.5, rms=1.857 (2.508%) 012: dt: 0.2500, sse=256039.6, rms=1.568 (15.523%) rms = 1.5275/1.5683, sse=254241.6/256039.6, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=254241.6, rms=1.527 (2.605%) rms = 1.4993/1.5275, sse=250067.5/254241.6, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=250067.5, rms=1.499 (1.846%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; 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=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 414 vertices, nripped=8648 mean border=92.9, 365 (107) missing vertices, mean dist -0.1 [0.3 (%58.5)->0.2 (%41.5))] %83 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0126 min Finding expansion regions mean absolute distance = 0.29 +- 0.47 3110 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=shark, 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=310268.8, rms=2.270 rms = 1.8784/2.2696, sse=312613.5/310268.8, time step reduction 1 of 3 to 0.250 0 1 0 015: dt: 0.5000, sse=312613.5, rms=1.878 (17.233%) 016: dt: 0.2500, sse=262126.1, rms=1.568 (16.512%) 017: dt: 0.2500, sse=249423.8, rms=1.479 (5.693%) rms = 1.4729/1.4790, sse=254068.9/249423.8, time step reduction 2 of 3 to 0.125 0 1 1 018: dt: 0.2500, sse=254068.9, rms=1.473 (0.414%) rms = 1.4241/1.4729, sse=251631.8/254068.9, time step reduction 3 of 3 to 0.062 0 0 1 019: dt: 0.1250, sse=251631.8, rms=1.424 (3.309%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; 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=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 413 vertices, nripped=8648 mean border=93.1, 416 (90) missing vertices, mean dist -0.0 [0.3 (%52.1)->0.2 (%47.9))] %85 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0082 min Finding expansion regions mean absolute distance = 0.25 +- 0.38 3003 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=shark, 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=260985.7, rms=1.600 rms = 1.6195/1.6000, sse=271700.7/260985.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=245642.8, rms=1.388 (13.250%) rms = 1.3487/1.3880, sse=256445.0/245642.8, time step reduction 2 of 3 to 0.125 0 1 1 021: dt: 0.2500, sse=256445.0, rms=1.349 (2.836%) 022: dt: 0.1250, sse=240611.7, rms=1.268 (5.956%) rms = 1.2490/1.2683, sse=234586.8/240611.7, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=234586.8, rms=1.249 (1.525%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 29 intersecting step 1 with no progress (num=60, old_num=29) 001: 60 intersecting step 2 with no progress (num=73, old_num=60) 002: 73 intersecting step 3 with no progress (num=81, old_num=73) 003: 81 intersecting 004: 78 intersecting step 1 with no progress (num=79, old_num=78) 005: 79 intersecting step 2 with no progress (num=79, old_num=79) 006: 79 intersecting step 3 with no progress (num=79, old_num=79) 007: 79 intersecting step 4 with no progress (num=79, old_num=79) 008: 79 intersecting step 5 with no progress (num=79, old_num=79) 009: 79 intersecting step 6 with no progress (num=79, old_num=79) 010: 79 intersecting step 7 with no progress (num=79, old_num=79) 011: 79 intersecting step 8 with no progress (num=79, old_num=79) 012: 79 intersecting step 9 with no progress (num=79, old_num=79) 013: 79 intersecting step 10 with no progress (num=79, old_num=79) 014: 79 intersecting step 11 with no progress (num=79, old_num=79) 015: 79 intersecting step 12 with no progress (num=79, old_num=79) 016: 79 intersecting step 13 with no progress (num=79, old_num=79) 017: 79 intersecting step 14 with no progress (num=79, old_num=79) 018: 79 intersecting step 15 with no progress (num=79, old_num=79) 019: 79 intersecting step 16 with no progress (num=79, old_num=79) terminating search with 29 intersecting Writing output to ../surf/lh.white #ET# mris_place_surface 1.56 minutes #VMPC# mris_place_surfaces VmPeak 1963028 mris_place_surface done #-------------------------------------------- #@# WhiteSurfs rh Tue Jan 10 13:05:33 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --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 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --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 removing intersecting faces 000: 90 intersecting step 1 with no progress (num=93, old_num=90) 001: 93 intersecting step 2 with no progress (num=94, old_num=93) 002: 94 intersecting step 3 with no progress (num=108, old_num=94) 003: 108 intersecting 004: 101 intersecting 005: 98 intersecting step 1 with no progress (num=98, old_num=98) 006: 98 intersecting 007: 92 intersecting step 1 with no progress (num=95, old_num=92) 008: 95 intersecting 009: 93 intersecting step 1 with no progress (num=96, old_num=93) 010: 96 intersecting 011: 94 intersecting 012: 91 intersecting step 1 with no progress (num=96, old_num=91) 013: 96 intersecting step 2 with no progress (num=103, old_num=96) 014: 103 intersecting 015: 90 intersecting step 1 with no progress (num=99, old_num=90) 016: 99 intersecting 017: 98 intersecting step 1 with no progress (num=103, old_num=98) 018: 103 intersecting 019: 100 intersecting step 1 with no progress (num=119, old_num=100) 020: 119 intersecting 021: 118 intersecting 022: 116 intersecting 023: 111 intersecting step 1 with no progress (num=113, old_num=111) 024: 113 intersecting step 2 with no progress (num=113, old_num=113) 025: 113 intersecting step 3 with no progress (num=114, old_num=113) 026: 114 intersecting step 4 with no progress (num=114, old_num=114) 027: 114 intersecting step 5 with no progress (num=114, old_num=114) 028: 114 intersecting step 6 with no progress (num=114, old_num=114) 029: 114 intersecting step 7 with no progress (num=114, old_num=114) 030: 114 intersecting step 8 with no progress (num=114, old_num=114) 031: 114 intersecting step 9 with no progress (num=114, old_num=114) 032: 114 intersecting step 10 with no progress (num=114, old_num=114) 033: 114 intersecting step 11 with no progress (num=114, old_num=114) 034: 114 intersecting step 12 with no progress (num=114, old_num=114) 035: 114 intersecting step 13 with no progress (num=114, old_num=114) 036: 114 intersecting step 14 with no progress (num=114, old_num=114) 037: 114 intersecting step 15 with no progress (num=114, old_num=114) 038: 114 intersecting step 16 with no progress (num=114, old_num=114) terminating search with 90 intersecting Area 224814 0.33700 0.12790 0.000000 2.9271 Corner 674442 60.00000 15.49886 0.000090 179.9997 Edge 337221 0.89480 0.21381 0.000094 4.1707 Hinge 337221 12.05696 15.04408 0.000049 179.9982 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 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 MRISripNotLabel() ripped 7619/112409 vertices (104790 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 524 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56205: xyz = (-0.162842,-15.8119,75.9733) oxyz = (-0.162842,-15.8119,75.9733) wxzy = (-0.162842,-15.8119,75.9733) pxyz = (0,0,0) CBVO Creating mask 112409 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=2 had to be increased for 505 vertices, nripped=8143 mean border=91.0, 446 (446) missing vertices, mean dist 0.2 [0.9 (%27.9)->0.6 (%72.1))] %56 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0336 min Finding expansion regions mean absolute distance = 0.67 +- 1.09 3104 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=shark, 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=796553.8, rms=4.480 001: dt: 0.5000, sse=621458.5, rms=2.949 (34.161%) 002: dt: 0.5000, sse=542369.4, rms=2.315 (21.502%) 003: dt: 0.5000, sse=518860.1, rms=2.214 (4.366%) 004: dt: 0.5000, sse=502241.8, rms=2.139 (3.401%) rms = 2.1643/2.1388, sse=502617.6/502241.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=476436.6, rms=1.887 (11.782%) 006: dt: 0.2500, sse=471859.9, rms=1.749 (7.292%) 007: dt: 0.2500, sse=463117.1, rms=1.691 (3.307%) 008: dt: 0.2500, sse=458150.7, rms=1.639 (3.072%) rms = 1.5997/1.6394, sse=456214.8/458150.7, time step reduction 2 of 3 to 0.125 0 0 1 009: dt: 0.2500, sse=456214.8, rms=1.600 (2.420%) rms = 1.5652/1.5997, sse=456732.0/456214.8, time step reduction 3 of 3 to 0.062 0 1 1 010: dt: 0.1250, sse=456732.0, rms=1.565 (2.159%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=1 had to be increased for 448 vertices, nripped=8143 mean border=92.4, 413 (163) missing vertices, mean dist -0.2 [0.5 (%62.0)->0.3 (%38.0))] %72 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0230 min Finding expansion regions mean absolute distance = 0.40 +- 0.73 2887 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=shark, 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=588178.2, rms=2.911 011: dt: 0.5000, sse=495200.3, rms=2.022 (30.554%) 012: dt: 0.5000, sse=472649.2, rms=1.777 (12.099%) rms = 1.7615/1.7772, sse=483556.2/472649.2, time step reduction 1 of 3 to 0.250 0 1 1 013: dt: 0.5000, sse=483556.2, rms=1.762 (0.880%) 014: dt: 0.2500, sse=448022.4, rms=1.453 (17.524%) rms = 1.4007/1.4528, sse=461092.7/448022.4, time step reduction 2 of 3 to 0.125 0 1 0 015: dt: 0.2500, sse=461092.8, rms=1.401 (3.587%) rms = 1.3833/1.4007, sse=446132.5/461092.7, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=446132.5, rms=1.383 (1.240%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; 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=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 469 vertices, nripped=8143 mean border=93.2, 479 (117) missing vertices, mean dist -0.1 [0.4 (%56.9)->0.2 (%43.1))] %80 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0124 min Finding expansion regions mean absolute distance = 0.30 +- 0.50 3168 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=shark, 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=498557.9, rms=2.124 017: dt: 0.5000, sse=468136.2, rms=1.687 (20.571%) 018: dt: 0.5000, sse=462933.0, rms=1.591 (5.729%) rms = 1.6676/1.5906, sse=457847.4/462933.0, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 019: dt: 0.2500, sse=446380.1, rms=1.402 (11.829%) 020: dt: 0.2500, sse=375439.2, rms=1.328 (5.290%) rms = 1.3126/1.3283, sse=349855.4/375439.3, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=349855.4, rms=1.313 (1.176%) rms = 1.2813/1.3126, sse=325019.3/349855.4, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=325019.3, rms=1.281 (2.389%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; 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=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 427 vertices, nripped=8143 mean border=93.5, 558 (99) missing vertices, mean dist -0.0 [0.3 (%51.4)->0.2 (%48.6))] %83 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0079 min Finding expansion regions mean absolute distance = 0.27 +- 0.41 2711 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=shark, 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=333140.6, rms=1.458 rms = 1.3950/1.4584, sse=418397.6/333140.6, time step reduction 1 of 3 to 0.250 0 1 0 023: dt: 0.5000, sse=418397.6, rms=1.395 (4.345%) 024: dt: 0.2500, sse=400958.5, rms=1.204 (13.701%) rms = 1.1684/1.2039, sse=388542.4/400958.5, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=388542.4, rms=1.168 (2.949%) 026: dt: 0.1250, sse=385319.8, rms=1.088 (6.909%) rms = 1.0658/1.0877, sse=379845.2/385319.9, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=379845.2, rms=1.066 (2.014%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 69 intersecting step 1 with no progress (num=74, old_num=69) 001: 74 intersecting 002: 65 intersecting 003: 63 intersecting 004: 60 intersecting step 1 with no progress (num=60, old_num=60) 005: 60 intersecting step 2 with no progress (num=65, old_num=60) 006: 65 intersecting step 3 with no progress (num=67, old_num=65) 007: 67 intersecting step 4 with no progress (num=69, old_num=67) 008: 69 intersecting step 5 with no progress (num=71, old_num=69) 009: 71 intersecting step 6 with no progress (num=71, old_num=71) 010: 71 intersecting step 7 with no progress (num=71, old_num=71) 011: 71 intersecting step 8 with no progress (num=71, old_num=71) 012: 71 intersecting step 9 with no progress (num=71, old_num=71) 013: 71 intersecting step 10 with no progress (num=71, old_num=71) 014: 71 intersecting step 11 with no progress (num=71, old_num=71) 015: 71 intersecting step 12 with no progress (num=71, old_num=71) 016: 71 intersecting step 13 with no progress (num=71, old_num=71) 017: 71 intersecting step 14 with no progress (num=71, old_num=71) 018: 71 intersecting step 15 with no progress (num=71, old_num=71) 019: 71 intersecting step 16 with no progress (num=71, old_num=71) terminating search with 60 intersecting Writing output to ../surf/rh.white #ET# mris_place_surface 1.68 minutes #VMPC# mris_place_surfaces VmPeak 2065736 mris_place_surface done #-------------------------------------------- #@# T1PialSurf lh Tue Jan 10 13:07:58 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --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 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --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 removing intersecting faces 000: 29 intersecting step 1 with no progress (num=31, old_num=29) 001: 31 intersecting step 2 with no progress (num=31, old_num=31) 002: 31 intersecting step 3 with no progress (num=31, old_num=31) 003: 31 intersecting step 4 with no progress (num=31, old_num=31) 004: 31 intersecting step 5 with no progress (num=31, old_num=31) 005: 31 intersecting step 6 with no progress (num=31, old_num=31) 006: 31 intersecting step 7 with no progress (num=31, old_num=31) 007: 31 intersecting step 8 with no progress (num=31, old_num=31) 008: 31 intersecting step 9 with no progress (num=31, old_num=31) 009: 31 intersecting step 10 with no progress (num=31, old_num=31) 010: 31 intersecting step 11 with no progress (num=31, old_num=31) 011: 31 intersecting step 12 with no progress (num=31, old_num=31) 012: 31 intersecting step 13 with no progress (num=31, old_num=31) 013: 31 intersecting step 14 with no progress (num=31, old_num=31) 014: 31 intersecting step 15 with no progress (num=31, old_num=31) 015: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 29 intersecting Area 231308 0.34327 0.14591 0.001039 2.7281 Corner 693924 60.00000 16.77840 0.248217 178.3999 Edge 346962 0.90552 0.23823 0.019084 4.0142 Hinge 346962 12.10726 14.72363 0.000004 179.9709 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.2749 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 MRISripNotLabel() ripped 6179/115656 vertices (109477 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (-3.05528,-18.0059,9.12601) CBVO Creating mask 115656 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=2 had to be increased for 655 vertices, nripped=6179 mean border=70.9, 633 (633) missing vertices, mean dist 1.3 [2.6 (%0.0)->3.4 (%100.0))] %12 local maxima, %23 large gradients and %59 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0279 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=shark, 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=12007999.0, rms=23.320 001: dt: 0.5000, sse=8754423.0, rms=19.859 (14.844%) 002: dt: 0.5000, sse=6432347.0, rms=16.960 (14.595%) 003: dt: 0.5000, sse=4937740.0, rms=14.796 (12.763%) 004: dt: 0.5000, sse=4021807.8, rms=13.294 (10.146%) 005: dt: 0.5000, sse=3435274.5, rms=12.235 (7.966%) 006: dt: 0.5000, sse=3017495.0, rms=11.420 (6.665%) 007: dt: 0.5000, sse=2650916.5, rms=10.652 (6.722%) 008: dt: 0.5000, sse=2298476.8, rms=9.857 (7.461%) 009: dt: 0.5000, sse=1954841.5, rms=9.015 (8.544%) 010: dt: 0.5000, sse=1659048.0, rms=8.221 (8.812%) 011: dt: 0.5000, sse=1446838.0, rms=7.598 (7.575%) 012: dt: 0.5000, sse=1287439.2, rms=7.093 (6.644%) 013: dt: 0.5000, sse=1173536.1, rms=6.707 (5.441%) 014: dt: 0.5000, sse=1095549.5, rms=6.428 (4.158%) 015: dt: 0.5000, sse=1045492.8, rms=6.240 (2.928%) 016: dt: 0.5000, sse=1009427.8, rms=6.100 (2.242%) 017: dt: 0.5000, sse=980996.2, rms=5.986 (1.867%) rms = 5.9426/5.9864, sse=971138.9/980996.2, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=971138.9, rms=5.943 (0.733%) 019: dt: 0.2500, sse=827378.3, rms=5.340 (10.138%) 020: dt: 0.2500, sse=793743.4, rms=5.190 (2.814%) rms = 5.1546/5.1899, sse=786471.9/793743.4, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=786471.9, rms=5.155 (0.680%) 022: dt: 0.1250, sse=734018.4, rms=4.910 (4.743%) 023: dt: 0.1250, sse=718588.6, rms=4.836 (1.518%) rms = 4.8338/4.8356, sse=718502.4/718588.6, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=718502.4, rms=4.834 (0.037%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=1 had to be increased for 14001 vertices, nripped=6179 mean border=69.4, 7755 (214) missing vertices, mean dist 0.2 [0.2 (%28.1)->0.7 (%71.9))] %20 local maxima, %19 large gradients and %49 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0087 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=shark, 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=969434.4, rms=5.737 rms = 6.0205/5.7369, sse=1041879.4/969434.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=883120.4, rms=5.378 (6.247%) 026: dt: 0.2500, sse=848454.6, rms=5.226 (2.829%) rms = 5.3865/5.2263, sse=885090.8/848454.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 027: dt: 0.1250, sse=829474.4, rms=5.141 (1.627%) 028: dt: 0.1250, sse=815317.6, rms=5.076 (1.271%) rms = 5.0444/5.0759, sse=808424.4/815317.6, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=808424.4, rms=5.044 (0.622%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; 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=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 14685 vertices, nripped=6179 mean border=68.9, 7935 (185) missing vertices, mean dist 0.1 [0.2 (%31.5)->0.6 (%68.5))] %25 local maxima, %13 large gradients and %49 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0050 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=shark, 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=849586.1, rms=5.230 rms = 6.0317/5.2302, sse=1043842.8/849586.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=819025.4, rms=5.094 (2.595%) rms = 5.2374/5.0944, sse=850462.7/819025.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 5.0734/5.0944, sse=814421.0/819025.5, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=814421.1, rms=5.073 (0.414%) maximum number of reductions reached, breaking from loop positioning took 0.1 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; 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=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 10984 vertices, nripped=6179 mean border=68.5, 12469 (174) missing vertices, mean dist 0.1 [0.2 (%33.0)->0.4 (%67.0))] %26 local maxima, %11 large gradients and %46 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0031 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=shark, 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=835280.9, rms=5.166 rms = 5.4379/5.1664, sse=892951.9/835281.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=795526.3, rms=4.989 (3.426%) 033: dt: 0.2500, sse=769570.1, rms=4.879 (2.208%) rms = 4.8848/4.8792, sse=769241.0/769570.1, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step 034: dt: 0.1250, sse=751081.4, rms=4.791 (1.805%) 035: dt: 0.1250, sse=721680.4, rms=4.650 (2.955%) 036: dt: 0.1250, sse=703251.8, rms=4.560 (1.923%) 037: dt: 0.1250, sse=691693.9, rms=4.504 (1.233%) rms = 4.4578/4.5039, sse=682244.2/691693.9, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=682244.2, rms=4.458 (1.024%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 113 intersecting 001: 64 intersecting 002: 35 intersecting 003: 29 intersecting step 1 with no progress (num=29, old_num=29) 004: 29 intersecting step 2 with no progress (num=29, old_num=29) 005: 29 intersecting step 3 with no progress (num=29, old_num=29) 006: 29 intersecting step 4 with no progress (num=29, old_num=29) 007: 29 intersecting step 5 with no progress (num=29, old_num=29) 008: 29 intersecting step 6 with no progress (num=29, old_num=29) 009: 29 intersecting step 7 with no progress (num=29, old_num=29) 010: 29 intersecting step 8 with no progress (num=29, old_num=29) 011: 29 intersecting step 9 with no progress (num=29, old_num=29) 012: 29 intersecting step 10 with no progress (num=29, old_num=29) 013: 29 intersecting step 11 with no progress (num=29, old_num=29) 014: 29 intersecting step 12 with no progress (num=29, old_num=29) 015: 29 intersecting step 13 with no progress (num=29, old_num=29) 016: 29 intersecting step 14 with no progress (num=29, old_num=29) 017: 29 intersecting step 15 with no progress (num=29, old_num=29) 018: 29 intersecting step 16 with no progress (num=29, old_num=29) terminating search with 29 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.18 minutes #VMPC# mris_place_surfaces VmPeak 1462436 mris_place_surface done #-------------------------------------------- #@# T1PialSurf rh Tue Jan 10 13:10:32 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --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 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --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 removing intersecting faces 000: 60 intersecting step 1 with no progress (num=60, old_num=60) 001: 60 intersecting step 2 with no progress (num=65, old_num=60) 002: 65 intersecting step 3 with no progress (num=67, old_num=65) 003: 67 intersecting step 4 with no progress (num=69, old_num=67) 004: 69 intersecting step 5 with no progress (num=71, old_num=69) 005: 71 intersecting step 6 with no progress (num=71, old_num=71) 006: 71 intersecting step 7 with no progress (num=71, old_num=71) 007: 71 intersecting step 8 with no progress (num=71, old_num=71) 008: 71 intersecting step 9 with no progress (num=71, old_num=71) 009: 71 intersecting step 10 with no progress (num=71, old_num=71) 010: 71 intersecting step 11 with no progress (num=71, old_num=71) 011: 71 intersecting step 12 with no progress (num=71, old_num=71) 012: 71 intersecting step 13 with no progress (num=71, old_num=71) 013: 71 intersecting step 14 with no progress (num=71, old_num=71) 014: 71 intersecting step 15 with no progress (num=71, old_num=71) 015: 71 intersecting step 16 with no progress (num=71, old_num=71) terminating search with 60 intersecting Area 224814 0.33931 0.13822 0.000000 2.9271 Corner 674442 60.00000 16.42539 0.001250 179.9963 Edge 337221 0.89957 0.22928 0.000199 5.4013 Hinge 337221 12.09284 14.94323 0.000033 179.9510 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.7749 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 MRISripNotLabel() ripped 6561/112409 vertices (105848 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56205: xyz = (-0.203856,-15.8081,75.992) oxyz = (-0.203856,-15.8081,75.992) wxzy = (-0.203856,-15.8081,75.992) pxyz = (-0.203856,-15.8081,75.992) CBVO Creating mask 112409 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=2 had to be increased for 577 vertices, nripped=6561 mean border=71.4, 485 (485) missing vertices, mean dist 1.4 [1.7 (%0.0)->3.4 (%100.0))] %13 local maxima, %24 large gradients and %57 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0277 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=shark, 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=11460107.0, rms=23.156 001: dt: 0.5000, sse=8400183.0, rms=19.774 (14.607%) 002: dt: 0.5000, sse=6193826.0, rms=16.920 (14.436%) 003: dt: 0.5000, sse=4763092.0, rms=14.775 (12.675%) 004: dt: 0.5000, sse=3882076.5, rms=13.282 (10.106%) 005: dt: 0.5000, sse=3301672.2, rms=12.197 (8.167%) 006: dt: 0.5000, sse=2874972.8, rms=11.332 (7.089%) 007: dt: 0.5000, sse=2513100.5, rms=10.543 (6.969%) 008: dt: 0.5000, sse=2166704.0, rms=9.726 (7.743%) 009: dt: 0.5000, sse=1841396.1, rms=8.891 (8.589%) 010: dt: 0.5000, sse=1565537.5, rms=8.115 (8.727%) 011: dt: 0.5000, sse=1362249.4, rms=7.490 (7.702%) 012: dt: 0.5000, sse=1217705.8, rms=7.010 (6.408%) 013: dt: 0.5000, sse=1122897.6, rms=6.674 (4.790%) 014: dt: 0.5000, sse=1059217.9, rms=6.437 (3.551%) 015: dt: 0.5000, sse=1015586.1, rms=6.268 (2.635%) 016: dt: 0.5000, sse=981835.1, rms=6.132 (2.162%) 017: dt: 0.5000, sse=962517.1, rms=6.051 (1.323%) 018: dt: 0.5000, sse=940839.9, rms=5.960 (1.506%) rms = 5.9130/5.9599, sse=930397.2/940840.0, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=930397.2, rms=5.913 (0.788%) 020: dt: 0.2500, sse=794076.9, rms=5.320 (10.020%) 021: dt: 0.2500, sse=760106.7, rms=5.163 (2.955%) rms = 5.1336/5.1632, sse=754385.6/760106.7, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=754385.6, rms=5.134 (0.574%) 023: dt: 0.1250, sse=703975.6, rms=4.890 (4.738%) 024: dt: 0.1250, sse=689836.1, rms=4.820 (1.445%) rms = 4.8002/4.8197, sse=686146.3/689836.2, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=686146.3, rms=4.800 (0.405%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=1 had to be increased for 13490 vertices, nripped=6561 mean border=69.9, 7688 (146) missing vertices, mean dist 0.2 [0.3 (%28.5)->0.8 (%71.5))] %21 local maxima, %19 large gradients and %47 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0095 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=shark, 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=952723.7, rms=5.796 rms = 6.0408/5.7963, sse=1013155.1/952723.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=869633.7, rms=5.444 (6.076%) 027: dt: 0.2500, sse=838099.1, rms=5.304 (2.576%) rms = 5.4364/5.3039, sse=867771.2/838099.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 028: dt: 0.1250, sse=820233.1, rms=5.222 (1.537%) 029: dt: 0.1250, sse=803380.1, rms=5.144 (1.508%) rms = 5.1168/5.1436, sse=797670.3/803380.1, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=797670.3, rms=5.117 (0.521%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; 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=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 13989 vertices, nripped=6561 mean border=69.4, 7806 (126) missing vertices, mean dist 0.2 [0.3 (%31.0)->0.6 (%69.0))] %26 local maxima, %14 large gradients and %48 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0055 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=shark, 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=850283.2, rms=5.357 rms = 6.1159/5.3567, sse=1031429.5/850283.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=821706.7, rms=5.229 (2.386%) rms = 5.3887/5.2289, sse=856711.5/821706.7, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 5.2113/5.2289, sse=817893.7/821706.7, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=817893.8, rms=5.211 (0.335%) maximum number of reductions reached, breaking from loop positioning took 0.1 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; 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=112409 Gdiag_no=-1 vno start=0, stop=112409 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 10042 vertices, nripped=6561 mean border=68.9, 12536 (125) missing vertices, mean dist 0.1 [0.2 (%32.1)->0.5 (%67.9))] %27 local maxima, %11 large gradients and %45 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0033 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=shark, 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=846070.2, rms=5.338 rms = 5.5182/5.3375, sse=882186.5/846070.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=803572.2, rms=5.148 (3.548%) 034: dt: 0.2500, sse=765749.4, rms=4.982 (3.230%) rms = 4.9602/4.9819, sse=759824.3/765749.4, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=759824.3, rms=4.960 (0.435%) 036: dt: 0.1250, sse=698313.6, rms=4.656 (6.131%) 037: dt: 0.1250, sse=674519.4, rms=4.536 (2.589%) 038: dt: 0.1250, sse=664554.5, rms=4.485 (1.114%) rms = 4.4469/4.4850, sse=657050.7/664554.5, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=657050.8, rms=4.447 (0.851%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 43 intersecting step 1 with no progress (num=64, old_num=43) 001: 64 intersecting step 2 with no progress (num=80, old_num=64) 002: 80 intersecting 003: 78 intersecting step 1 with no progress (num=148, old_num=78) 004: 148 intersecting 005: 119 intersecting 006: 109 intersecting step 1 with no progress (num=154, old_num=109) 007: 154 intersecting 008: 136 intersecting step 1 with no progress (num=149, old_num=136) 009: 149 intersecting 010: 145 intersecting 011: 132 intersecting step 1 with no progress (num=136, old_num=132) 012: 136 intersecting step 2 with no progress (num=140, old_num=136) 013: 140 intersecting 014: 136 intersecting 015: 132 intersecting step 1 with no progress (num=132, old_num=132) 016: 132 intersecting step 2 with no progress (num=132, old_num=132) 017: 132 intersecting step 3 with no progress (num=132, old_num=132) 018: 132 intersecting step 4 with no progress (num=132, old_num=132) 019: 132 intersecting step 5 with no progress (num=132, old_num=132) 020: 132 intersecting step 6 with no progress (num=132, old_num=132) 021: 132 intersecting step 7 with no progress (num=132, old_num=132) 022: 132 intersecting step 8 with no progress (num=132, old_num=132) 023: 132 intersecting step 9 with no progress (num=132, old_num=132) 024: 132 intersecting step 10 with no progress (num=132, old_num=132) 025: 132 intersecting step 11 with no progress (num=132, old_num=132) 026: 132 intersecting step 12 with no progress (num=132, old_num=132) 027: 132 intersecting step 13 with no progress (num=132, old_num=132) 028: 132 intersecting step 14 with no progress (num=132, old_num=132) 029: 132 intersecting step 15 with no progress (num=132, old_num=132) 030: 132 intersecting step 16 with no progress (num=132, old_num=132) terminating search with 43 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.38 minutes #VMPC# mris_place_surfaces VmPeak 1456592 mris_place_surface done #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Jan 10 13:13:17 CET 2023 bbregister --s Test_withT2 --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz --lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask tmp /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032 Log file is /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.log Tue Jan 10 13:13:17 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/bin/bbregister --s Test_withT2 --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz --lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask bbregister 7.3.2 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00118486, -0.999997, 0.00188591) j_ras = (0.0980046, -0.00176071, -0.995184) k_ras = (0.995185, 0.00136398, 0.0980023) writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii... mri_coreg --s Test_withT2 --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --regdat /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.init.dat --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts cmdline mri_coreg --s Test_withT2 --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --regdat /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.init.dat --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname sharky machine x86_64 user brainstimmaps dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii INFO: This is an unsigined short. Reading in ref /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/brainmask.mgz Setting cras translation parameters to align volume centers Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Init matrix params -1.0474 1.0278 -0.0515 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial parameters to be opt -1.0474 1.0278 -0.0515 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 4 movsat = 819.0000 mov gstd 1.8908 1.8908 1.8914 Smoothing mov refsat = 241.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0482998704 nhits = 180123 out of 16777216, Percent Overlap: 68.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -1.04744; 0.00000 1.00000 0.00000 1.02782; 0.00000 0.00000 1.00000 -0.05146; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -0.00118 -0.00188 -0.99556 350.82333; -0.09757 0.99077 -0.00175 109.84100; -0.99518 -0.09800 0.00136 226.70732; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -1.04744 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0407441 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -1.047440 1.027817 -0.051460 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0482999086 #@# 4 188 -1.04744 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0482999 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.048300 #@# 4 190 -0.04744 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0485200 #@# 4 194 -0.42941 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0486172 #@# 4 196 -0.39856 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0486178 #@# 4 205 -0.40856 0.99300 -0.05146 0.00000 0.00000 0.00000 -1.0486192 #@# 4 206 -0.40856 0.96334 -0.05146 0.00000 0.00000 0.00000 -1.0486197 #@# 4 217 -0.40856 0.95334 -0.21759 0.00000 0.00000 0.00000 -1.0486393 #@# 4 218 -0.40856 0.95334 -0.22759 0.00000 0.00000 0.00000 -1.0486394 #@# 4 219 -0.40856 0.95334 -0.23759 0.00000 0.00000 0.00000 -1.0486398 #@# 4 229 -0.40856 0.95334 -0.23759 0.38197 0.00000 0.00000 -1.0486951 #@# 4 230 -0.40856 0.95334 -0.23759 0.35166 0.00000 0.00000 -1.0486959 #@# 4 232 -0.40856 0.95334 -0.23759 0.32872 0.00000 0.00000 -1.0486960 #@# 4 240 -0.40856 0.95334 -0.23759 0.32872 -0.61803 0.00000 -1.0487163 #@# 4 242 -0.40856 0.95334 -0.23759 0.32872 -0.39161 0.00000 -1.0487279 #@# 4 253 -0.40856 0.95334 -0.23759 0.32872 -0.39161 -0.22387 -1.0487548 #@# 4 254 -0.40856 0.95334 -0.23759 0.32872 -0.39161 -0.23387 -1.0487549 powell nthiter 1: fret = -1.048755 #@# 4 272 -0.39856 0.94334 -0.23759 0.32872 -0.39161 -0.23387 -1.0487550 #@# 4 282 -0.39856 0.93334 -0.44359 0.32872 -0.39161 -0.23387 -1.0487845 #@# 4 290 -0.39856 0.93334 -0.44359 0.71069 -0.39161 -0.23387 -1.0487889 #@# 4 291 -0.39856 0.93334 -0.44359 0.53261 -0.39161 -0.23387 -1.0488014 #@# 4 300 -0.39856 0.93334 -0.44359 0.54261 -0.54299 -0.23387 -1.0488060 #@# 4 301 -0.39856 0.93334 -0.44359 0.54261 -0.53299 -0.23387 -1.0488065 #@# 4 302 -0.39856 0.93334 -0.44359 0.54261 -0.49092 -0.23387 -1.0488069 #@# 4 304 -0.39856 0.93334 -0.44359 0.54261 -0.50762 -0.23387 -1.0488071 #@# 4 305 -0.39856 0.93334 -0.44359 0.54261 -0.51762 -0.23387 -1.0488074 Powell done niters total = 1 OptTimeSec 4.0 sec OptTimeMin 0.07 min nEvals 315 Final optimized parameters -0.39855793 0.93334097 -0.44359189 0.54261124 -0.51762331 -0.23386888 Final matrix parameters -0.3986 0.9333 -0.4436 0.5426 -0.5176 -0.2439 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.048807331110246 --------------------------------- Final RefRAS-to-MovRAS 0.99995 -0.00408 -0.00903 -0.39856; 0.00417 0.99995 0.00947 0.93334; 0.00899 -0.00951 0.99991 -0.44359; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.00295 0.00756 -0.99553 349.24756; -0.08865 0.99158 0.00727 107.80823; -0.99602 -0.08902 -0.00363 227.02847; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.3986 0.9333 -0.4436 0.5426 -0.5176 -0.2339 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.3986 0.9333 -0.4436 0.5426 -0.5176 -0.2339 nhits = 179917 out of 16777216, Percent Overlap: 68.6 mri_coreg RunTimeSec 73.2 sec To check run: tkregisterfv --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --targ /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/brainmask.mgz --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/mri_coreg.lta --s Test_withT2 --surfs mri_coreg done mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.init.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 7.3.2 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.init.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 sysname Linux hostname sharky machine x86_64 user brainstimmaps movvol /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii regfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.init.dat subject Test_withT2 dof 6 outregfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1673452464 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00297 0.99997 0.00759 0.83787; 0.99602 -0.00363 0.08902 -0.32104; -0.08904 -0.00730 0.99600 -0.31540; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.015006 1 -25.0 -25.0 25.0 0.994432 2 -25.0 25.0 -25.0 1.020178 3 -25.0 25.0 25.0 1.022865 4 25.0 -25.0 -25.0 0.991715 5 25.0 -25.0 25.0 0.983959 6 25.0 25.0 -25.0 0.986725 7 25.0 25.0 25.0 0.984726 REL: 8 0.111109 7.999604 0.999951 rel = 0.111114 Initial costs ---------------- Number of surface hits 2108 WM Intensity 239.6409 +/- 37.4446 Ctx Intensity 334.7417 +/- 77.1559 Pct Contrast 31.1872 +/- 24.6615 Cost 0.1111 RelCost 0.1111 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0003 1.0003 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9898 0.9898 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9841 0.9841 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9613 0.9613 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.8876 0.8876 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8473 0.8473 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.7509 0.7509 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.6228 0.6228 0.0 121 -4.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6191 0.6191 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5679 0.5679 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1111 0.1111 0.0 Brute Force -------------------------- Min cost was 0.111109 Number of iterations 729 Search time 0.749474 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.111109 5 -0.618 0.000 0.000 0.000 0.000 0.000 0.0977183936 7 -0.496 0.000 0.000 0.000 0.000 0.000 0.0958709371 8 -0.455 0.000 0.000 0.000 0.000 0.000 0.0956132070 10 -0.465 0.000 0.000 0.000 0.000 0.000 0.0955997696 11 -0.463 0.000 0.000 0.000 0.000 0.000 0.0955929202 12 -0.461 0.000 0.000 0.000 0.000 0.000 0.0955919240 24 -0.461 -0.007 0.000 0.000 0.000 0.000 0.0955808201 25 -0.461 -0.006 0.000 0.000 0.000 0.000 0.0955799233 31 -0.461 -0.006 -0.618 0.000 0.000 0.000 0.0953541959 33 -0.461 -0.006 -0.312 0.000 0.000 0.000 0.0898394522 35 -0.461 -0.006 -0.193 0.000 0.000 0.000 0.0871224827 37 -0.461 -0.006 -0.202 0.000 0.000 0.000 0.0870444803 39 -0.461 -0.006 -0.212 0.000 0.000 0.000 0.0870009721 41 -0.461 -0.006 -0.210 0.000 0.000 0.000 0.0869943956 42 -0.461 -0.006 -0.208 0.000 0.000 0.000 0.0869941605 58 -0.461 -0.006 -0.208 -0.001 0.000 0.000 0.0869936344 72 -0.461 -0.006 -0.208 -0.001 0.004 0.000 0.0869697320 73 -0.461 -0.006 -0.208 -0.001 0.005 0.000 0.0869691010 81 -0.461 -0.006 -0.208 -0.001 0.005 -0.144 0.0866908590 88 -0.461 -0.006 -0.208 -0.001 0.005 -0.154 0.0866123201 90 -0.461 -0.006 -0.208 -0.001 0.005 -0.152 0.0866086052 92 -0.461 -0.006 -0.208 -0.001 0.005 -0.153 0.0866079781 powell nthiter 1: fret = 0.086608 100 -0.531 -0.006 -0.208 -0.001 0.005 -0.153 0.0858391133 104 -0.536 -0.006 -0.208 -0.001 0.005 -0.153 0.0858324845 105 -0.535 -0.006 -0.208 -0.001 0.005 -0.153 0.0858320585 114 -0.535 -0.035 -0.208 -0.001 0.005 -0.153 0.0853730780 117 -0.535 -0.029 -0.208 -0.001 0.005 -0.153 0.0853510734 118 -0.535 -0.030 -0.208 -0.001 0.005 -0.153 0.0853510672 127 -0.535 -0.030 -0.221 -0.001 0.005 -0.153 0.0851650491 128 -0.535 -0.030 -0.259 -0.001 0.005 -0.153 0.0851511382 130 -0.535 -0.030 -0.241 -0.001 0.005 -0.153 0.0850516844 132 -0.535 -0.030 -0.242 -0.001 0.005 -0.153 0.0850510149 141 -0.535 -0.030 -0.242 0.152 0.005 -0.153 0.0843202874 142 -0.535 -0.030 -0.242 0.141 0.005 -0.153 0.0842986286 155 -0.535 -0.030 -0.242 0.141 -0.105 -0.153 0.0840909518 156 -0.535 -0.030 -0.242 0.141 -0.058 -0.153 0.0831741902 157 -0.535 -0.030 -0.242 0.141 -0.053 -0.153 0.0830999274 159 -0.535 -0.030 -0.242 0.141 -0.044 -0.153 0.0830524023 169 -0.535 -0.030 -0.242 0.141 -0.044 -0.168 0.0828589009 171 -0.535 -0.030 -0.242 0.141 -0.044 -0.167 0.0828577215 powell nthiter 2: fret = 0.082858 187 -0.539 -0.030 -0.242 0.141 -0.044 -0.167 0.0828389202 198 -0.539 -0.005 -0.242 0.141 -0.044 -0.167 0.0827085173 199 -0.539 -0.006 -0.242 0.141 -0.044 -0.167 0.0826992654 200 -0.539 -0.014 -0.242 0.141 -0.044 -0.167 0.0826693303 211 -0.539 -0.014 -0.196 0.141 -0.044 -0.167 0.0821506121 213 -0.539 -0.014 -0.200 0.141 -0.044 -0.167 0.0821421532 223 -0.539 -0.014 -0.200 0.166 -0.044 -0.167 0.0820767932 225 -0.539 -0.014 -0.200 0.158 -0.044 -0.167 0.0820552886 238 -0.539 -0.014 -0.200 0.158 -0.041 -0.167 0.0820501269 250 -0.539 -0.014 -0.200 0.158 -0.041 -0.170 0.0820424229 powell nthiter 3: fret = 0.082042 265 -0.531 -0.014 -0.200 0.158 -0.041 -0.170 0.0819591099 266 -0.528 -0.014 -0.200 0.158 -0.041 -0.170 0.0819459551 267 -0.526 -0.014 -0.200 0.158 -0.041 -0.170 0.0819450850 277 -0.526 -0.012 -0.200 0.158 -0.041 -0.170 0.0819330758 278 -0.526 -0.004 -0.200 0.158 -0.041 -0.170 0.0819028579 280 -0.526 -0.005 -0.200 0.158 -0.041 -0.170 0.0819022291 292 -0.526 -0.005 -0.197 0.158 -0.041 -0.170 0.0819010498 294 -0.526 -0.005 -0.198 0.158 -0.041 -0.170 0.0819009503 302 -0.526 -0.005 -0.198 0.185 -0.041 -0.170 0.0818069250 304 -0.526 -0.005 -0.198 0.178 -0.041 -0.170 0.0817848674 318 -0.526 -0.005 -0.198 0.178 -0.044 -0.170 0.0817821615 330 -0.526 -0.005 -0.198 0.178 -0.044 -0.171 0.0817782489 331 -0.526 -0.005 -0.198 0.178 -0.044 -0.172 0.0817753738 334 -0.514 0.003 -0.196 0.198 -0.046 -0.174 0.0816273599 339 -0.506 0.008 -0.195 0.210 -0.048 -0.176 0.0816164634 341 -0.509 0.006 -0.196 0.205 -0.047 -0.175 0.0816109282 345 -0.509 0.006 -0.196 0.205 -0.047 -0.175 0.0816109120 346 -0.509 0.006 -0.196 0.205 -0.047 -0.175 0.0816107230 powell nthiter 4: fret = 0.081611 359 -0.517 0.006 -0.196 0.205 -0.047 -0.175 0.0815867993 360 -0.514 0.006 -0.196 0.205 -0.047 -0.175 0.0815785191 371 -0.514 0.014 -0.196 0.205 -0.047 -0.175 0.0815013366 372 -0.514 0.015 -0.196 0.205 -0.047 -0.175 0.0814964098 374 -0.514 0.016 -0.196 0.205 -0.047 -0.175 0.0814963292 385 -0.514 0.016 -0.185 0.205 -0.047 -0.175 0.0814610935 386 -0.514 0.016 -0.186 0.205 -0.047 -0.175 0.0814601632 397 -0.514 0.016 -0.186 0.205 -0.047 -0.167 0.0814468528 399 -0.514 0.016 -0.186 0.205 -0.047 -0.171 0.0814444339 400 -0.514 0.016 -0.186 0.205 -0.047 -0.170 0.0814437157 411 -0.514 0.016 -0.186 0.205 -0.054 -0.170 0.0814352253 412 -0.514 0.016 -0.186 0.205 -0.052 -0.170 0.0814318445 416 -0.501 0.024 -0.184 0.225 -0.054 -0.172 0.0812990697 419 -0.494 0.029 -0.183 0.237 -0.056 -0.173 0.0812881109 421 -0.497 0.027 -0.183 0.232 -0.055 -0.173 0.0812830027 422 -0.496 0.028 -0.183 0.233 -0.055 -0.173 0.0812822329 423 -0.496 0.028 -0.183 0.234 -0.055 -0.173 0.0812817784 432 -0.465 0.061 -0.168 0.290 -0.067 -0.174 0.0812736970 powell nthiter 5: fret = 0.081282 442 -0.500 0.028 -0.183 0.234 -0.055 -0.173 0.0812590622 456 -0.500 0.030 -0.183 0.234 -0.055 -0.173 0.0812588046 468 -0.500 0.030 -0.179 0.234 -0.055 -0.173 0.0812512815 469 -0.500 0.030 -0.178 0.234 -0.055 -0.173 0.0812505353 481 -0.500 0.030 -0.177 0.234 -0.055 -0.167 0.0812323100 482 -0.500 0.030 -0.177 0.234 -0.055 -0.169 0.0812302233 493 -0.500 0.030 -0.177 0.234 -0.065 -0.169 0.0812270064 494 -0.500 0.030 -0.177 0.234 -0.060 -0.169 0.0812068631 498 -0.487 0.038 -0.176 0.254 -0.063 -0.171 0.0811482791 502 -0.492 0.035 -0.176 0.246 -0.062 -0.170 0.0811343091 504 -0.491 0.035 -0.176 0.247 -0.062 -0.170 0.0811329196 507 -0.491 0.035 -0.176 0.248 -0.062 -0.170 0.0811324780 510 -0.487 0.043 -0.169 0.261 -0.069 -0.168 0.0810048004 513 -0.480 0.054 -0.158 0.284 -0.080 -0.163 0.0808495582 518 -0.478 0.056 -0.156 0.287 -0.081 -0.162 0.0808462400 519 -0.478 0.056 -0.156 0.287 -0.081 -0.162 0.0808461388 522 -0.479 0.056 -0.157 0.287 -0.081 -0.162 0.0808460416 523 -0.479 0.056 -0.157 0.287 -0.081 -0.162 0.0808459346 525 -0.479 0.056 -0.157 0.287 -0.081 -0.162 0.0808458094 527 -0.479 0.056 -0.157 0.287 -0.081 -0.162 0.0808457319 powell nthiter 6: fret = 0.080846 537 -0.473 0.056 -0.157 0.287 -0.081 -0.162 0.0808292291 548 -0.473 0.061 -0.157 0.287 -0.081 -0.162 0.0807177546 549 -0.473 0.072 -0.157 0.287 -0.081 -0.162 0.0804504381 551 -0.473 0.074 -0.157 0.287 -0.081 -0.162 0.0804424126 552 -0.473 0.075 -0.157 0.287 -0.081 -0.162 0.0804422164 564 -0.473 0.075 -0.150 0.287 -0.081 -0.162 0.0804115754 565 -0.473 0.075 -0.146 0.287 -0.081 -0.162 0.0804067887 566 -0.473 0.075 -0.147 0.287 -0.081 -0.162 0.0804063534 576 -0.473 0.075 -0.147 0.287 -0.081 -0.161 0.0803864931 577 -0.473 0.075 -0.147 0.287 -0.081 -0.154 0.0803314150 579 -0.473 0.075 -0.147 0.287 -0.081 -0.155 0.0803303206 589 -0.473 0.075 -0.147 0.287 -0.087 -0.155 0.0802871073 594 -0.469 0.082 -0.140 0.300 -0.094 -0.152 0.0802596126 598 -0.471 0.080 -0.143 0.295 -0.091 -0.153 0.0802577368 599 -0.470 0.081 -0.142 0.297 -0.093 -0.153 0.0802551543 600 -0.470 0.081 -0.142 0.297 -0.093 -0.153 0.0802548915 603 -0.470 0.081 -0.142 0.297 -0.093 -0.153 0.0802548344 604 -0.470 0.081 -0.142 0.297 -0.093 -0.153 0.0802545643 powell nthiter 7: fret = 0.080255 614 -0.437 0.081 -0.142 0.297 -0.093 -0.153 0.0801643030 616 -0.448 0.081 -0.142 0.297 -0.093 -0.153 0.0801605766 617 -0.456 0.081 -0.142 0.297 -0.093 -0.153 0.0801369441 620 -0.457 0.081 -0.142 0.297 -0.093 -0.153 0.0801358230 630 -0.457 0.083 -0.142 0.297 -0.093 -0.153 0.0800910705 631 -0.457 0.094 -0.142 0.297 -0.093 -0.153 0.0800886390 633 -0.457 0.089 -0.142 0.297 -0.093 -0.153 0.0800265869 646 -0.457 0.089 -0.146 0.297 -0.093 -0.153 0.0800236519 647 -0.457 0.089 -0.144 0.297 -0.093 -0.153 0.0800229998 658 -0.457 0.089 -0.144 0.297 -0.093 -0.150 0.0800144458 670 -0.457 0.089 -0.144 0.297 -0.098 -0.150 0.0799675072 671 -0.457 0.089 -0.144 0.297 -0.099 -0.150 0.0799659869 679 -0.457 0.090 -0.143 0.300 -0.100 -0.150 0.0799636050 686 -0.457 0.090 -0.143 0.300 -0.100 -0.150 0.0799634993 687 -0.443 0.099 -0.145 0.302 -0.107 -0.147 0.0797422739 690 -0.422 0.114 -0.148 0.306 -0.119 -0.142 0.0792636147 691 -0.386 0.138 -0.152 0.312 -0.139 -0.134 0.0785164001 698 -0.384 0.139 -0.152 0.312 -0.140 -0.134 0.0785157392 699 -0.385 0.139 -0.152 0.312 -0.140 -0.134 0.0785155963 704 -0.385 0.139 -0.152 0.312 -0.140 -0.134 0.0785153501 706 -0.385 0.139 -0.152 0.312 -0.140 -0.134 0.0785149478 powell nthiter 8: fret = 0.078515 708 -0.380 0.146 -0.145 0.326 -0.146 -0.131 0.0784652983 713 -0.379 0.148 -0.144 0.329 -0.148 -0.130 0.0784633672 717 -0.379 0.148 -0.143 0.330 -0.148 -0.130 0.0784631329 730 -0.379 0.147 -0.143 0.330 -0.148 -0.130 0.0784274648 731 -0.379 0.117 -0.143 0.330 -0.148 -0.130 0.0783406291 732 -0.379 0.131 -0.143 0.330 -0.148 -0.130 0.0779562458 734 -0.379 0.130 -0.143 0.330 -0.148 -0.130 0.0779529222 747 -0.379 0.130 -0.125 0.330 -0.148 -0.130 0.0778751839 748 -0.379 0.130 -0.130 0.330 -0.148 -0.130 0.0778695969 749 -0.379 0.130 -0.129 0.330 -0.148 -0.130 0.0778689574 762 -0.379 0.130 -0.129 0.330 -0.148 -0.129 0.0778667658 774 -0.379 0.130 -0.129 0.330 -0.147 -0.129 0.0778648949 777 -0.366 0.139 -0.130 0.332 -0.154 -0.126 0.0777241818 782 -0.363 0.141 -0.131 0.333 -0.156 -0.126 0.0777183737 783 -0.363 0.141 -0.131 0.333 -0.156 -0.126 0.0777181258 798 -0.348 0.149 -0.129 0.338 -0.165 -0.122 0.0777170363 799 -0.355 0.145 -0.130 0.335 -0.161 -0.124 0.0777121800 801 -0.353 0.146 -0.129 0.336 -0.162 -0.123 0.0777112378 803 -0.353 0.146 -0.129 0.336 -0.162 -0.123 0.0777108311 powell nthiter 9: fret = 0.077711 811 -0.355 0.142 -0.134 0.328 -0.158 -0.125 0.0776990473 813 -0.355 0.143 -0.133 0.329 -0.159 -0.124 0.0776981574 814 -0.355 0.143 -0.133 0.329 -0.159 -0.124 0.0776980363 815 -0.355 0.142 -0.133 0.329 -0.158 -0.125 0.0776980146 821 -0.355 0.142 -0.133 0.328 -0.158 -0.125 0.0776979462 822 -0.355 0.142 -0.133 0.328 -0.158 -0.125 0.0776978205 823 -0.355 0.142 -0.133 0.328 -0.158 -0.125 0.0776976223 829 -0.363 0.137 -0.132 0.327 -0.154 -0.127 0.0776548777 833 -0.363 0.137 -0.132 0.327 -0.154 -0.126 0.0776547721 835 -0.363 0.137 -0.132 0.327 -0.154 -0.126 0.0776546350 850 -0.363 0.137 -0.120 0.327 -0.154 -0.126 0.0776402230 851 -0.363 0.137 -0.125 0.327 -0.154 -0.126 0.0776373275 865 -0.363 0.137 -0.125 0.327 -0.154 -0.123 0.0776124488 877 -0.363 0.137 -0.125 0.327 -0.161 -0.123 0.0775815532 886 -0.348 0.145 -0.123 0.332 -0.170 -0.119 0.0775681301 887 -0.353 0.142 -0.123 0.331 -0.167 -0.120 0.0775640489 891 -0.353 0.142 -0.123 0.331 -0.167 -0.120 0.0775640481 894 -0.343 0.144 -0.116 0.329 -0.178 -0.115 0.0774777295 897 -0.326 0.147 -0.104 0.326 -0.196 -0.105 0.0773868032 900 -0.320 0.148 -0.099 0.325 -0.203 -0.102 0.0773763740 906 -0.320 0.147 -0.099 0.325 -0.203 -0.102 0.0773762396 907 -0.320 0.147 -0.099 0.325 -0.203 -0.102 0.0773762378 908 -0.320 0.147 -0.099 0.325 -0.203 -0.102 0.0773761358 powell nthiter 10: fret = 0.077376 914 -0.323 0.143 -0.104 0.316 -0.199 -0.104 0.0773408788 916 -0.323 0.143 -0.104 0.316 -0.199 -0.104 0.0773407046 917 -0.323 0.143 -0.104 0.316 -0.199 -0.104 0.0773406357 929 -0.321 0.144 -0.104 0.317 -0.200 -0.103 0.0773382658 930 -0.320 0.144 -0.104 0.317 -0.200 -0.103 0.0773377082 943 -0.320 0.144 -0.103 0.317 -0.200 -0.103 0.0773309412 944 -0.320 0.144 -0.095 0.317 -0.200 -0.103 0.0773129660 946 -0.320 0.144 -0.096 0.317 -0.200 -0.103 0.0773121700 957 -0.320 0.144 -0.096 0.317 -0.200 -0.111 0.0772782452 958 -0.320 0.144 -0.096 0.317 -0.200 -0.109 0.0772726112 969 -0.320 0.144 -0.096 0.317 -0.205 -0.109 0.0772562409 970 -0.320 0.144 -0.096 0.317 -0.206 -0.109 0.0772562051 973 -0.310 0.146 -0.089 0.315 -0.217 -0.104 0.0772355165 978 -0.311 0.146 -0.090 0.315 -0.216 -0.104 0.0772348088 979 -0.312 0.146 -0.090 0.315 -0.215 -0.105 0.0772347503 powell nthiter 11: fret = 0.077235 992 -0.314 0.141 -0.094 0.307 -0.211 -0.106 0.0772323642 994 -0.313 0.143 -0.092 0.311 -0.213 -0.106 0.0772266893 995 -0.313 0.143 -0.092 0.311 -0.213 -0.106 0.0772264351 997 -0.313 0.143 -0.093 0.310 -0.213 -0.106 0.0772261656 1018 -0.313 0.143 -0.093 0.310 -0.213 -0.106 0.0772261331 1028 -0.313 0.143 -0.086 0.310 -0.213 -0.106 0.0772044849 1040 -0.313 0.143 -0.086 0.310 -0.213 -0.107 0.0772008624 1051 -0.313 0.143 -0.086 0.310 -0.212 -0.107 0.0771995131 1054 -0.303 0.145 -0.078 0.308 -0.223 -0.102 0.0771879921 1059 -0.302 0.145 -0.077 0.308 -0.224 -0.101 0.0771868798 1061 -0.301 0.145 -0.077 0.308 -0.225 -0.100 0.0771866106 1062 -0.301 0.145 -0.077 0.308 -0.225 -0.100 0.0771866020 1064 -0.301 0.145 -0.077 0.308 -0.225 -0.101 0.0771864024 1070 -0.291 0.144 -0.064 0.301 -0.234 -0.096 0.0771665581 1076 -0.295 0.144 -0.069 0.304 -0.231 -0.098 0.0771652483 1077 -0.293 0.144 -0.067 0.302 -0.232 -0.097 0.0771632422 1078 -0.293 0.144 -0.066 0.302 -0.232 -0.097 0.0771628351 1080 -0.293 0.144 -0.066 0.302 -0.233 -0.097 0.0771627109 1081 -0.293 0.144 -0.066 0.302 -0.233 -0.097 0.0771624380 powell nthiter 12: fret = 0.077162 1091 -0.296 0.140 -0.070 0.294 -0.228 -0.099 0.0771590557 1093 -0.294 0.142 -0.068 0.297 -0.230 -0.098 0.0771536711 1094 -0.294 0.142 -0.068 0.297 -0.230 -0.098 0.0771534757 1107 -0.290 0.144 -0.068 0.299 -0.233 -0.097 0.0771470780 1110 -0.290 0.144 -0.068 0.299 -0.233 -0.097 0.0771470491 1112 -0.290 0.144 -0.068 0.299 -0.233 -0.097 0.0771467527 1119 -0.296 0.143 -0.072 0.300 -0.226 -0.101 0.0771380915 1121 -0.296 0.143 -0.072 0.300 -0.226 -0.100 0.0771377379 1125 -0.296 0.143 -0.072 0.300 -0.226 -0.100 0.0771375505 1138 -0.296 0.143 -0.072 0.300 -0.226 -0.102 0.0771365688 1147 -0.296 0.143 -0.072 0.300 -0.225 -0.102 0.0771333255 1150 -0.296 0.143 -0.072 0.300 -0.224 -0.102 0.0771315755 1153 -0.286 0.142 -0.059 0.293 -0.233 -0.098 0.0771255436 1157 -0.290 0.142 -0.064 0.295 -0.229 -0.099 0.0771213376 1159 -0.290 0.142 -0.064 0.295 -0.230 -0.099 0.0771212971 1161 -0.290 0.142 -0.064 0.295 -0.230 -0.099 0.0771211977 powell nthiter 13: fret = 0.077121 1172 -0.290 0.141 -0.065 0.293 -0.228 -0.100 0.0771185716 1177 -0.291 0.141 -0.065 0.293 -0.228 -0.100 0.0771182358 1189 -0.294 0.139 -0.065 0.292 -0.226 -0.100 0.0771140023 1190 -0.296 0.138 -0.066 0.291 -0.225 -0.101 0.0771129873 1193 -0.295 0.138 -0.066 0.291 -0.225 -0.101 0.0771126206 1203 -0.296 0.138 -0.066 0.291 -0.225 -0.101 0.0771126096 1205 -0.296 0.138 -0.066 0.291 -0.225 -0.101 0.0771125196 1220 -0.296 0.138 -0.066 0.291 -0.225 -0.102 0.0771123034 1231 -0.296 0.138 -0.066 0.291 -0.224 -0.102 0.0771118662 1239 -0.295 0.138 -0.065 0.291 -0.225 -0.102 0.0771114178 1241 -0.295 0.138 -0.065 0.291 -0.225 -0.102 0.0771113520 1242 -0.295 0.138 -0.065 0.291 -0.225 -0.102 0.0771112501 powell nthiter 14: fret = 0.077111 1260 -0.295 0.138 -0.065 0.291 -0.225 -0.102 0.0771112130 1262 -0.295 0.138 -0.065 0.291 -0.225 -0.102 0.0771111109 1279 -0.293 0.139 -0.064 0.290 -0.227 -0.101 0.0771107862 1280 -0.294 0.139 -0.064 0.290 -0.226 -0.101 0.0771107385 1282 -0.294 0.139 -0.064 0.290 -0.226 -0.101 0.0771106018 1284 -0.294 0.139 -0.064 0.290 -0.226 -0.101 0.0771104955 1285 -0.294 0.139 -0.064 0.290 -0.226 -0.101 0.0771104223 1286 -0.294 0.139 -0.064 0.290 -0.226 -0.101 0.0771101421 1329 -0.294 0.139 -0.064 0.290 -0.226 -0.101 0.0771101400 Powell done niters = 14 Computing relative cost 0 -25.0 -25.0 -25.0 1.024358 1 -25.0 -25.0 25.0 0.980000 2 -25.0 25.0 -25.0 1.019607 3 -25.0 25.0 25.0 1.022277 4 25.0 -25.0 -25.0 1.000674 5 25.0 -25.0 25.0 1.002508 6 25.0 25.0 -25.0 0.984433 7 25.0 25.0 25.0 1.010278 REL: 8 0.077110 8.044135 1.005517 rel = 0.0766871 Number of iterations 14 Min cost was 0.077110 Number of FunctionCalls 1330 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.478446 sec Parameters at optimum (transmm) -0.29374 0.13851 -0.06408 Parameters at optimum (rotdeg) 0.29037 -0.22622 -0.10118 Final costs ---------------- Number of surface hits 2108 WM Intensity 239.0587 +/- 37.2665 Ctx Intensity 334.4167 +/- 73.4545 Pct Contrast 31.5038 +/- 24.6050 Cost 0.0771 RelCost 0.1111 Reg at min cost was 0.00506 0.99998 0.00381 0.54480; 0.99645 -0.00536 0.08396 -0.18241; -0.08398 -0.00337 0.99646 -0.37779; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat, type = 14 Original Reg 0.00297 0.99997 0.00759 0.83787; 0.99602 -0.00363 0.08902 -0.32104; -0.08904 -0.00730 0.99600 -0.31540; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00209 -0.00001 0.00379 0.29307; -0.00043 0.00173 0.00506 -0.13863; -0.00506 -0.00393 -0.00046 0.06239; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.614813 Computing change in rh position Surface-RMS-Diff-mm 0.536021 0.125304 0.794672 mri_segreg done mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 7.3.2 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/scripts mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname sharky machine x86_64 user brainstimmaps movvol /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/template.nii regfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/tmp.bbregister.740032/bbr.pass1.dat subject Test_withT2 dof 6 outregfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 1.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1673735425 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00506 0.99998 0.00381 0.54480; 0.99645 -0.00536 0.08396 -0.18241; -0.08398 -0.00337 0.99646 -0.37779; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 1.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.027200 1 -25.0 -25.0 25.0 1.014589 2 -25.0 25.0 -25.0 1.010787 3 -25.0 25.0 25.0 1.009442 4 25.0 -25.0 -25.0 1.000706 5 25.0 -25.0 25.0 1.023112 6 25.0 25.0 -25.0 1.007425 7 25.0 25.0 25.0 1.005691 REL: 8 0.084466 8.098952 1.012369 rel = 0.0834336 Initial costs ---------------- Number of surface hits 212218 WM Intensity 236.9106 +/- 31.4969 Ctx Intensity 336.4732 +/- 72.8486 Pct Contrast 32.9093 +/- 23.5703 Cost 0.0845 RelCost 0.0834 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0801 0.0801 0.0 84 -0.1000 0.0000 -0.1000 -0.1000 0.0000 -0.1000 0.0791 0.0791 0.0 Brute Force -------------------------- Min cost was 0.079133 Number of iterations 729 Search time 0.794320 sec Parameters at best (transmm, rotdeg) -0.100 0.000 -0.100 -0.100 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 0 2 -0.1 3 -0.1 4 0 5 -0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.083036 7 -0.037 0.000 -0.100 -0.100 0.000 -0.100 0.0828898255 9 -0.049 0.000 -0.100 -0.100 0.000 -0.100 0.0828715927 20 -0.049 -0.134 -0.100 -0.100 0.000 -0.100 0.0826612230 21 -0.049 -0.098 -0.100 -0.100 0.000 -0.100 0.0826084726 22 -0.049 -0.092 -0.100 -0.100 0.000 -0.100 0.0826036801 24 -0.049 -0.087 -0.100 -0.100 0.000 -0.100 0.0825999304 27 -0.049 -0.085 -0.100 -0.100 0.000 -0.100 0.0825996580 35 -0.049 -0.085 -0.203 -0.100 0.000 -0.100 0.0822116759 37 -0.049 -0.085 -0.194 -0.100 0.000 -0.100 0.0822058621 41 -0.049 -0.085 -0.195 -0.100 0.000 -0.100 0.0822045175 48 -0.049 -0.085 -0.195 -0.284 0.000 -0.100 0.0812941437 49 -0.049 -0.085 -0.195 -0.286 0.000 -0.100 0.0812927552 50 -0.049 -0.085 -0.195 -0.316 0.000 -0.100 0.0812756914 54 -0.049 -0.085 -0.195 -0.330 0.000 -0.100 0.0812720018 56 -0.049 -0.085 -0.195 -0.328 0.000 -0.100 0.0812717266 57 -0.049 -0.085 -0.195 -0.325 0.000 -0.100 0.0812716621 60 -0.049 -0.085 -0.195 -0.326 0.000 -0.100 0.0812715800 78 -0.049 -0.085 -0.195 -0.326 0.000 0.027 0.0808289695 79 -0.049 -0.085 -0.195 -0.326 0.000 0.021 0.0808157316 80 -0.049 -0.085 -0.195 -0.326 0.000 0.002 0.0808079819 82 -0.049 -0.085 -0.195 -0.326 0.000 0.008 0.0808029463 83 -0.049 -0.085 -0.195 -0.326 0.000 0.009 0.0808025543 85 -0.049 -0.085 -0.195 -0.326 0.000 0.010 0.0808024704 powell nthiter 1: fret = 0.080802 94 -0.028 -0.085 -0.195 -0.326 0.000 0.010 0.0807464877 96 -0.022 -0.085 -0.195 -0.326 0.000 0.010 0.0807447693 97 -0.023 -0.085 -0.195 -0.326 0.000 0.010 0.0807443854 98 -0.024 -0.085 -0.195 -0.326 0.000 0.010 0.0807443747 106 -0.024 -0.223 -0.195 -0.326 0.000 0.010 0.0806580901 107 -0.024 -0.168 -0.195 -0.326 0.000 0.010 0.0805538143 109 -0.024 -0.179 -0.195 -0.326 0.000 0.010 0.0805520513 111 -0.024 -0.174 -0.195 -0.326 0.000 0.010 0.0805499587 120 -0.024 -0.174 -0.220 -0.326 0.000 0.010 0.0805348856 121 -0.024 -0.174 -0.217 -0.326 0.000 0.010 0.0805348499 123 -0.024 -0.174 -0.218 -0.326 0.000 0.010 0.0805347447 132 -0.024 -0.174 -0.218 -0.341 0.000 0.010 0.0805316643 133 -0.024 -0.174 -0.218 -0.338 0.000 0.010 0.0805289123 134 -0.024 -0.174 -0.218 -0.335 0.000 0.010 0.0805279542 135 -0.024 -0.174 -0.218 -0.336 0.000 0.010 0.0805278995 144 -0.024 -0.174 -0.218 -0.336 -0.019 0.010 0.0805194611 146 -0.024 -0.174 -0.218 -0.336 -0.020 0.010 0.0805194166 147 -0.024 -0.174 -0.218 -0.336 -0.021 0.010 0.0805189435 151 -0.024 -0.174 -0.218 -0.336 -0.034 0.010 0.0805060033 162 -0.024 -0.174 -0.218 -0.336 -0.034 -0.004 0.0804957772 163 -0.024 -0.174 -0.218 -0.336 -0.034 -0.010 0.0804884722 166 -0.024 -0.174 -0.218 -0.336 -0.034 -0.043 0.0804274575 169 -0.024 -0.174 -0.218 -0.336 -0.034 -0.047 0.0804236592 171 -0.024 -0.174 -0.218 -0.336 -0.034 -0.048 0.0804232067 powell nthiter 2: fret = 0.080423 180 -0.013 -0.174 -0.218 -0.336 -0.034 -0.048 0.0804100461 182 -0.010 -0.174 -0.218 -0.336 -0.034 -0.048 0.0804091185 183 -0.009 -0.174 -0.218 -0.336 -0.034 -0.048 0.0804090506 191 -0.009 -0.254 -0.218 -0.336 -0.034 -0.048 0.0803609735 192 -0.009 -0.223 -0.218 -0.336 -0.034 -0.048 0.0803310292 193 -0.009 -0.224 -0.218 -0.336 -0.034 -0.048 0.0803300964 194 -0.009 -0.231 -0.218 -0.336 -0.034 -0.048 0.0803255359 196 -0.009 -0.232 -0.218 -0.336 -0.034 -0.048 0.0803253512 197 -0.009 -0.233 -0.218 -0.336 -0.034 -0.048 0.0803251483 208 -0.009 -0.233 -0.230 -0.336 -0.034 -0.048 0.0803091220 209 -0.009 -0.233 -0.231 -0.336 -0.034 -0.048 0.0803089665 210 -0.009 -0.233 -0.232 -0.336 -0.034 -0.048 0.0803089637 220 -0.009 -0.233 -0.232 -0.371 -0.034 -0.048 0.0803027424 221 -0.009 -0.233 -0.232 -0.370 -0.034 -0.048 0.0803027378 222 -0.009 -0.233 -0.232 -0.369 -0.034 -0.048 0.0803026121 224 -0.009 -0.233 -0.232 -0.364 -0.034 -0.048 0.0803025194 225 -0.009 -0.233 -0.232 -0.366 -0.034 -0.048 0.0803022144 236 -0.009 -0.233 -0.232 -0.366 -0.032 -0.048 0.0803014401 246 -0.009 -0.233 -0.232 -0.366 -0.032 -0.069 0.0802663176 250 -0.009 -0.233 -0.232 -0.366 -0.032 -0.072 0.0802647560 253 0.005 -0.292 -0.247 -0.396 -0.030 -0.096 0.0802595964 259 -0.000 -0.270 -0.242 -0.384 -0.031 -0.087 0.0802442462 260 -0.001 -0.266 -0.241 -0.382 -0.031 -0.085 0.0802430509 261 -0.004 -0.256 -0.238 -0.378 -0.031 -0.081 0.0802425298 263 -0.003 -0.260 -0.239 -0.379 -0.031 -0.083 0.0802420858 265 -0.003 -0.260 -0.239 -0.379 -0.031 -0.083 0.0802420447 powell nthiter 3: fret = 0.080242 274 -0.018 -0.260 -0.239 -0.379 -0.031 -0.083 0.0802317077 276 -0.014 -0.260 -0.239 -0.379 -0.031 -0.083 0.0802303681 289 -0.014 -0.260 -0.239 -0.379 -0.031 -0.085 0.0802293155 298 -0.014 -0.260 -0.197 -0.379 -0.031 -0.085 0.0802201123 299 -0.014 -0.260 -0.214 -0.379 -0.031 -0.085 0.0802117279 301 -0.014 -0.260 -0.220 -0.379 -0.031 -0.085 0.0802111765 303 -0.014 -0.260 -0.221 -0.379 -0.031 -0.085 0.0802111042 313 -0.014 -0.260 -0.221 -0.397 -0.031 -0.085 0.0802048760 314 -0.014 -0.260 -0.221 -0.396 -0.031 -0.085 0.0802042093 315 -0.014 -0.260 -0.221 -0.391 -0.031 -0.085 0.0802025026 317 -0.014 -0.260 -0.221 -0.390 -0.031 -0.085 0.0802023321 318 -0.014 -0.260 -0.221 -0.389 -0.031 -0.085 0.0802022529 328 -0.014 -0.260 -0.221 -0.389 -0.027 -0.085 0.0801999869 336 -0.009 -0.282 -0.226 -0.401 -0.026 -0.094 0.0801924152 337 -0.010 -0.278 -0.225 -0.399 -0.026 -0.092 0.0801915428 338 -0.010 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801915168 339 -0.010 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801915000 340 -0.010 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801914939 342 -0.010 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801914452 powell nthiter 4: fret = 0.080191 352 -0.022 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801795981 354 -0.021 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801793448 355 -0.020 -0.277 -0.225 -0.398 -0.026 -0.092 0.0801792980 365 -0.020 -0.277 -0.225 -0.398 -0.026 -0.093 0.0801787314 376 -0.020 -0.277 -0.222 -0.398 -0.026 -0.093 0.0801786086 377 -0.020 -0.277 -0.223 -0.398 -0.026 -0.093 0.0801784614 384 -0.020 -0.277 -0.223 -0.428 -0.026 -0.093 0.0801744422 388 -0.020 -0.277 -0.223 -0.460 -0.026 -0.093 0.0801484726 390 -0.020 -0.277 -0.223 -0.454 -0.026 -0.093 0.0801432173 392 -0.020 -0.277 -0.223 -0.453 -0.026 -0.093 0.0801427852 393 -0.020 -0.277 -0.223 -0.452 -0.026 -0.093 0.0801426865 403 -0.020 -0.277 -0.223 -0.452 -0.031 -0.093 0.0801390312 405 -0.020 -0.277 -0.223 -0.452 -0.032 -0.093 0.0801389685 412 -0.014 -0.300 -0.229 -0.463 -0.031 -0.102 0.0801154986 413 -0.013 -0.306 -0.230 -0.466 -0.031 -0.105 0.0801124829 415 -0.012 -0.309 -0.231 -0.468 -0.031 -0.106 0.0801120961 417 -0.012 -0.309 -0.231 -0.468 -0.031 -0.106 0.0801120823 powell nthiter 5: fret = 0.080112 429 -0.019 -0.309 -0.231 -0.468 -0.031 -0.106 0.0800965776 432 -0.025 -0.309 -0.231 -0.468 -0.031 -0.106 0.0800911485 443 -0.025 -0.309 -0.231 -0.468 -0.031 -0.104 0.0800902020 454 -0.025 -0.309 -0.222 -0.468 -0.031 -0.104 0.0800862865 455 -0.025 -0.309 -0.224 -0.468 -0.031 -0.104 0.0800857291 467 -0.025 -0.309 -0.224 -0.469 -0.031 -0.104 0.0800854473 468 -0.025 -0.309 -0.224 -0.470 -0.031 -0.104 0.0800853593 478 -0.025 -0.309 -0.224 -0.470 -0.030 -0.104 0.0800847163 479 -0.025 -0.309 -0.224 -0.470 -0.027 -0.104 0.0800842539 481 -0.025 -0.309 -0.224 -0.470 -0.028 -0.104 0.0800751720 496 -0.025 -0.309 -0.224 -0.470 -0.028 -0.105 0.0800750388 499 -0.025 -0.309 -0.224 -0.470 -0.028 -0.105 0.0800749639 powell nthiter 6: fret = 0.080075 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.027506 1 -25.0 -25.0 25.0 1.015938 2 -25.0 25.0 -25.0 1.013929 3 -25.0 25.0 25.0 1.011014 4 25.0 -25.0 -25.0 0.997886 5 25.0 -25.0 25.0 1.022869 6 25.0 25.0 -25.0 1.006479 7 25.0 25.0 25.0 1.004277 REL: 8 0.080075 8.099899 1.012487 rel = 0.0790874 Number of iterations 6 Min cost was 0.080075 Number of FunctionCalls 576 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 15.381946 sec Parameters at optimum (transmm) -0.02539 -0.30890 -0.22392 Parameters at optimum (rotdeg) -0.46973 -0.02814 -0.10461 Final costs ---------------- Number of surface hits 212215 WM Intensity 235.9934 +/- 31.6510 Ctx Intensity 336.0701 +/- 71.8580 Pct Contrast 33.2448 +/- 23.4789 Cost 0.0801 RelCost 0.0834 Reg at min cost was 0.00692 0.99997 0.00349 0.51926; 0.99572 -0.00721 0.09212 -0.49540; -0.09214 -0.00284 0.99574 -0.59993; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat, type = 14 Original Reg 0.00506 0.99998 0.00381 0.54480; 0.99645 -0.00536 0.08396 -0.18241; -0.08398 -0.00337 0.99646 -0.37779; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00186 0.00001 0.00032 0.02554; 0.00073 0.00185 -0.00816 0.31299; 0.00816 -0.00054 0.00072 0.22214; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.234486 Computing change in rh position Surface-RMS-Diff-mm 0.355311 0.156353 0.727184 mri_segreg done MinCost: 0.080075 235.993385 336.070057 33.244776 tkregister2_cmdl --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat --noedit --ltaout /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz reg file /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 ---- Input registration matrix -------- 0.00692 0.99997 0.00349 0.51926; 0.99572 -0.00721 0.09212 -0.49540; -0.09214 -0.00284 0.99574 -0.59993; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz Tmov: -------------------- -1.00446 0.00000 0.00000 224.99904; 0.00000 0.00000 1.00000 -88.00012; 0.00000 -1.00446 0.00000 224.99904; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.00692 0.99997 0.00349 0.51926; 0.99572 -0.00721 0.09212 -0.49540; -0.09214 -0.00284 0.99574 -0.59993; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = Test_withT2 RegMat --------------------------- 0.00692 0.99997 0.00349 0.51926; 0.99572 -0.00721 0.09212 -0.49540; -0.09214 -0.00284 0.99574 -0.59993; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jan 10 13:13:17 CET 2023 Ended at Tue Jan 10 13:14:54 CET 2023 BBR-Run-Time-Sec 97 bbregister Done To check results, run: tkregisterfv --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.lta --surfs --sd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects cp /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.auto.lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.lta mri_convert -odt float -at /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.lta -rl /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.prenorm.mgz reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00118486, -0.999997, 0.00188591) j_ras = (0.0980046, -0.00176071, -0.995184) k_ras = (0.995185, 0.00136398, 0.0980023) INFO: Reading transformation from file /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/orig.mgz... INFO: Applying transformation from file /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99995 0.00812 0.00587 0.54312; -0.00808 0.99995 -0.00541 -0.57283; -0.00591 0.00537 0.99997 0.69818; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from ushrt to float (noscale = 0)... MRIchangeType: Building histogram 0 928 1000, flo=0, fhi=0.999, dest_type=3 writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.prenorm.mgz... mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/aseg.presurf.mgz -surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/lh.white identity.nofile -surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/surf/rh.white identity.nofile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.prenorm.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.norm.mgz setting seed for random number genererator to 1234 using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading mri_src from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.prenorm.mgz... Copying mri_dst from mri_src computing distance transform computing distance transform min_dist = 1 Erasing Border planes 4 Removing non-wm voxels 47601 non wm control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 MRIapplyBiasCorrectionSameGeometry() NaN found at voxel (0, 0, 0, 0) error: Numerical argument out of domain error: WARNING: 16777216 NaNs found in volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.prenorm.mgz... writing normalized volume to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 1018988 mri_normalize done mri_mask -transfer 255 -keep_mask_deletion_edits /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.norm.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/brain.finalsurfs.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri/T2.mgz...done. #-------------------------------------------- #@# MMPialSurf lh Tue Jan 10 13:15:17 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 7.3.2 7.3.2 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects/Test_withT2/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.3.2_testing/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface removing intersecting faces 000: 29 intersecting step 1 with no progress (num=29, old_num=29) 001: 29 intersecting step 2 with no progress (num=29, old_num=29) 002: 29 intersecting step 3 with no progress (num=29, old_num=29) 003: 29 intersecting step 4 with no progress (num=29, old_num=29) 004: 29 intersecting step 5 with no progress (num=29, old_num=29) 005: 29 intersecting step 6 with no progress (num=29, old_num=29) 006: 29 intersecting step 7 with no progress (num=29, old_num=29) 007: 29 intersecting step 8 with no progress (num=29, old_num=29) 008: 29 intersecting step 9 with no progress (num=29, old_num=29) 009: 29 intersecting step 10 with no progress (num=29, old_num=29) 010: 29 intersecting step 11 with no progress (num=29, old_num=29) 011: 29 intersecting step 12 with no progress (num=29, old_num=29) 012: 29 intersecting step 13 with no progress (num=29, old_num=29) 013: 29 intersecting step 14 with no progress (num=29, old_num=29) 014: 29 intersecting step 15 with no progress (num=29, old_num=29) 015: 29 intersecting step 16 with no progress (num=29, old_num=29) terminating search with 29 intersecting Area 231308 0.41456 0.33635 0.000197 6.4502 Corner 693924 60.00000 32.43870 0.055483 179.8686 Edge 346962 1.03824 0.49701 0.007399 6.5232 Hinge 346962 24.72730 30.06492 0.000044 179.9979 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.2749 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 MRISripNotLabel() ripped 6179/115656 vertices (109477 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume T2.mgz using multi modal weights vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (-3.05528,-18.0059,9.12601) CBVO Creating mask 115656 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 50, T2_max_inside 200, T2_min_outside = 10, T2_max_outside 50 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 Changed 526842 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0221587 Creating white distance volumes t=0.38687 (box.dx, box.dy, box.dz) = (130, 234, 308) (region->dx, region->dy, region->dz) = (130, 234, 308) (region->dx, region->dy, region->dz) = (130, 234, 308) Creating pial distance volumes t=0.777426 (box.dx, box.dy, box.dz) = (138, 242, 316) (region->dx, region->dy, region->dz) = (138, 242, 316) (region->dx, region->dy, region->dz) = (138, 242, 316) locating cortical regions not in interior range [50.0 --> 200.0], and not in exterior range [10.0 --> 50.0] t = 1.23221 Starting loop over 115656 vertices vno = 0, t = 1.23221 error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image Segmentation fault Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux recon-all -s Test_withT2 exited with ERRORS at Tue Jan 10 13:17:00 CET 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting