Fri Jan 6 17:07:14 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training /usr/local/freesurfer/bin/recon-all -s New_patient_test3_bugfix -i t1.nii.gz -T2 t2.nii.gz -all -parallel subjid New_patient_test3_bugfix setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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 8.7Gi 1.2Gi 113Mi 52Gi 53Gi Swap: 976Mi 101Mi 875Mi ######################################## program versions used 7.3.0 (freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89) 7.3.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.3.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.3.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.3.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.0 TimeStamp: 2023/01/06-16:07:14-GMT BuildTime: Jul 18 2022 00:12:13 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 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 /usr/local/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix mri_convert /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/t1.nii.gz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/001.mgz mri_convert /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/t1.nii.gz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/001.mgz reading from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Jan 6 17:07:16 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix mri_convert --no_scale 1 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/t2.nii.gz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz mri_convert --no_scale 1 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/t2.nii.gz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz reading from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Jan 6 17:07:19 CET 2023 Found 1 runs /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/001.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/rawavg.mgz mri_info /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix mri_convert /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz --conform mri_convert /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz --conform reading from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz... mri_add_xform_to_header -c /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/talairach.xfm /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz INFO: extension is mgz mri_info /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz orig.mgz ======================================== Volume information for /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 Fri Jan 6 17:07:28 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.3.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux Fri Jan 6 17:07:28 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.288344 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.288344/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.288344/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.288344/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.288344/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... Fri Jan 6 17:09:53 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Fri Jan 6 17:09:53 CET 2023 Ended at Fri Jan 6 17:11:10 CET 2023 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.3.0 --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 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 Fri Jan 6 17:11:13 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/talairach_avi.log tal_QC_AZS /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/talairach_avi.log TalAviQA: 0.96375 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Fri Jan 6 17:11:13 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.3.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux Fri Jan 6 17:11:13 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.289143 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.289143/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.289143/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.289143/ones.mgz 7.3.0 cwd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.289143/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.289143/ones.mgz sysname Linux hostname sharky machine x86_64 user brainstimmaps input ./tmp.mri_nu_correct.mni.289143/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.289143/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.289143/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.289143/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.289143/sum.junk --avgwf ./tmp.mri_nu_correct.mni.289143/input.mean.dat 7.3.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.289143/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.289143/sum.junk --avgwf ./tmp.mri_nu_correct.mni.289143/input.mean.dat sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.289143/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.289143/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.289143/ones.mgz --i ./tmp.mri_nu_correct.mni.289143/nu0.mgz --sum ./tmp.mri_nu_correct.mni.289143/sum.junk --avgwf ./tmp.mri_nu_correct.mni.289143/output.mean.dat 7.3.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.289143/ones.mgz --i ./tmp.mri_nu_correct.mni.289143/nu0.mgz --sum ./tmp.mri_nu_correct.mni.289143/sum.junk --avgwf ./tmp.mri_nu_correct.mni.289143/output.mean.dat sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.289143/ones.mgz Loading ./tmp.mri_nu_correct.mni.289143/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.289143/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.289143/nu0.mgz ./tmp.mri_nu_correct.mni.289143/nu0.mgz mul 1.19718070388619721578 Saving result to './tmp.mri_nu_correct.mni.289143/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.289143/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.289143/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.289143/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 Fri Jan 6 17:13:55 CET 2023 mri_nu_correct.mni done mri_add_xform_to_header -c /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Jan 6 17:13:56 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 11 seconds. #-------------------------------------------- #@# Skull Stripping Fri Jan 6 17:15:07 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=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 14 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 14 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 14 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 0.0378 hours 4 threads registration took 2 minutes and 16 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=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=8144905506 voxels, voxel volume =1.000 = 8144905506 mmm3 = 8144905.728 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 Fri Jan 6 17:17:34 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=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 795592 FSRUNTIME@ mri_em_register 0.0358 hours 4 threads registration took 2 minutes and 9 seconds. #-------------------------------------- #@# CA Normalize Fri Jan 6 17:19:43 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... 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 2 seconds. #-------------------------------------- #@# CA Reg Fri Jan 6 17:20:45 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.973061 #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 6.5390 tGradient 5.0130 tsec 11.9450 #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 5.2280 tGradient 4.8790 tsec 10.5000 #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 5.1920 tGradient 4.8860 tsec 10.4730 #GCMRL# 3 dt 369.920000 rms 0.893 0.000% neg 0 invalid 762 tFOTS 5.2080 tGradient 4.8260 tsec 10.4500 #GCMRL# 4 dt 369.920000 rms 0.888 0.560% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8490 tsec 5.2390 #GCMRL# 5 dt 369.920000 rms 0.884 0.398% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8760 tsec 5.2640 #GCMRL# 6 dt 369.920000 rms 0.883 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8110 tsec 5.1980 #GCMRL# 7 dt 369.920000 rms 0.882 0.196% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8450 tsec 5.2300 #GCMRL# 8 dt 369.920000 rms 0.881 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8920 tsec 5.2800 #GCMRL# 9 dt 369.920000 rms 0.880 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8100 tsec 5.1980 #GCMRL# 10 dt 369.920000 rms 0.880 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8250 tsec 5.2370 #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 5.2290 tGradient 4.8120 tsec 10.4520 #GCMRL# 12 dt 73.984000 rms 0.879 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8810 tsec 5.2760 #GCMRL# 13 dt 73.984000 rms 0.879 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8770 tsec 5.2630 #GCMRL# 14 dt 73.984000 rms 0.879 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8590 tsec 5.2490 #GCMRL# 15 dt 73.984000 rms 0.878 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9190 tsec 5.3070 #GCMRL# 16 dt 73.984000 rms 0.877 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9190 tsec 5.3070 #GCAMreg# pass 0 level1 5 level2 1 tsec 129.127 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 5.2130 tGradient 4.8230 tsec 10.4300 #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 5.2180 tGradient 4.8360 tsec 10.4700 #GCMRL# 20 dt 129.472000 rms 0.874 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7990 tsec 5.1900 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 5.2460 tGradient 3.3820 tsec 9.0270 #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 5.2290 tGradient 3.4030 tsec 9.0250 #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 5.2090 tGradient 3.3190 tsec 8.9550 #GCMRL# 25 dt 31.104000 rms 0.864 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3800 tsec 3.7750 #GCAMreg# pass 0 level1 4 level2 1 tsec 41.896 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 5.2260 tGradient 3.4070 tsec 9.0290 #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 5.2350 tGradient 3.3790 tsec 9.0290 #GCMRL# 29 dt 9.072000 rms 0.862 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4110 tsec 3.8060 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 4.9470 tGradient 2.6580 tsec 8.0020 #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 5.2660 tGradient 2.6050 tsec 8.2800 #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 7.1320 tGradient 2.6720 tsec 10.3050 #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 5.2320 tGradient 2.6590 tsec 8.3070 #GCMRL# 35 dt 6.400000 rms 0.874 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5830 tsec 2.9720 #GCAMreg# pass 0 level1 3 level2 1 tsec 48.121 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 4.8830 tGradient 2.5910 tsec 7.8650 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 4.8650 tGradient 2.0030 tsec 7.2580 #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 4.7140 tGradient 1.9990 tsec 7.1380 #GCAMreg# pass 0 level1 2 level2 1 tsec 24.133 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 4.9140 tGradient 2.0180 tsec 7.3280 #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 4.9040 tGradient 1.6240 tsec 6.9210 #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 4.9700 tGradient 1.5940 tsec 6.9650 #GCMRL# 46 dt 0.320000 rms 0.950 0.331% neg 0 invalid 762 tFOTS 4.9170 tGradient 1.5930 tsec 6.9000 #GCMRL# 47 dt 0.320000 rms 0.949 0.000% neg 0 invalid 762 tFOTS 4.9240 tGradient 1.6220 tsec 6.9570 #GCMRL# 48 dt 0.320000 rms 0.947 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6040 tsec 2.0150 #GCMRL# 49 dt 0.320000 rms 0.945 0.216% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6170 tsec 2.0300 #GCMRL# 50 dt 0.320000 rms 0.943 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6250 tsec 2.0400 #GCMRL# 51 dt 0.320000 rms 0.943 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6160 tsec 2.0500 #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 4.9810 tGradient 1.6320 tsec 7.0120 #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 4.9950 tGradient 1.6140 tsec 7.0300 #GCMRL# 54 dt 0.112000 rms 0.940 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5820 tsec 1.9920 #GCMRL# 55 dt 0.112000 rms 0.940 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5920 tsec 2.0060 #GCMRL# 56 dt 0.112000 rms 0.939 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5840 tsec 1.9950 #GCMRL# 57 dt 0.112000 rms 0.939 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5570 tsec 1.9740 #GCMRL# 58 dt 0.112000 rms 0.938 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5620 tsec 2.0700 #GCMRL# 59 dt 0.112000 rms 0.938 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6570 tsec 2.0610 #GCAMreg# pass 0 level1 1 level2 1 tsec 71.081 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 4.9250 tGradient 1.5600 tsec 6.8840 #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 4.9780 tGradient 1.5800 tsec 6.9740 #GCMRL# 63 dt 0.256000 rms 0.936 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5690 tsec 1.9860 #GCMRL# 64 dt 0.256000 rms 0.935 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5810 tsec 2.0950 #GCMRL# 65 dt 0.256000 rms 0.935 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5870 tsec 1.9970 #GCMRL# 66 dt 0.256000 rms 0.934 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5980 tsec 2.0060 #GCMRL# 67 dt 0.256000 rms 0.934 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5910 tsec 2.0050 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 4.9730 tGradient 1.1840 tsec 6.5520 #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 4.9830 tGradient 1.1900 tsec 6.5880 #GCAMreg# pass 0 level1 0 level2 1 tsec 21.958 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 4.9760 tGradient 1.1920 tsec 6.5670 #FOTS# QuadFit found better minimum quadopt=(dt=0.00175,rms=0.901349) vs oldopt=(dt=0.00125,rms=0.901349) GCAMregister done in 7.88037 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 2.86372 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 5.3010 tGradient 2.1990 tsec 7.8950 #GCMRL# 75 dt 369.920000 rms 0.850 2.158% neg 0 invalid 762 tFOTS 5.3000 tGradient 2.1620 tsec 7.8580 #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 6.8880 tGradient 2.1360 tsec 9.4320 #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 5.2290 tGradient 2.1630 tsec 7.7860 #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 5.3160 tGradient 2.1380 tsec 7.8490 #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 5.2370 tGradient 2.1430 tsec 7.7770 #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 5.1970 tGradient 2.3120 tsec 7.9000 #GCMRL# 81 dt 369.920000 rms 0.830 0.290% neg 0 invalid 762 tFOTS 5.3530 tGradient 2.2130 tsec 7.9750 #GCMRL# 82 dt 92.480000 rms 0.830 0.000% neg 0 invalid 762 tFOTS 5.1950 tGradient 2.2210 tsec 7.8290 #GCMRL# 83 dt 92.480000 rms 0.829 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2320 tsec 2.6200 #GCMRL# 84 dt 92.480000 rms 0.829 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2040 tsec 2.7170 #GCMRL# 85 dt 92.480000 rms 0.828 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2140 tsec 2.6020 #GCMRL# 86 dt 92.480000 rms 0.827 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1560 tsec 2.5500 #GCMRL# 87 dt 92.480000 rms 0.826 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1640 tsec 2.5520 #GCMRL# 88 dt 92.480000 rms 0.824 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1430 tsec 2.5320 #GCMRL# 89 dt 92.480000 rms 0.823 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1560 tsec 2.5460 #GCMRL# 90 dt 92.480000 rms 0.822 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1540 tsec 2.6590 #GCMRL# 91 dt 92.480000 rms 0.821 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1660 tsec 2.5550 #GCMRL# 92 dt 92.480000 rms 0.820 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1560 tsec 2.5450 #GCMRL# 93 dt 92.480000 rms 0.819 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1990 tsec 2.5920 #GCMRL# 94 dt 92.480000 rms 0.818 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1160 tsec 2.6160 #GCMRL# 95 dt 92.480000 rms 0.817 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1420 tsec 2.5340 #GCMRL# 96 dt 92.480000 rms 0.816 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1510 tsec 2.6300 #GCMRL# 97 dt 92.480000 rms 0.815 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1280 tsec 2.5120 #GCMRL# 98 dt 92.480000 rms 0.814 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1580 tsec 2.6350 #GCMRL# 99 dt 92.480000 rms 0.813 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1670 tsec 2.5520 #GCMRL# 100 dt 92.480000 rms 0.812 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1740 tsec 2.5680 #GCMRL# 101 dt 92.480000 rms 0.811 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1960 tsec 2.5930 #GCMRL# 102 dt 92.480000 rms 0.810 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1060 tsec 2.6150 #GCMRL# 103 dt 92.480000 rms 0.809 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1090 tsec 2.5040 #GCMRL# 104 dt 92.480000 rms 0.808 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1760 tsec 2.5700 #GCMRL# 105 dt 92.480000 rms 0.807 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1990 tsec 2.7070 #GCMRL# 106 dt 92.480000 rms 0.806 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1390 tsec 2.6410 #GCMRL# 107 dt 92.480000 rms 0.806 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1870 tsec 2.5770 #GCMRL# 108 dt 92.480000 rms 0.805 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2130 tsec 2.7180 #GCMRL# 109 dt 92.480000 rms 0.804 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1830 tsec 2.5700 #GCMRL# 110 dt 92.480000 rms 0.803 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2020 tsec 2.5920 #GCMRL# 111 dt 92.480000 rms 0.802 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1320 tsec 2.6400 #GCMRL# 112 dt 92.480000 rms 0.802 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1390 tsec 2.6270 #GCMRL# 113 dt 92.480000 rms 0.801 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1030 tsec 2.6080 #GCMRL# 114 dt 92.480000 rms 0.801 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1590 tsec 2.5480 #GCMRL# 115 dt 92.480000 rms 0.801 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1580 tsec 2.5520 #GCMRL# 116 dt 92.480000 rms 0.800 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2400 tsec 2.6350 #GCMRL# 117 dt 92.480000 rms 0.799 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2030 tsec 2.5980 #GCMRL# 118 dt 92.480000 rms 0.799 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2010 tsec 2.5940 #GCMRL# 119 dt 92.480000 rms 0.798 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2320 tsec 2.7140 #GCMRL# 120 dt 92.480000 rms 0.798 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2220 tsec 2.6160 #GCMRL# 121 dt 92.480000 rms 0.798 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2600 tsec 2.7780 #GCMRL# 122 dt 92.480000 rms 0.797 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2530 tsec 2.6540 #GCMRL# 123 dt 92.480000 rms 0.797 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2460 tsec 2.7530 #GCMRL# 124 dt 92.480000 rms 0.796 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2210 tsec 2.7280 #GCMRL# 125 dt 92.480000 rms 0.796 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3040 tsec 2.8130 #GCMRL# 126 dt 92.480000 rms 0.795 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3380 tsec 2.8480 #GCMRL# 127 dt 92.480000 rms 0.795 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3260 tsec 2.8260 #GCMRL# 128 dt 92.480000 rms 0.795 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2130 tsec 2.7170 #GCMRL# 129 dt 92.480000 rms 0.794 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3090 tsec 2.8140 #GCMRL# 130 dt 92.480000 rms 0.794 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1950 tsec 2.5880 #GCMRL# 131 dt 92.480000 rms 0.794 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1800 tsec 2.5760 #GCMRL# 132 dt 92.480000 rms 0.793 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1720 tsec 2.5650 #GCMRL# 133 dt 92.480000 rms 0.793 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1890 tsec 2.5790 #GCMRL# 134 dt 92.480000 rms 0.793 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1840 tsec 2.5760 #GCMRL# 135 dt 92.480000 rms 0.792 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2140 tsec 2.6460 #GCMRL# 136 dt 92.480000 rms 0.792 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2040 tsec 2.6500 #GCMRL# 137 dt 92.480000 rms 0.792 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2960 tsec 2.6890 #GCMRL# 138 dt 92.480000 rms 0.791 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2960 tsec 2.6880 #GCMRL# 139 dt 92.480000 rms 0.791 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1710 tsec 2.6140 #GCMRL# 140 dt 92.480000 rms 0.791 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1840 tsec 2.6900 #GCMRL# 141 dt 92.480000 rms 0.791 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1910 tsec 2.6980 #GCMRL# 142 dt 92.480000 rms 0.790 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1970 tsec 2.7010 #GCMRL# 143 dt 92.480000 rms 0.790 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1880 tsec 2.6900 #GCMRL# 144 dt 92.480000 rms 0.790 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1860 tsec 2.5820 #GCMRL# 145 dt 92.480000 rms 0.790 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1690 tsec 2.5610 #GCMRL# 146 dt 92.480000 rms 0.789 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1980 tsec 2.5950 #GCMRL# 147 dt 92.480000 rms 0.789 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1880 tsec 2.6310 #GCMRL# 148 dt 92.480000 rms 0.789 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1830 tsec 2.5800 #GCMRL# 149 dt 92.480000 rms 0.789 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1720 tsec 2.5660 #GCMRL# 150 dt 92.480000 rms 0.789 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1790 tsec 2.6890 #GCMRL# 151 dt 92.480000 rms 0.788 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2610 tsec 2.6580 #GCMRL# 152 dt 92.480000 rms 0.788 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1850 tsec 2.5800 #GCMRL# 153 dt 92.480000 rms 0.788 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1640 tsec 2.6280 #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 271.409 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 5.0140 tGradient 2.1950 tsec 7.6080 #GCMRL# 156 dt 23.120000 rms 0.788 0.000% neg 0 invalid 762 tFOTS 5.5720 tGradient 2.1840 tsec 8.4820 #GCMRL# 157 dt 23.120000 rms 0.788 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1900 tsec 2.5860 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 4.8940 tGradient 1.8590 tsec 7.1480 #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 5.2370 tGradient 1.8520 tsec 7.4840 #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 5.2610 tGradient 1.8150 tsec 7.4760 #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 5.2800 tGradient 1.8730 tsec 7.5540 #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 5.3120 tGradient 1.8800 tsec 7.5920 #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 5.2490 tGradient 1.8650 tsec 7.5090 #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 6.8030 tGradient 1.8630 tsec 9.0780 #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 6.5950 tGradient 1.8120 tsec 8.8110 #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 6.8040 tGradient 1.8180 tsec 9.0240 #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 6.6990 tGradient 1.8270 tsec 8.9250 #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 4.5840 tGradient 1.8780 tsec 6.8550 #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 6.3460 tGradient 1.8530 tsec 8.5990 #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 5.2900 tGradient 1.8710 tsec 7.5630 #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 4.9200 tGradient 1.8800 tsec 7.1950 #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 4.8390 tGradient 1.8580 tsec 7.0910 #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 6.3820 tGradient 1.8360 tsec 8.6290 #GCMRL# 175 dt 82.944000 rms 0.743 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8740 tsec 2.3830 #GCMRL# 176 dt 82.944000 rms 0.742 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8610 tsec 2.2490 #GCMRL# 177 dt 82.944000 rms 0.742 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8280 tsec 2.4190 #GCMRL# 178 dt 82.944000 rms 0.741 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8320 tsec 2.2230 #GCMRL# 179 dt 10.368000 rms 0.741 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8730 tsec 2.9880 #GCMRL# 180 dt 5.184000 rms 0.741 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8280 tsec 2.6000 #GCMRL# 181 dt 1.620000 rms 0.741 0.000% neg 0 invalid 762 tFOTS 3.9000 tGradient 1.8700 tsec 6.1790 #GCMRL# 182 dt 0.202500 rms 0.741 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8650 tsec 2.9940 #GCMRL# 183 dt 0.050625 rms 0.741 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8480 tsec 2.7840 #GCAMreg# pass 0 level1 4 level2 1 tsec 158.549 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 4.8650 tGradient 1.8520 tsec 7.1020 #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 5.1720 tGradient 1.8470 tsec 7.4030 #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 5.1690 tGradient 1.9040 tsec 7.4620 #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 5.1230 tGradient 1.7830 tsec 7.3000 #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 5.2010 tGradient 1.8080 tsec 7.3960 #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 5.0950 tGradient 1.8320 tsec 7.3150 #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 5.1790 tGradient 1.8360 tsec 7.4060 #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 5.1630 tGradient 1.8490 tsec 7.4230 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 4.9350 tGradient 1.7120 tsec 7.0450 #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 4.9640 tGradient 1.7290 tsec 7.0930 #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 4.9390 tGradient 1.7590 tsec 7.0920 #GCMRL# 197 dt 32.000000 rms 0.708 0.433% neg 0 invalid 762 tFOTS 4.8890 tGradient 1.7630 tsec 7.0460 #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 4.8690 tGradient 1.7270 tsec 6.9850 #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 4.8450 tGradient 1.7200 tsec 6.9560 #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 4.8580 tGradient 1.7070 tsec 6.9580 #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 4.5270 tGradient 1.7380 tsec 6.6550 #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 4.5330 tGradient 1.7480 tsec 6.6700 #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 4.5760 tGradient 1.7540 tsec 6.7190 #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 4.5710 tGradient 1.7600 tsec 6.7240 #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 3.6340 tGradient 1.7660 tsec 5.8110 #GCMRL# 206 dt 0.175000 rms 0.695 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7470 tsec 2.1320 #GCMRL# 207 dt 0.021875 rms 0.695 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7550 tsec 2.9910 #GCMRL# 208 dt 0.010937 rms 0.695 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7740 tsec 2.5720 #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 96.734 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 5.1810 tGradient 1.7840 tsec 7.3590 #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 5.1670 tGradient 1.7870 tsec 7.3470 #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 5.1860 tGradient 1.7160 tsec 7.3090 #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 4.5670 tGradient 1.6920 tsec 6.6480 #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 5.1650 tGradient 1.8220 tsec 7.3760 #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 5.2010 tGradient 1.7990 tsec 7.3920 #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 5.1900 tGradient 1.9730 tsec 7.5550 #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 4.8470 tGradient 1.7220 tsec 6.9600 #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 5.1350 tGradient 1.7290 tsec 7.2560 #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 5.1480 tGradient 1.6940 tsec 7.2310 #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 5.1580 tGradient 1.6790 tsec 7.2260 #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 4.8550 tGradient 1.6780 tsec 6.9270 #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 5.1360 tGradient 1.7470 tsec 7.2770 #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 5.1600 tGradient 1.7890 tsec 7.3400 #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 5.1470 tGradient 1.6800 tsec 7.2160 #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 4.8410 tGradient 1.6960 tsec 6.9260 #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 4.8500 tGradient 1.7090 tsec 6.9560 #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 5.2490 tGradient 1.8010 tsec 7.4470 #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 4.9260 tGradient 1.7270 tsec 7.0640 #GCMRL# 229 dt 19.200000 rms 0.670 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6840 tsec 2.0660 #GCMRL# 230 dt 19.200000 rms 0.670 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6610 tsec 2.0470 #GCMRL# 231 dt 19.200000 rms 0.669 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6940 tsec 2.0810 #GCMRL# 232 dt 19.200000 rms 0.668 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6850 tsec 2.0730 #GCMRL# 233 dt 19.200000 rms 0.667 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6650 tsec 2.0520 #GCMRL# 234 dt 19.200000 rms 0.666 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7080 tsec 2.0930 #GCMRL# 235 dt 19.200000 rms 0.664 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6580 tsec 2.0620 #GCMRL# 236 dt 19.200000 rms 0.663 0.212% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6280 tsec 2.0160 #GCMRL# 237 dt 19.200000 rms 0.661 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6620 tsec 2.0490 #GCMRL# 238 dt 19.200000 rms 0.660 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6760 tsec 2.0620 #GCMRL# 239 dt 19.200000 rms 0.659 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6690 tsec 2.0570 #GCMRL# 240 dt 19.200000 rms 0.657 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6680 tsec 2.0520 #GCMRL# 241 dt 19.200000 rms 0.656 0.225% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6120 tsec 2.0150 #GCMRL# 242 dt 19.200000 rms 0.654 0.203% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6220 tsec 2.0050 #GCMRL# 243 dt 19.200000 rms 0.653 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6260 tsec 2.0100 #GCMRL# 244 dt 19.200000 rms 0.652 0.173% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6200 tsec 2.0040 #GCMRL# 245 dt 19.200000 rms 0.651 0.180% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6200 tsec 2.1210 #GCMRL# 246 dt 19.200000 rms 0.650 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6560 tsec 2.0380 #GCMRL# 247 dt 19.200000 rms 0.649 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6550 tsec 2.0380 #GCMRL# 248 dt 19.200000 rms 0.648 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6300 tsec 2.0140 #GCMRL# 249 dt 19.200000 rms 0.647 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6800 tsec 2.0630 #GCMRL# 250 dt 19.200000 rms 0.646 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6040 tsec 1.9850 #GCMRL# 251 dt 19.200000 rms 0.645 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6210 tsec 2.0050 #GCMRL# 252 dt 19.200000 rms 0.645 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6920 tsec 2.0870 #GCMRL# 253 dt 19.200000 rms 0.644 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6590 tsec 2.0430 #GCMRL# 254 dt 19.200000 rms 0.644 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6080 tsec 2.1140 #GCMRL# 255 dt 19.200000 rms 0.643 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6200 tsec 2.0210 #GCMRL# 256 dt 19.200000 rms 0.642 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6230 tsec 2.0050 #GCMRL# 257 dt 19.200000 rms 0.642 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6490 tsec 2.1440 #GCMRL# 258 dt 19.200000 rms 0.641 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6230 tsec 2.0070 #GCMRL# 259 dt 19.200000 rms 0.641 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6100 tsec 1.9950 #GCMRL# 260 dt 19.200000 rms 0.640 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6090 tsec 1.9980 #GCMRL# 261 dt 19.200000 rms 0.640 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6080 tsec 2.0110 #GCMRL# 262 dt 19.200000 rms 0.639 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6300 tsec 2.0120 #GCMRL# 263 dt 19.200000 rms 0.639 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6390 tsec 2.0210 #GCMRL# 264 dt 19.200000 rms 0.639 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7200 tsec 2.1030 #GCMRL# 265 dt 19.200000 rms 0.638 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6710 tsec 2.0640 #GCMRL# 266 dt 19.200000 rms 0.638 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6730 tsec 2.0730 #GCMRL# 267 dt 19.200000 rms 0.638 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6290 tsec 2.0280 #GCMRL# 268 dt 19.200000 rms 0.637 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5680 tsec 2.0680 #GCMRL# 269 dt 19.200000 rms 0.637 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5950 tsec 1.9780 #GCMRL# 270 dt 19.200000 rms 0.637 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5660 tsec 1.9510 #GCMRL# 271 dt 19.200000 rms 0.637 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5710 tsec 1.9560 #GCMRL# 272 dt 19.200000 rms 0.636 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6450 tsec 2.0290 #GCMRL# 273 dt 19.200000 rms 0.636 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6410 tsec 2.0290 #GCMRL# 274 dt 19.200000 rms 0.636 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6840 tsec 2.0740 #GCMRL# 275 dt 19.200000 rms 0.635 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6610 tsec 2.0440 #GCMRL# 276 dt 19.200000 rms 0.635 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6320 tsec 2.0330 #GCMRL# 277 dt 19.200000 rms 0.635 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6220 tsec 2.0070 #GCMRL# 278 dt 19.200000 rms 0.635 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6180 tsec 2.0190 #GCMRL# 279 dt 19.200000 rms 0.634 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6140 tsec 1.9960 #GCMRL# 280 dt 19.200000 rms 0.634 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6880 tsec 2.0720 #GCMRL# 281 dt 19.200000 rms 0.634 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6530 tsec 2.0350 #GCMRL# 282 dt 19.200000 rms 0.634 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6470 tsec 2.0290 #GCMRL# 283 dt 19.200000 rms 0.633 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6240 tsec 2.0140 #GCMRL# 284 dt 19.200000 rms 0.633 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6260 tsec 2.0080 #GCMRL# 285 dt 19.200000 rms 0.633 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6060 tsec 1.9900 #GCMRL# 286 dt 19.200000 rms 0.633 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6150 tsec 1.9970 #GCMRL# 287 dt 19.200000 rms 0.632 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6180 tsec 2.0010 #GCMRL# 288 dt 19.200000 rms 0.632 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6070 tsec 1.9910 #GCMRL# 289 dt 19.200000 rms 0.632 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6420 tsec 2.0320 #GCMRL# 290 dt 19.200000 rms 0.632 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6110 tsec 2.0000 #GCMRL# 291 dt 19.200000 rms 0.631 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6290 tsec 2.0100 #GCMRL# 292 dt 19.200000 rms 0.631 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6110 tsec 1.9930 #GCMRL# 293 dt 19.200000 rms 0.631 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6440 tsec 2.0270 #GCMRL# 294 dt 19.200000 rms 0.631 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6180 tsec 2.0050 #GCMRL# 295 dt 19.200000 rms 0.631 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6540 tsec 2.0570 #GCMRL# 296 dt 19.200000 rms 0.631 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6130 tsec 2.0200 #GCMRL# 297 dt 32.000000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 4.8270 tGradient 1.5900 tsec 6.8270 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 4.5660 tGradient 1.5800 tsec 6.5350 #GCMRL# 300 dt 0.150000 rms 0.654 0.000% neg 0 invalid 762 tFOTS 4.5630 tGradient 1.5720 tsec 6.8400 #GCAMreg# pass 0 level1 2 level2 1 tsec 17.793 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 4.8840 tGradient 1.5570 tsec 6.8370 #GCMRL# 303 dt 0.150000 rms 0.654 0.000% neg 0 invalid 762 tFOTS 4.8920 tGradient 1.5670 tsec 7.1680 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 4.5620 tGradient 1.5300 tsec 6.4830 #GCMRL# 306 dt 0.320000 rms 0.698 0.000% neg 0 invalid 762 tFOTS 4.8580 tGradient 1.5420 tsec 6.8060 #GCAMreg# pass 0 level1 1 level2 1 tsec 17.664 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 4.9490 tGradient 1.5410 tsec 6.8830 #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 4.9550 tGradient 1.5210 tsec 6.8950 #GCMRL# 310 dt 0.448000 rms 0.697 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5360 tsec 1.9470 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 4.6160 tGradient 1.1460 tsec 6.1540 #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 4.5380 tGradient 1.1310 tsec 6.0610 #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 4.6280 tGradient 1.1250 tsec 6.1530 #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 4.5550 tGradient 1.1260 tsec 6.0720 #GCMRL# 316 dt 0.320000 rms 0.598 0.250% neg 0 invalid 762 tFOTS 4.6510 tGradient 1.1430 tsec 6.1950 #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 4.5980 tGradient 1.1420 tsec 6.1320 #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 4.5870 tGradient 1.1300 tsec 6.1070 #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 4.5630 tGradient 1.1350 tsec 6.0920 #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 4.5630 tGradient 1.1340 tsec 6.0870 #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 4.5560 tGradient 1.1290 tsec 6.0760 #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 4.6630 tGradient 1.1330 tsec 6.1950 #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 4.5640 tGradient 1.1320 tsec 6.1060 #GCMRL# 324 dt 0.448000 rms 0.593 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1220 tsec 1.5130 #GCMRL# 325 dt 0.448000 rms 0.593 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1640 tsec 1.5650 #GCMRL# 326 dt 0.224000 rms 0.593 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1260 tsec 1.8920 #GCMRL# 327 dt 0.224000 rms 0.593 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1550 tsec 1.5460 #GCMRL# 328 dt 0.224000 rms 0.592 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1370 tsec 1.5270 #GCMRL# 329 dt 0.224000 rms 0.592 -0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1390 tsec 2.0540 #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 91.469 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 4.5640 tGradient 1.1410 tsec 6.0990 #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 4.5620 tGradient 1.1300 tsec 6.0850 #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 4.5700 tGradient 1.1250 tsec 6.0910 #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 4.5650 tGradient 1.1340 tsec 6.0940 #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 4.5380 tGradient 1.1320 tsec 6.0570 #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 4.5400 tGradient 1.1330 tsec 6.0660 #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 4.5470 tGradient 1.1270 tsec 6.0850 #GCMRL# 338 dt 0.384000 rms 0.571 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1380 tsec 1.5270 #GCMRL# 339 dt 0.384000 rms 0.570 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1340 tsec 1.5250 #GCMRL# 340 dt 0.384000 rms 0.570 -0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1360 tsec 2.0310 #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 6.0490 tGradient 1.1330 tsec 7.5760 GCAMregister done in 18.7503 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 5.9020 tGradient 2.0400 tsec 8.3340 #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 20.571 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 5.5840 tGradient 2.0350 tsec 8.0130 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 5.8880 tGradient 1.7450 tsec 8.0260 #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 5.9490 tGradient 1.7130 tsec 8.0780 #GCAMreg# pass 0 level1 4 level2 1 tsec 20.601 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 5.8500 tGradient 1.7120 tsec 7.9530 #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 5.8390 tGradient 1.6760 tsec 7.9300 #GCMRL# 352 dt 9.072000 rms 0.567 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7130 tsec 2.1020 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 5.8920 tGradient 1.6350 tsec 8.9640 #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 5.9220 tGradient 1.7760 tsec 8.8440 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 26.196 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 5.8730 tGradient 1.7540 tsec 11.1760 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 5.8980 tGradient 1.7950 tsec 8.7900 #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 5.8560 tGradient 1.7430 tsec 8.7100 #GCMRL# 360 dt 9.600000 rms 0.553 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7390 tsec 2.1300 #GCMRL# 361 dt 9.600000 rms 0.552 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7350 tsec 2.1260 #GCMRL# 362 dt 9.600000 rms 0.551 0.205% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7370 tsec 2.1240 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 1.7360 tsec 3.6330 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 1.7310 tsec 3.9810 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 1.7580 tsec 3.2880 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 1.7250 tsec 3.6350 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 1.7590 tsec 3.9840 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 1.7520 tsec 4.3870 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 1.7460 tsec 6.4420 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 1.7400 tsec 3.2730 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 1.7340 tsec 3.9600 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 1.7420 tsec 5.0720 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 1.7600 tsec 4.7530 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 1.7990 tsec 3.7380 #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 7.1780 tGradient 1.7940 tsec 10.2010 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 7.9120 tGradient 1.6070 tsec 12.8120 #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 7.9240 tGradient 1.6150 tsec 11.8140 #GCMRL# 379 dt 1.008000 rms 0.541 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6110 tsec 2.0890 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 32.956 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 7.7710 tGradient 1.5970 tsec 9.7550 #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 7.3680 tGradient 1.5730 tsec 10.4930 #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 7.8400 tGradient 1.5860 tsec 11.3180 #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 7.7680 tGradient 1.6060 tsec 9.7640 #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 7.7700 tGradient 1.5840 tsec 9.7650 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 1.5900 tsec 3.5090 #GCMRL# 387 dt 4.545455 rms 0.531 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5700 tsec 2.0640 #GCMRL# 388 dt 4.545455 rms 0.529 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5800 tsec 2.0930 #GCMRL# 389 dt 4.545455 rms 0.528 0.257% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6390 tsec 2.1170 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 1.6040 tsec 2.7970 #GCMRL# 391 dt 4.545455 rms 0.525 0.289% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6320 tsec 2.1290 #GCMRL# 392 dt 4.545455 rms 0.524 0.279% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6000 tsec 2.0970 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 1.5780 tsec 3.4680 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 1.5910 tsec 3.4970 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 1.6100 tsec 2.8240 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 1.5870 tsec 2.8020 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 1.6150 tsec 4.5680 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 1.5740 tsec 4.5370 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 1.6020 tsec 5.9680 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 1.6240 tsec 6.7450 #GCMRL# 401 dt 11.520000 rms 0.517 0.000% neg 0 invalid 762 tFOTS 7.9040 tGradient 1.5980 tsec 9.9240 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 7.6620 tGradient 1.4960 tsec 9.5560 #GCAMreg# pass 0 level1 1 level2 1 tsec 27.84 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 7.6170 tGradient 1.4880 tsec 9.5150 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 5.7740 tGradient 1.1200 tsec 12.8250 #GCMRL# 408 dt 0.000013 rms 0.490 0.000% neg 0 invalid 762 tFOTS 7.3320 tGradient 1.0980 tsec 8.8390 #GCAMreg# pass 0 level1 0 level2 1 tsec 32.161 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 5.8330 tGradient 1.0970 tsec 7.3220 #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 5.8290 tGradient 1.0970 tsec 7.3410 #GCMRL# 412 dt 0.112000 rms 0.488 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.0720 tsec 1.4580 label assignment complete, 0 changed (0.00%) GCAMregister done in 7.64435 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 7.5150 tGradient 5.2030 tsec 13.0940 #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 9.6830 tGradient 5.2050 tsec 15.2860 #GCAMreg# pass 0 level1 5 level2 1 tsec 43.157 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 20.094 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 7.6120 tGradient 2.2850 tsec 10.2810 #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 7.6040 tGradient 2.3010 tsec 10.3020 #GCAMreg# pass 0 level1 3 level2 1 tsec 32.183 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 7.5400 tGradient 2.2880 tsec 10.2030 #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 7.5600 tGradient 2.2910 tsec 10.2270 #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 7.6930 tGradient 2.2740 tsec 10.3460 #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 7.6490 tGradient 2.3000 tsec 10.3520 #GCMRL# 427 dt 11.200000 rms 0.480 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3000 tsec 2.7990 #GCMRL# 428 dt 11.200000 rms 0.480 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3060 tsec 2.7960 #GCMRL# 429 dt 11.200000 rms 0.480 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2920 tsec 2.7850 #GCMRL# 430 dt 11.200000 rms 0.479 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2750 tsec 2.7690 #GCMRL# 431 dt 11.200000 rms 0.478 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2870 tsec 2.7790 #GCMRL# 432 dt 11.200000 rms 0.478 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3060 tsec 2.7920 #GCMRL# 433 dt 11.200000 rms 0.477 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2980 tsec 2.8080 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 7.7320 tGradient 1.5970 tsec 9.7120 #GCAMreg# pass 0 level1 2 level2 1 tsec 27.847 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 7.5870 tGradient 1.5700 tsec 9.5440 #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 6.4480 tGradient 1.5830 tsec 12.7800 #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 7.3870 tGradient 1.5830 tsec 9.3760 #GCMRL# 440 dt 4.032000 rms 0.473 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5930 tsec 2.0840 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 1.5750 tsec 2.8380 #GCMRL# 442 dt 4.032000 rms 0.471 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6000 tsec 2.0910 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 1.6100 tsec 5.6870 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 1.6000 tsec 3.9030 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 1.6080 tsec 3.9360 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 1.5940 tsec 3.4410 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 1.6010 tsec 3.9250 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 1.6190 tsec 6.3790 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 1.5990 tsec 4.2190 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 1.6120 tsec 4.2650 #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 6.4360 tGradient 1.6110 tsec 9.9930 #GCMRL# 452 dt 4.032000 rms 0.465 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6130 tsec 2.0690 #GCMRL# 453 dt 4.032000 rms 0.465 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5790 tsec 2.0010 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 17.602 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 5.5690 tGradient 0.6960 tsec 13.6180 #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 6.9660 tGradient 0.6910 tsec 8.0560 #GCAMreg# pass 0 level1 0 level2 1 tsec 31.478 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 5.5210 tGradient 0.6850 tsec 7.8320 #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 5.4980 tGradient 0.7000 tsec 8.1960 #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 5.5090 tGradient 0.7140 tsec 11.7590 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 5.5060 tGradient 0.7140 tsec 7.5100 #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 5.5440 tGradient 0.6900 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 5.5250 tGradient 0.7060 tsec 6.6290 #GCMRL# 466 dt 0.112000 rms 0.444 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7230 tsec 1.1020 #GCMRL# 467 dt 0.112000 rms 0.444 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7180 tsec 1.0890 #GCMRL# 468 dt 0.112000 rms 0.444 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7170 tsec 1.0910 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 0.7000 tsec 2.2740 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 0.7340 tsec 1.9420 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 0.7110 tsec 1.9180 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 0.7150 tsec 2.3490 #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 5.5690 tGradient 0.7170 tsec 6.6880 GCAMregister done in 7.4777 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 3949 tmin = 3.43828 Calls to gcamLabelEnergy 3287 tmin = 0.780483 Calls to gcamJacobianEnergy 3949 tmin = 1.94115 Calls to gcamSmoothnessEnergy 3949 tmin = 6.90693 Calls to gcamLogLikelihoodTerm 475 tmin = 1.19073 Calls to gcamLabelTerm 414 tmin = 3.41638 Calls to gcamJacobianTerm 475 tmin = 2.28672 Calls to gcamSmoothnessTerm 475 tmin = 1.1386 Calls to gcamComputeGradient 475 tmin = 15.3457 Calls to gcamComputeMetricProperties 5540 tmin = 4.16302 mri_ca_register took 0 hours, 44 minutes and 47 seconds. #VMPC# mri_ca_register VmPeak 2306084 FSRUNTIME@ mri_ca_register 0.7465 hours 4 threads #-------------------------------------- #@# SubCort Seg Fri Jan 6 18:05:33 CET 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname sharky machine x86_64 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.82 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.14999 ( 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 1698.793935 mri_ca_label stimesec 0.727909 mri_ca_label ru_maxrss 2128648 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 429354 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 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 539 mri_ca_label ru_nivcsw 5488 auto-labeling took 27 minutes and 31 seconds. #-------------------------------------- #@# CC Seg Fri Jan 6 18:33:04 CET 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/cc_up.lta New_patient_test3_bugfix 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/cc_up.lta reading aseg from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/aseg.auto_noCCseg.mgz reading norm from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #VMPC# mri_cc VmPeak 460152 mri_cc done #-------------------------------------- #@# Merge ASeg Fri Jan 6 18:33:42 CET 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Jan 6 18:33:42 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 23 seconds. #-------------------------------------------- #@# Mask BFS Fri Jan 6 18:36:06 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 Fri Jan 6 18:36:07 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 1.0 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 0.36 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 Fri Jan 6 18:38:00 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/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 0.9 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 Fri Jan 6 18:38:57 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 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 Fri Jan 6 18:39:00 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 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 Fri Jan 6 18:39:03 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Jan 6 18:39:03 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 290899 of (290899 290902) to complete... Waiting for PID 290902 of (290899 290902) 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 (290899 290902) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Jan 6 18:39:05 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Jan 6 18:39:05 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 290951 of (290951 290954) to complete... Waiting for PID 290954 of (290951 290954) 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 27.867298 mris_inflate stimesec 0.705095 mris_inflate ru_maxrss 199156 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 414247 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8680 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 889 mris_inflate ru_nivcsw 71 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 28.829951 mris_inflate stimesec 0.699465 mris_inflate ru_maxrss 201176 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 431420 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8768 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 850 mris_inflate ru_nivcsw 57 PIDs (290951 290954) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Jan 6 18:39:16 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Jan 6 18:39:16 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 291003 of (291003 291006) to complete... Waiting for PID 291006 of (291003 291006) 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: 7.3.0 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 0.0159 hours FSRUNTIME@ mris_sphere 0.0159 hours 4 threads #VMPC# mris_sphere VmPeak 713144 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: 7.3.0 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 0.0155 hours FSRUNTIME@ mris_sphere 0.0155 hours 4 threads #VMPC# mris_sphere VmPeak 779056 mris_sphere done PIDs (291003 291006) completed and logs appended. #@# Fix Topology lh Fri Jan 6 18:40:13 CET 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 New_patient_test3_bugfix lh #@# Fix Topology rh Fri Jan 6 18:40:13 CET 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 New_patient_test3_bugfix rh Waiting for PID 291051 of (291051 291054) to complete... Waiting for PID 291054 of (291051 291054) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 New_patient_test3_bugfix 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' 7.3.0 7.3.0 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 6.4 minutes FSRUNTIME@ mris_fix_topology lh 0.1069 hours 4 threads #VMPC# mris_fix_topology VmPeak 959160 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 New_patient_test3_bugfix 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' 7.3.0 7.3.0 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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!!!!(-113.859359 >= -113.839342 ) After retessellation of defect 42 (v0=56047), euler #=-33 (109214,326840,217593) : difference with theory (-33) = 0 CORRECTING DEFECT 43 (vertices=37, convex hull=29, v0=56408) After retessellation of defect 43 (v0=56408), euler #=-32 (109217,326858,217609) : difference with theory (-32) = 0 CORRECTING DEFECT 44 (vertices=46, convex hull=29, v0=56458) After retessellation of defect 44 (v0=56458), euler #=-31 (109225,326891,217635) : difference with theory (-31) = 0 CORRECTING DEFECT 45 (vertices=26, convex hull=29, v0=56976) After retessellation of defect 45 (v0=56976), euler #=-30 (109229,326912,217653) : difference with theory (-30) = 0 CORRECTING DEFECT 46 (vertices=187, convex hull=125, v0=64223) After retessellation of defect 46 (v0=64223), euler #=-29 (109275,327111,217807) : difference with theory (-29) = 0 CORRECTING DEFECT 47 (vertices=48, convex hull=67, v0=64550) After retessellation of defect 47 (v0=64550), euler #=-28 (109295,327196,217873) : difference with theory (-28) = 0 CORRECTING DEFECT 48 (vertices=45, convex hull=41, v0=67317) After retessellation of defect 48 (v0=67317), euler #=-27 (109301,327228,217900) : difference with theory (-27) = 0 CORRECTING DEFECT 49 (vertices=36, convex hull=53, v0=67750) After retessellation of defect 49 (v0=67750), euler #=-26 (109311,327279,217942) : difference with theory (-26) = 0 CORRECTING DEFECT 50 (vertices=34, convex hull=42, v0=67839) After retessellation of defect 50 (v0=67839), euler #=-26 (109322,327330,217982) : difference with theory (-25) = 1 CORRECTING DEFECT 51 (vertices=51, convex hull=38, v0=71899) After retessellation of defect 51 (v0=71899), euler #=-25 (109332,327374,218017) : difference with theory (-24) = 1 CORRECTING DEFECT 52 (vertices=75, convex hull=100, v0=75484) After retessellation of defect 52 (v0=75484), euler #=-24 (109372,327533,218137) : difference with theory (-23) = 1 CORRECTING DEFECT 53 (vertices=17, convex hull=58, v0=76350) After retessellation of defect 53 (v0=76350), euler #=-23 (109381,327577,218173) : difference with theory (-22) = 1 CORRECTING DEFECT 54 (vertices=50, convex hull=45, v0=76442) After retessellation of defect 54 (v0=76442), euler #=-22 (109403,327660,218235) : difference with theory (-21) = 1 CORRECTING DEFECT 55 (vertices=270, convex hull=69, v0=76700) After retessellation of defect 55 (v0=76700), euler #=-21 (109425,327755,218309) : difference with theory (-20) = 1 CORRECTING DEFECT 56 (vertices=30, convex hull=72, v0=81189) After retessellation of defect 56 (v0=81189), euler #=-20 (109446,327847,218381) : difference with theory (-19) = 1 CORRECTING DEFECT 57 (vertices=21, convex hull=30, v0=82149) After retessellation of defect 57 (v0=82149), euler #=-19 (109449,327862,218394) : difference with theory (-18) = 1 CORRECTING DEFECT 58 (vertices=18, convex hull=49, v0=82782) After retessellation of defect 58 (v0=82782), euler #=-18 (109459,327909,218432) : difference with theory (-17) = 1 CORRECTING DEFECT 59 (vertices=30, convex hull=34, v0=83311) After retessellation of defect 59 (v0=83311), euler #=-17 (109464,327935,218454) : difference with theory (-16) = 1 CORRECTING DEFECT 60 (vertices=132, convex hull=138, v0=92267) After retessellation of defect 60 (v0=92267), euler #=-16 (109522,328166,218628) : difference with theory (-15) = 1 CORRECTING DEFECT 61 (vertices=40, convex hull=51, v0=92355) After retessellation of defect 61 (v0=92355), euler #=-15 (109537,328232,218680) : difference with theory (-14) = 1 CORRECTING DEFECT 62 (vertices=18, convex hull=25, v0=97495) After retessellation of defect 62 (v0=97495), euler #=-14 (109542,328253,218697) : difference with theory (-13) = 1 CORRECTING DEFECT 63 (vertices=19, convex hull=44, v0=97634) After retessellation of defect 63 (v0=97634), euler #=-13 (109552,328298,218733) : difference with theory (-12) = 1 CORRECTING DEFECT 64 (vertices=101, convex hull=33, v0=97904) After retessellation of defect 64 (v0=97904), euler #=-12 (109560,328332,218760) : difference with theory (-11) = 1 CORRECTING DEFECT 65 (vertices=141, convex hull=171, v0=98776) After retessellation of defect 65 (v0=98776), euler #=-10 (109614,328572,218948) : difference with theory (-10) = 0 CORRECTING DEFECT 66 (vertices=79, convex hull=31, v0=100361) After retessellation of defect 66 (v0=100361), euler #=-9 (109627,328618,218982) : difference with theory (-9) = 0 CORRECTING DEFECT 67 (vertices=9, convex hull=22, v0=101123) After retessellation of defect 67 (v0=101123), euler #=-8 (109627,328624,218989) : difference with theory (-8) = 0 CORRECTING DEFECT 68 (vertices=40, convex hull=49, v0=101187) After retessellation of defect 68 (v0=101187), euler #=-7 (109638,328673,219028) : difference with theory (-7) = 0 CORRECTING DEFECT 69 (vertices=28, convex hull=36, v0=105321) After retessellation of defect 69 (v0=105321), euler #=-7 (109656,328743,219080) : difference with theory (-6) = 1 CORRECTING DEFECT 70 (vertices=249, convex hull=102, v0=108009) After retessellation of defect 70 (v0=108009), euler #=-6 (109705,328939,219228) : difference with theory (-5) = 1 CORRECTING DEFECT 71 (vertices=94, convex hull=54, v0=108653) After retessellation of defect 71 (v0=108653), euler #=-5 (109716,328993,219272) : difference with theory (-4) = 1 CORRECTING DEFECT 72 (vertices=50, convex hull=81, v0=108776) After retessellation of defect 72 (v0=108776), euler #=-4 (109748,329123,219371) : difference with theory (-3) = 1 CORRECTING DEFECT 73 (vertices=77, convex hull=110, v0=108953) After retessellation of defect 73 (v0=108953), euler #=-2 (109765,329224,219457) : difference with theory (-2) = 0 CORRECTING DEFECT 74 (vertices=29, convex hull=53, v0=111646) After retessellation of defect 74 (v0=111646), euler #=-1 (109777,329281,219503) : difference with theory (-1) = 0 CORRECTING DEFECT 75 (vertices=26, convex hull=29, v0=118540) After retessellation of defect 75 (v0=118540), euler #=0 (109782,329307,219525) : difference with theory (0) = 0 CORRECTING DEFECT 76 (vertices=103, convex hull=33, v0=122600) After retessellation of defect 76 (v0=122600), euler #=1 (109791,329348,219558) : difference with theory (1) = 0 CORRECTING DEFECT 77 (vertices=18, convex hull=50, v0=124007) After retessellation of defect 77 (v0=124007), euler #=2 (109799,329391,219594) : 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... 288 mutations (34.6%), 544 crossovers (65.4%), 1152 vertices were eliminated building final representation... 14671 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109799, nf=219594, ne=329391, g=0) writing corrected surface to /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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: 1672 intersecting 001: 178 intersecting 002: 52 intersecting 003: 12 intersecting 004: 7 intersecting step 1 with no progress (num=7, old_num=7) 005: 7 intersecting step 2 with no progress (num=7, old_num=7) 006: 7 intersecting step 3 with no progress (num=7, old_num=7) 007: 7 intersecting step 4 with no progress (num=7, old_num=7) 008: 7 intersecting step 5 with no progress (num=7, old_num=7) 009: 7 intersecting step 6 with no progress (num=7, old_num=7) 010: 7 intersecting step 7 with no progress (num=7, old_num=7) 011: 7 intersecting step 8 with no progress (num=7, old_num=7) 012: 7 intersecting step 9 with no progress (num=7, old_num=7) 013: 7 intersecting step 10 with no progress (num=7, old_num=7) 014: 7 intersecting step 11 with no progress (num=7, old_num=7) 015: 7 intersecting step 12 with no progress (num=7, old_num=7) 016: 7 intersecting step 13 with no progress (num=7, old_num=7) 017: 7 intersecting step 14 with no progress (num=7, old_num=7) 018: 7 intersecting step 15 with no progress (num=7, old_num=7) 019: 7 intersecting step 16 with no progress (num=7, old_num=7) terminating search with 7 intersecting topology fixing took 6.5 minutes FSRUNTIME@ mris_fix_topology rh 0.1085 hours 4 threads #VMPC# mris_fix_topology VmPeak 960780 PIDs (291051 291054) 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: 109799 - 329391 + 219594 = 2 --> 0 holes F =2V-4: 219594 = 219598-4 (0) 2E=3F: 658782 = 658782 (0) total defect index = 0 Fri Jan 6 18:46:45 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts /usr/local/freesurfer/bin/defect2seg --s New_patient_test3_bugfix --cortex freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 defect2seg 7.3.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux pid 291133 mri_label2label --label-cortex /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.orig.nofix /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/aseg.presurf.mgz 0 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.orig.nofix /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.defect_labels /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz 1000 0 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/surface.defects.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/surface.defects.mgz mris_defects_pointset -s /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.orig.nofix -d /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.defect_labels -o /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.defects.pointset --label /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/lh.nofix.cortex.label Reading in surface /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.orig.nofix Reading in defect segmentation /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.defect_labels Reading in label /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 536272 mris_defects_pointset done mri_label2label --label-cortex /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.orig.nofix /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/aseg.presurf.mgz 0 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.orig.nofix /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.defect_labels /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/surface.defects.mgz 2000 1 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/surface.defects.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/surface.defects.mgz mris_defects_pointset -s /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.orig.nofix -d /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.defect_labels -o /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.defects.pointset --label /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/rh.nofix.cortex.label Reading in surface /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.orig.nofix Reading in defect segmentation /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.defect_labels Reading in label /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 537268 mris_defects_pointset done Started at Fri Jan 6 18:46:45 CET 2023 Ended at Fri Jan 6 18:47:09 CET 2023 Defect2seg-Run-Time-Sec 24 Defect2seg-Run-Time-Min 0.48 Defect2seg-Run-Time-Hours 0.01 tkmeditfv New_patient_test3_bugfix brain.finalsurfs.mgz -defect defect2seg Done mris_remesh --remesh --iters 3 --input /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.orig.premesh --output /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.orig.premesh --output /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.717908 remeshing to edge length 0.717908 with 3 iterations avg qual before : 0.88204 after: 0.970619 Removing intersections removing intersecting faces 000: 288 intersecting 001: 149 intersecting 002: 101 intersecting step 1 with no progress (num=101, old_num=101) 003: 101 intersecting step 2 with no progress (num=101, old_num=101) 004: 101 intersecting step 3 with no progress (num=101, old_num=101) 005: 101 intersecting step 4 with no progress (num=101, old_num=101) 006: 101 intersecting step 5 with no progress (num=101, old_num=101) 007: 101 intersecting step 6 with no progress (num=101, old_num=101) 008: 101 intersecting step 7 with no progress (num=101, old_num=101) 009: 101 intersecting step 8 with no progress (num=101, old_num=101) 010: 101 intersecting step 9 with no progress (num=101, old_num=101) 011: 101 intersecting step 10 with no progress (num=101, old_num=101) 012: 101 intersecting step 11 with no progress (num=101, old_num=101) 013: 101 intersecting step 12 with no progress (num=101, old_num=101) 014: 101 intersecting step 13 with no progress (num=101, old_num=101) 015: 101 intersecting step 14 with no progress (num=101, old_num=101) 016: 101 intersecting step 15 with no progress (num=101, old_num=101) 017: 101 intersecting step 16 with no progress (num=101, old_num=101) terminating search with 101 intersecting Remeshed surface quality stats nv0 = 109799 nv = 112444 1.02409 Area 224884 0.30736 0.03639 0.001234 0.6958 Corner 674652 60.00000 9.10603 0.385882 179.1943 Edge 337326 0.85065 0.08558 0.025510 1.4955 Hinge 337326 10.85503 12.08229 0.000012 176.0807 mris_remesh done /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 101 intersecting step 1 with no progress (num=101, old_num=101) 001: 101 intersecting step 2 with no progress (num=101, old_num=101) 002: 101 intersecting step 3 with no progress (num=101, old_num=101) 003: 101 intersecting step 4 with no progress (num=101, old_num=101) 004: 101 intersecting step 5 with no progress (num=101, old_num=101) 005: 101 intersecting step 6 with no progress (num=101, old_num=101) 006: 101 intersecting step 7 with no progress (num=101, old_num=101) 007: 101 intersecting step 8 with no progress (num=101, old_num=101) 008: 101 intersecting step 9 with no progress (num=101, old_num=101) 009: 101 intersecting step 10 with no progress (num=101, old_num=101) 010: 101 intersecting step 11 with no progress (num=101, old_num=101) 011: 101 intersecting step 12 with no progress (num=101, old_num=101) 012: 101 intersecting step 13 with no progress (num=101, old_num=101) 013: 101 intersecting step 14 with no progress (num=101, old_num=101) 014: 101 intersecting step 15 with no progress (num=101, old_num=101) 015: 101 intersecting step 16 with no progress (num=101, old_num=101) terminating search with 101 intersecting writing corrected surface to ../surf/rh.orig rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Fri Jan 6 18:49:16 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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 Fri Jan 6 18:49:18 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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 561884 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Fri Jan 6 18:49:21 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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 0.0367 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 0.7 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=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 0.0239 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 0.0128 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 0.0082 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 1.97 minutes #VMPC# mris_place_surfaces VmPeak 2096168 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Fri Jan 6 18:51:42 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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: 175 intersecting step 1 with no progress (num=196, old_num=175) 001: 196 intersecting 002: 186 intersecting 003: 182 intersecting 004: 168 intersecting 005: 146 intersecting 006: 145 intersecting 007: 139 intersecting step 1 with no progress (num=154, old_num=139) 008: 154 intersecting 009: 150 intersecting 010: 142 intersecting 011: 141 intersecting step 1 with no progress (num=145, old_num=141) 012: 145 intersecting step 2 with no progress (num=149, old_num=145) 013: 149 intersecting step 3 with no progress (num=178, old_num=149) 014: 178 intersecting 015: 166 intersecting 016: 158 intersecting step 1 with no progress (num=162, old_num=158) 017: 162 intersecting 018: 154 intersecting step 1 with no progress (num=161, old_num=154) 019: 161 intersecting step 2 with no progress (num=161, old_num=161) 020: 161 intersecting 021: 157 intersecting 022: 155 intersecting step 1 with no progress (num=183, old_num=155) 023: 183 intersecting 024: 180 intersecting 025: 172 intersecting 026: 159 intersecting step 1 with no progress (num=164, old_num=159) 027: 164 intersecting step 2 with no progress (num=174, old_num=164) 028: 174 intersecting 029: 166 intersecting step 1 with no progress (num=173, old_num=166) 030: 173 intersecting step 2 with no progress (num=174, old_num=173) 031: 174 intersecting 032: 165 intersecting 033: 164 intersecting step 1 with no progress (num=169, old_num=164) 034: 169 intersecting step 2 with no progress (num=171, old_num=169) 035: 171 intersecting 036: 158 intersecting step 1 with no progress (num=172, old_num=158) 037: 172 intersecting 038: 168 intersecting step 1 with no progress (num=172, old_num=168) 039: 172 intersecting step 2 with no progress (num=177, old_num=172) 040: 177 intersecting 041: 165 intersecting step 1 with no progress (num=178, old_num=165) 042: 178 intersecting 043: 165 intersecting step 1 with no progress (num=165, old_num=165) 044: 165 intersecting step 2 with no progress (num=175, old_num=165) 045: 175 intersecting 046: 171 intersecting 047: 165 intersecting step 1 with no progress (num=167, old_num=165) 048: 167 intersecting 049: 160 intersecting step 1 with no progress (num=173, old_num=160) 050: 173 intersecting step 2 with no progress (num=173, old_num=173) 051: 173 intersecting 052: 167 intersecting step 1 with no progress (num=168, old_num=167) 053: 168 intersecting step 2 with no progress (num=171, old_num=168) 054: 171 intersecting 055: 165 intersecting step 1 with no progress (num=165, old_num=165) 056: 165 intersecting step 2 with no progress (num=167, old_num=165) 057: 167 intersecting 058: 162 intersecting step 1 with no progress (num=167, old_num=162) 059: 167 intersecting step 2 with no progress (num=170, old_num=167) 060: 170 intersecting 061: 169 intersecting 062: 161 intersecting step 1 with no progress (num=171, old_num=161) 063: 171 intersecting 064: 166 intersecting 065: 165 intersecting step 1 with no progress (num=165, old_num=165) 066: 165 intersecting 067: 161 intersecting step 1 with no progress (num=176, old_num=161) 068: 176 intersecting 069: 163 intersecting step 1 with no progress (num=172, old_num=163) 070: 172 intersecting step 2 with no progress (num=172, old_num=172) 071: 172 intersecting 072: 170 intersecting step 1 with no progress (num=173, old_num=170) 073: 173 intersecting step 2 with no progress (num=176, old_num=173) 074: 176 intersecting 075: 169 intersecting step 1 with no progress (num=172, old_num=169) 076: 172 intersecting 077: 169 intersecting step 1 with no progress (num=182, old_num=169) 078: 182 intersecting 079: 175 intersecting step 1 with no progress (num=180, old_num=175) 080: 180 intersecting 081: 171 intersecting step 1 with no progress (num=180, old_num=171) 082: 180 intersecting 083: 174 intersecting step 1 with no progress (num=174, old_num=174) 084: 174 intersecting step 2 with no progress (num=175, old_num=174) 085: 175 intersecting step 3 with no progress (num=175, old_num=175) 086: 175 intersecting step 4 with no progress (num=175, old_num=175) 087: 175 intersecting step 5 with no progress (num=175, old_num=175) 088: 175 intersecting step 6 with no progress (num=175, old_num=175) 089: 175 intersecting step 7 with no progress (num=175, old_num=175) 090: 175 intersecting step 8 with no progress (num=175, old_num=175) 091: 175 intersecting step 9 with no progress (num=175, old_num=175) 092: 175 intersecting step 10 with no progress (num=175, old_num=175) 093: 175 intersecting step 11 with no progress (num=175, old_num=175) 094: 175 intersecting step 12 with no progress (num=175, old_num=175) 095: 175 intersecting step 13 with no progress (num=175, old_num=175) 096: 175 intersecting step 14 with no progress (num=175, old_num=175) 097: 175 intersecting step 15 with no progress (num=175, old_num=175) 098: 175 intersecting step 16 with no progress (num=175, old_num=175) terminating search with 139 intersecting Area 224884 0.26770 0.06845 0.000000 0.6922 Corner 674652 60.00000 10.65057 0.000035 179.9999 Edge 337326 0.78943 0.12513 0.000073 1.6004 Hinge 337326 6.83663 7.88644 0.000008 179.9657 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 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6555, nmarked2=4, nripped=6555 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56222: xyz = (12.4893,-15.7155,71.0168) oxyz = (12.4893,-15.7155,71.0168) wxzy = (12.4893,-15.7155,71.0168) pxyz = (0,0,0) CBVO Creating mask 112444 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=6555 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 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6555, nmarked2=4, nripped=6555 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=2 had to be increased for 553 vertices, nripped=6555 mean border=91.0, 364 (364) missing vertices, mean dist 0.0 [0.9 (%44.7)->0.8 (%55.3))] %59 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0353 min Finding expansion regions mean absolute distance = 0.87 +- 1.14 3413 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=5258062.5, rms=10.478 001: dt: 0.5000, sse=3969260.8, rms=8.218 (21.573%) 002: dt: 0.5000, sse=2893397.8, rms=6.534 (20.495%) 003: dt: 0.5000, sse=2731374.2, rms=5.213 (20.215%) 004: dt: 0.5000, sse=2435550.8, rms=4.150 (20.396%) 005: dt: 0.5000, sse=2407199.2, rms=3.386 (18.405%) 006: dt: 0.5000, sse=2316108.0, rms=2.950 (12.866%) 007: dt: 0.5000, sse=2278339.2, rms=2.739 (7.162%) rms = 2.6167/2.7389, sse=2290594.1/2278339.2, time step reduction 1 of 3 to 0.250 0 1 0 008: dt: 0.5000, sse=2290594.0, rms=2.617 (4.465%) 009: dt: 0.2500, sse=2198154.0, rms=1.982 (24.260%) 010: dt: 0.2500, sse=2169689.0, rms=1.874 (5.456%) rms = 1.8354/1.8737, sse=2022936.3/2169689.1, time step reduction 2 of 3 to 0.125 0 0 1 011: dt: 0.2500, sse=2022936.4, rms=1.835 (2.047%) rms = 1.7867/1.8354, sse=2007513.0/2022936.3, time step reduction 3 of 3 to 0.062 0 0 1 012: dt: 0.1250, sse=2007513.0, rms=1.787 (2.651%) maximum number of reductions reached, breaking from loop positioning took 0.5 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=6555 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 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 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 #FML# MRISripMidline(): nmarked=7013, nmarked2=18, nripped=7013 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=1 had to be increased for 434 vertices, nripped=7013 mean border=92.5, 482 (174) missing vertices, mean dist -0.2 [0.5 (%63.8)->0.3 (%36.2))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0234 min Finding expansion regions mean absolute distance = 0.41 +- 0.73 3294 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=2209726.2, rms=3.339 rms = 2.3473/3.3388, sse=2270593.9/2209726.3, time step reduction 1 of 3 to 0.250 0 1 0 013: dt: 0.5000, sse=2270594.0, rms=2.347 (29.697%) 014: dt: 0.2500, sse=2101509.2, rms=1.938 (17.429%) rms = 1.7744/1.9382, sse=2215877.2/2101509.2, time step reduction 2 of 3 to 0.125 0 1 0 015: dt: 0.2500, sse=2215877.2, rms=1.774 (8.451%) rms = 1.7064/1.7744, sse=2222752.1/2215877.2, time step reduction 3 of 3 to 0.062 0 1 0 016: dt: 0.1250, sse=2222752.2, rms=1.706 (3.831%) maximum number of reductions reached, breaking from loop positioning took 0.2 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=7013 removing 2 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 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 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7090, nmarked2=22, nripped=7090 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 459 vertices, nripped=7090 mean border=93.3, 499 (137) missing vertices, mean dist -0.1 [0.4 (%57.5)->0.2 (%42.5))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0126 min Finding expansion regions mean absolute distance = 0.31 +- 0.51 3617 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=2282170.5, rms=2.403 017: dt: 0.5000, sse=2257350.8, rms=1.939 (19.288%) 018: dt: 0.5000, sse=2234551.8, rms=1.782 (8.102%) rms = 1.8264/1.7823, sse=2242211.3/2234551.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=2211504.5, rms=1.589 (10.862%) rms = 1.5001/1.5887, sse=2213939.4/2211504.5, time step reduction 2 of 3 to 0.125 0 1 0 020: dt: 0.2500, sse=2213939.5, rms=1.500 (5.576%) rms = 1.4576/1.5001, sse=2208462.5/2213939.4, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=2208462.5, rms=1.458 (2.835%) maximum number of reductions reached, breaking from loop positioning took 0.2 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=7090 removing 1 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 removing 1 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 #FML# MRISripMidline(): nmarked=7116, nmarked2=21, nripped=7116 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 508 vertices, nripped=7116 mean border=93.6, 562 (120) missing vertices, mean dist -0.1 [0.3 (%52.0)->0.2 (%48.0))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0080 min Finding expansion regions mean absolute distance = 0.27 +- 0.41 2818 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=2219256.5, rms=1.650 022: dt: 0.5000, sse=1586814.0, rms=1.596 (3.274%) rms = 1.5807/1.5956, sse=2225041.2/1586814.1, time step reduction 1 of 3 to 0.250 0 1 1 023: dt: 0.5000, sse=2225041.2, rms=1.581 (0.938%) 024: dt: 0.2500, sse=2215068.5, rms=1.380 (12.688%) 025: dt: 0.2500, sse=2205225.8, rms=1.327 (3.837%) rms = 1.3372/1.3272, sse=2201161.7/2205225.7, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 1.2936/1.3272, sse=2199350.5/2205225.7, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=2199350.5, rms=1.294 (2.530%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 119 intersecting step 1 with no progress (num=138, old_num=119) 001: 138 intersecting 002: 125 intersecting 003: 107 intersecting 004: 99 intersecting step 1 with no progress (num=102, old_num=99) 005: 102 intersecting step 2 with no progress (num=105, old_num=102) 006: 105 intersecting step 3 with no progress (num=105, old_num=105) 007: 105 intersecting step 4 with no progress (num=108, old_num=105) 008: 108 intersecting 009: 107 intersecting step 1 with no progress (num=110, old_num=107) 010: 110 intersecting 011: 108 intersecting step 1 with no progress (num=117, old_num=108) 012: 117 intersecting 013: 115 intersecting step 1 with no progress (num=117, old_num=115) 014: 117 intersecting step 2 with no progress (num=124, old_num=117) 015: 124 intersecting step 3 with no progress (num=132, old_num=124) 016: 132 intersecting step 4 with no progress (num=132, old_num=132) 017: 132 intersecting 018: 121 intersecting step 1 with no progress (num=124, old_num=121) 019: 124 intersecting 020: 113 intersecting 021: 106 intersecting step 1 with no progress (num=112, old_num=106) 022: 112 intersecting step 2 with no progress (num=113, old_num=112) 023: 113 intersecting 024: 112 intersecting step 1 with no progress (num=113, old_num=112) 025: 113 intersecting step 2 with no progress (num=120, old_num=113) 026: 120 intersecting step 3 with no progress (num=124, old_num=120) 027: 124 intersecting step 4 with no progress (num=132, old_num=124) 028: 132 intersecting step 5 with no progress (num=153, old_num=132) 029: 153 intersecting step 6 with no progress (num=165, old_num=153) 030: 165 intersecting step 7 with no progress (num=167, old_num=165) 031: 167 intersecting 032: 152 intersecting step 1 with no progress (num=156, old_num=152) 033: 156 intersecting step 2 with no progress (num=175, old_num=156) 034: 175 intersecting 035: 172 intersecting 036: 155 intersecting step 1 with no progress (num=156, old_num=155) 037: 156 intersecting 038: 155 intersecting step 1 with no progress (num=159, old_num=155) 039: 159 intersecting step 2 with no progress (num=169, old_num=159) 040: 169 intersecting step 3 with no progress (num=171, old_num=169) 041: 171 intersecting 042: 160 intersecting 043: 153 intersecting step 1 with no progress (num=153, old_num=153) 044: 153 intersecting 045: 152 intersecting step 1 with no progress (num=161, old_num=152) 046: 161 intersecting 047: 156 intersecting 048: 152 intersecting step 1 with no progress (num=152, old_num=152) 049: 152 intersecting step 2 with no progress (num=154, old_num=152) 050: 154 intersecting step 3 with no progress (num=156, old_num=154) 051: 156 intersecting step 4 with no progress (num=157, old_num=156) 052: 157 intersecting 053: 155 intersecting 054: 150 intersecting step 1 with no progress (num=152, old_num=150) 055: 152 intersecting step 2 with no progress (num=158, old_num=152) 056: 158 intersecting 057: 153 intersecting 058: 147 intersecting step 1 with no progress (num=150, old_num=147) 059: 150 intersecting step 2 with no progress (num=150, old_num=150) 060: 150 intersecting 061: 149 intersecting step 1 with no progress (num=154, old_num=149) 062: 154 intersecting step 2 with no progress (num=155, old_num=154) 063: 155 intersecting 064: 148 intersecting step 1 with no progress (num=154, old_num=148) 065: 154 intersecting step 2 with no progress (num=168, old_num=154) 066: 168 intersecting 067: 165 intersecting step 1 with no progress (num=166, old_num=165) 068: 166 intersecting 069: 154 intersecting 070: 149 intersecting step 1 with no progress (num=149, old_num=149) 071: 149 intersecting step 2 with no progress (num=153, old_num=149) 072: 153 intersecting step 3 with no progress (num=159, old_num=153) 073: 159 intersecting 074: 143 intersecting step 1 with no progress (num=155, old_num=143) 075: 155 intersecting 076: 148 intersecting step 1 with no progress (num=150, old_num=148) 077: 150 intersecting 078: 146 intersecting step 1 with no progress (num=158, old_num=146) 079: 158 intersecting 080: 157 intersecting step 1 with no progress (num=157, old_num=157) 081: 157 intersecting step 2 with no progress (num=170, old_num=157) 082: 170 intersecting 083: 166 intersecting step 1 with no progress (num=171, old_num=166) 084: 171 intersecting step 2 with no progress (num=180, old_num=171) 085: 180 intersecting step 3 with no progress (num=187, old_num=180) 086: 187 intersecting step 4 with no progress (num=199, old_num=187) 087: 199 intersecting step 5 with no progress (num=199, old_num=199) 088: 199 intersecting step 6 with no progress (num=199, old_num=199) 089: 199 intersecting 090: 198 intersecting step 1 with no progress (num=198, old_num=198) 091: 198 intersecting 092: 197 intersecting 093: 196 intersecting step 1 with no progress (num=196, old_num=196) 094: 196 intersecting step 2 with no progress (num=196, old_num=196) 095: 196 intersecting step 3 with no progress (num=196, old_num=196) 096: 196 intersecting step 4 with no progress (num=196, old_num=196) 097: 196 intersecting step 5 with no progress (num=196, old_num=196) 098: 196 intersecting step 6 with no progress (num=196, old_num=196) 099: 196 intersecting step 7 with no progress (num=196, old_num=196) 100: 196 intersecting step 8 with no progress (num=196, old_num=196) 101: 196 intersecting terminating search with 99 intersecting Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.90 minutes #VMPC# mris_place_surfaces VmPeak 2229996 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Fri Jan 6 18:56:10 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 Fri Jan 6 18:56:21 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 Fri Jan 6 18:56:32 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7 non-cortical segments detected only using segment with 7075 vertices erasing segment 1 (vno[0] = 68676) erasing segment 2 (vno[0] = 70055) erasing segment 3 (vno[0] = 73479) erasing segment 4 (vno[0] = 77938) erasing segment 5 (vno[0] = 81677) erasing segment 6 (vno[0] = 103234) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Fri Jan 6 18:56:42 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7 non-cortical segments detected only using segment with 5992 vertices erasing segment 1 (vno[0] = 68676) erasing segment 2 (vno[0] = 70055) erasing segment 3 (vno[0] = 73479) erasing segment 4 (vno[0] = 77938) erasing segment 5 (vno[0] = 81677) erasing segment 6 (vno[0] = 103234) #-------------------------------------------- #@# Smooth2 lh Fri Jan 6 18:56:52 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Fri Jan 6 18:56:52 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 291732 of (291732 291735) to complete... Waiting for PID 291735 of (291732 291735) 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 (291732 291735) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Fri Jan 6 18:56:54 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Fri Jan 6 18:56:54 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 291784 of (291784 291787) to complete... Waiting for PID 291787 of (291784 291787) 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 28.023678 mris_inflate stimesec 0.096067 mris_inflate ru_maxrss 181608 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29061 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 932 mris_inflate ru_nivcsw 42 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.8 mm, total surface area = 67472 mm^2 step 000: RMS=0.174 (target=0.015) step 005: RMS=0.115 (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=0.039 (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=0.028 (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 28.128951 mris_inflate stimesec 0.504017 mris_inflate ru_maxrss 175964 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 360402 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 904 mris_inflate ru_nivcsw 50 PIDs (291784 291787) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Fri Jan 6 18:57:05 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 Fri Jan 6 18:57:05 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf reconbatchjobs /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 291873 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291876 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291879 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291882 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291885 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291888 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291891 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291894 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291897 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291900 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291903 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) to complete... Waiting for PID 291906 of (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) 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 = 44.056*4pi (553.618) --> -43 handles ICI = 178.5, FI = 1532.4, variation=24819.045 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 146 vertices thresholded to be in k1 ~ [-1.42 1.45], k2 ~ [-0.26 0.85] total integrated curvature = 0.512*4pi (6.436) --> 0 handles ICI = 1.5, FI = 8.3, variation=147.145 108 vertices thresholded to be in [-0.35 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = -0.000, std = 0.006 82 vertices thresholded to be in [-0.37 0.66] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.026 done. PIDs (291873 291876 291879 291882 291885 291888 291891 291894 291897 291900 291903 291906) completed and logs appended. #-------------------------------------------- #@# Sphere lh Fri Jan 6 18:57:34 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Fri Jan 6 18:57:34 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 291982 of (291982 291985) to complete... Waiting for PID 291985 of (291982 291985) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.3.0 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 0.0586 hours FSRUNTIME@ mris_sphere 0.0586 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: 7.3.0 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.330... 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 %20.49 pass 1: epoch 2 of 3 starting distance error %20.46 unfolding complete - removing small folds... starting distance error %20.31 removing remaining folds... final distance error %20.36 MRISunfold() return, current seed 1234 -01: dt=0.0000, 439 negative triangles VmPeak 768940 250: dt=0.9900, 439 negative triangles 251: dt=0.9900, 373 negative triangles 252: dt=0.9900, 373 negative triangles 253: dt=0.9900, 379 negative triangles 254: dt=0.9900, 371 negative triangles 255: dt=0.9900, 369 negative triangles 256: dt=0.9900, 368 negative triangles 257: dt=0.9900, 361 negative triangles 258: dt=0.9900, 363 negative triangles 259: dt=0.9900, 349 negative triangles 260: dt=0.9900, 354 negative triangles 261: dt=0.9900, 352 negative triangles 262: dt=0.9900, 352 negative triangles 263: dt=0.9900, 345 negative triangles 264: dt=0.9900, 354 negative triangles 265: dt=0.9900, 342 negative triangles 266: dt=0.9900, 346 negative triangles 267: dt=0.9900, 346 negative triangles 268: dt=0.9900, 348 negative triangles 269: dt=0.9900, 348 negative triangles 270: dt=0.9900, 350 negative triangles 271: dt=0.9900, 342 negative triangles 272: dt=0.9900, 351 negative triangles 273: dt=0.9900, 337 negative triangles 274: dt=0.9900, 349 negative triangles 275: dt=0.9900, 352 negative triangles 276: dt=0.9900, 344 negative triangles 277: dt=0.9900, 346 negative triangles 278: dt=0.9900, 339 negative triangles 279: dt=0.9900, 347 negative triangles 280: dt=0.9900, 344 negative triangles 281: dt=0.9900, 342 negative triangles 282: dt=0.9900, 341 negative triangles 283: dt=0.9405, 343 negative triangles 284: dt=0.9405, 343 negative triangles 285: dt=0.9405, 345 negative triangles 286: dt=0.9405, 343 negative triangles 287: dt=0.9405, 344 negative triangles 288: dt=0.9405, 344 negative triangles 289: dt=0.9405, 344 negative triangles 290: dt=0.9405, 340 negative triangles 291: dt=0.9405, 342 negative triangles 292: dt=0.9405, 348 negative triangles 293: dt=0.8935, 340 negative triangles 294: dt=0.8935, 339 negative triangles 295: dt=0.8935, 342 negative triangles 296: dt=0.8935, 345 negative triangles 297: dt=0.8935, 342 negative triangles 298: dt=0.8935, 339 negative triangles 299: dt=0.8935, 343 negative triangles 300: dt=0.8935, 341 negative triangles 301: dt=0.8935, 343 negative triangles 302: dt=0.8935, 345 negative triangles 303: dt=0.8488, 340 negative triangles 304: dt=0.8488, 344 negative triangles 305: dt=0.8488, 346 negative triangles 306: dt=0.8488, 347 negative triangles 307: dt=0.8488, 343 negative triangles 308: dt=0.8488, 345 negative triangles 309: dt=0.8488, 344 negative triangles 310: dt=0.8488, 343 negative triangles 311: dt=0.8488, 343 negative triangles 312: dt=0.8488, 339 negative triangles 313: dt=0.8064, 340 negative triangles 314: dt=0.8064, 345 negative triangles 315: dt=0.8064, 344 negative triangles 316: dt=0.8064, 342 negative triangles 317: dt=0.8064, 347 negative triangles 318: dt=0.8064, 341 negative triangles 319: dt=0.8064, 337 negative triangles 320: dt=0.8064, 341 negative triangles 321: dt=0.8064, 340 negative triangles 322: dt=0.8064, 333 negative triangles 323: dt=0.8064, 340 negative triangles 324: dt=0.8064, 337 negative triangles 325: dt=0.8064, 341 negative triangles 326: dt=0.8064, 337 negative triangles 327: dt=0.8064, 337 negative triangles 328: dt=0.8064, 336 negative triangles 329: dt=0.8064, 345 negative triangles 330: dt=0.8064, 338 negative triangles 331: dt=0.8064, 347 negative triangles 332: dt=0.7660, 343 negative triangles 333: dt=0.7660, 340 negative triangles 334: dt=0.7660, 341 negative triangles 335: dt=0.7660, 352 negative triangles 336: dt=0.7660, 343 negative triangles 337: dt=0.7660, 343 negative triangles 338: dt=0.7660, 340 negative triangles 339: dt=0.7660, 337 negative triangles 340: dt=0.7660, 339 negative triangles 341: dt=0.7660, 344 negative triangles 342: dt=0.7277, 334 negative triangles 343: dt=0.7277, 338 negative triangles 344: dt=0.7277, 339 negative triangles 345: dt=0.7277, 340 negative triangles 346: dt=0.7277, 340 negative triangles 347: dt=0.7277, 340 negative triangles 348: dt=0.7277, 340 negative triangles 349: dt=0.7277, 346 negative triangles 350: dt=0.7277, 341 negative triangles 351: dt=0.7277, 345 negative triangles 352: dt=0.6914, 336 negative triangles 353: dt=0.6914, 343 negative triangles 354: dt=0.6914, 333 negative triangles 355: dt=0.6914, 342 negative triangles 356: dt=0.6914, 334 negative triangles 357: dt=0.6914, 338 negative triangles 358: dt=0.6914, 339 negative triangles 359: dt=0.6914, 342 negative triangles 360: dt=0.6914, 337 negative triangles 361: dt=0.6914, 340 negative triangles 362: dt=0.6568, 340 negative triangles 363: dt=0.6568, 344 negative triangles 364: dt=0.6568, 337 negative triangles 365: dt=0.6568, 334 negative triangles 366: dt=0.6568, 337 negative triangles 367: dt=0.6568, 338 negative triangles 368: dt=0.6568, 339 negative triangles 369: dt=0.6568, 340 negative triangles 370: dt=0.6568, 337 negative triangles 371: dt=0.6568, 341 negative triangles 372: dt=0.6239, 336 negative triangles expanding nbhd size to 1 373: dt=0.9900, 336 negative triangles 374: dt=0.9900, 337 negative triangles 375: dt=0.9900, 343 negative triangles 376: dt=0.9900, 341 negative triangles 377: dt=0.9900, 342 negative triangles 378: dt=0.9900, 349 negative triangles 379: dt=0.9900, 347 negative triangles 380: dt=0.9900, 347 negative triangles 381: dt=0.9900, 346 negative triangles 382: dt=0.9405, 347 negative triangles 383: dt=0.9405, 348 negative triangles 384: dt=0.9405, 348 negative triangles 385: dt=0.9405, 349 negative triangles 386: dt=0.9405, 347 negative triangles 387: dt=0.9405, 349 negative triangles 388: dt=0.9405, 350 negative triangles 389: dt=0.9405, 348 negative triangles 390: dt=0.9405, 345 negative triangles 391: dt=0.9405, 351 negative triangles 392: dt=0.8935, 345 negative triangles 393: dt=0.8935, 347 negative triangles 394: dt=0.8935, 345 negative triangles 395: dt=0.8935, 345 negative triangles 396: dt=0.8935, 342 negative triangles 397: dt=0.8935, 345 negative triangles 398: dt=0.8935, 345 negative triangles 399: dt=0.8935, 345 negative triangles 400: dt=0.8935, 345 negative triangles 401: dt=0.8935, 344 negative triangles 402: dt=0.8488, 344 negative triangles 403: dt=0.8488, 346 negative triangles 404: dt=0.8488, 341 negative triangles 405: dt=0.8488, 342 negative triangles 406: dt=0.8488, 344 negative triangles 407: dt=0.8488, 345 negative triangles 408: dt=0.8488, 341 negative triangles 409: dt=0.8488, 344 negative triangles 410: dt=0.8488, 340 negative triangles 411: dt=0.8488, 341 negative triangles 412: dt=0.8064, 342 negative triangles 413: dt=0.8064, 338 negative triangles 414: dt=0.8064, 339 negative triangles 415: dt=0.8064, 339 negative triangles 416: dt=0.8064, 340 negative triangles 417: dt=0.8064, 338 negative triangles 418: dt=0.8064, 340 negative triangles 419: dt=0.8064, 339 negative triangles 420: dt=0.8064, 339 negative triangles 421: dt=0.8064, 339 negative triangles 422: dt=0.7660, 344 negative triangles 423: dt=0.7660, 340 negative triangles 424: dt=0.7660, 344 negative triangles 425: dt=0.7660, 341 negative triangles 426: dt=0.7660, 339 negative triangles 427: dt=0.7660, 341 negative triangles 428: dt=0.7660, 340 negative triangles 429: dt=0.7660, 341 negative triangles 430: dt=0.7660, 338 negative triangles 431: dt=0.7660, 337 negative triangles 432: dt=0.7277, 339 negative triangles 433: dt=0.7277, 340 negative triangles 434: dt=0.7277, 336 negative triangles 435: dt=0.7277, 337 negative triangles 436: dt=0.7277, 340 negative triangles 437: dt=0.7277, 340 negative triangles 438: dt=0.7277, 339 negative triangles 439: dt=0.7277, 341 negative triangles 440: dt=0.7277, 337 negative triangles 441: dt=0.7277, 340 negative triangles 442: dt=0.6914, 337 negative triangles 443: dt=0.6914, 335 negative triangles 444: dt=0.6914, 337 negative triangles 445: dt=0.6914, 336 negative triangles 446: dt=0.6914, 334 negative triangles 447: dt=0.6914, 335 negative triangles 448: dt=0.6914, 334 negative triangles 449: dt=0.6914, 334 negative triangles 450: dt=0.6914, 334 negative triangles 451: dt=0.6914, 334 negative triangles 452: dt=0.6568, 334 negative triangles 453: dt=0.6568, 332 negative triangles 454: dt=0.6568, 330 negative triangles 455: dt=0.6568, 328 negative triangles 456: dt=0.6568, 328 negative triangles 457: dt=0.6568, 332 negative triangles 458: dt=0.6568, 333 negative triangles 459: dt=0.6568, 332 negative triangles 460: dt=0.6568, 329 negative triangles 461: dt=0.6568, 330 negative triangles 462: dt=0.6568, 330 negative triangles 463: dt=0.6568, 329 negative triangles 464: dt=0.6568, 326 negative triangles 465: dt=0.6568, 332 negative triangles 466: dt=0.6568, 335 negative triangles 467: dt=0.6568, 327 negative triangles 468: dt=0.6568, 328 negative triangles 469: dt=0.6568, 330 negative triangles 470: dt=0.6568, 332 negative triangles 471: dt=0.6568, 332 negative triangles 472: dt=0.6568, 331 negative triangles 473: dt=0.6568, 327 negative triangles 474: dt=0.6239, 327 negative triangles 475: dt=0.6239, 325 negative triangles 476: dt=0.6239, 330 negative triangles 477: dt=0.6239, 326 negative triangles 478: dt=0.6239, 326 negative triangles 479: dt=0.6239, 325 negative triangles 480: dt=0.6239, 325 negative triangles 481: dt=0.6239, 325 negative triangles 482: dt=0.6239, 330 negative triangles 483: dt=0.6239, 328 negative triangles 484: dt=0.6239, 330 negative triangles 485: dt=0.5927, 329 negative triangles 486: dt=0.5927, 325 negative triangles 487: dt=0.5927, 325 negative triangles 488: dt=0.5927, 330 negative triangles 489: dt=0.5927, 326 negative triangles 490: dt=0.5927, 331 negative triangles 491: dt=0.5927, 329 negative triangles 492: dt=0.5927, 329 negative triangles 493: dt=0.5927, 328 negative triangles 494: dt=0.5927, 329 negative triangles 495: dt=0.5631, 333 negative triangles 496: dt=0.5631, 331 negative triangles 497: dt=0.5631, 330 negative triangles 498: dt=0.5631, 330 negative triangles 499: dt=0.5631, 330 negative triangles 500: dt=0.5631, 330 negative triangles 501: dt=0.5631, 330 negative triangles 502: dt=0.5631, 326 negative triangles 503: dt=0.5631, 330 negative triangles 504: dt=0.5631, 329 negative triangles 505: dt=0.5350, 325 negative triangles 506: dt=0.5350, 327 negative triangles 507: dt=0.5350, 324 negative triangles 508: dt=0.5350, 328 negative triangles 509: dt=0.5350, 326 negative triangles 510: dt=0.5350, 325 negative triangles 511: dt=0.5350, 326 negative triangles 512: dt=0.5350, 329 negative triangles 513: dt=0.5350, 330 negative triangles 514: dt=0.5350, 324 negative triangles 515: dt=0.5350, 327 negative triangles 516: dt=0.5350, 330 negative triangles 517: dt=0.5082, 326 negative triangles 518: dt=0.5082, 326 negative triangles 519: dt=0.5082, 330 negative triangles 520: dt=0.5082, 328 negative triangles 521: dt=0.5082, 329 negative triangles 522: dt=0.5082, 326 negative triangles 523: dt=0.5082, 327 negative triangles 524: dt=0.5082, 327 negative triangles 525: dt=0.5082, 326 negative triangles 526: dt=0.5082, 325 negative triangles 527: dt=0.4828, 325 negative triangles 528: dt=0.4828, 322 negative triangles 529: dt=0.4828, 328 negative triangles 530: dt=0.4828, 322 negative triangles 531: dt=0.4828, 325 negative triangles 532: dt=0.4828, 323 negative triangles 533: dt=0.4828, 326 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322 negative triangles 995: dt=0.0505, 324 negative triangles 996: dt=0.0505, 319 negative triangles 997: dt=0.0505, 326 negative triangles 998: dt=0.0505, 320 negative triangles 999: dt=0.0505, 315 negative triangles 1000: dt=0.0505, 320 negative triangles 1001: dt=0.0505, 323 negative triangles 1002: dt=0.0505, 320 negative triangles 1003: dt=0.0505, 326 negative triangles 1004: dt=0.0480, 321 negative triangles 1005: dt=0.0480, 316 negative triangles 1006: dt=0.0480, 325 negative triangles 1007: dt=0.0480, 322 negative triangles 1008: dt=0.0480, 320 negative triangles 1009: dt=0.0480, 321 negative triangles 1010: dt=0.0480, 326 negative triangles 1011: dt=0.0480, 327 negative triangles 1012: dt=0.0480, 327 negative triangles 1013: dt=0.0480, 329 negative triangles 1014: dt=0.0456, 329 negative triangles 1015: dt=0.0456, 324 negative triangles 1016: dt=0.0456, 325 negative triangles 1017: dt=0.0456, 326 negative triangles 1018: dt=0.0456, 324 negative triangles 1019: dt=0.0456, 318 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negative triangles 1070: dt=0.0353, 333 negative triangles 1071: dt=0.0353, 332 negative triangles 1072: dt=0.0353, 327 negative triangles 1073: dt=0.0353, 329 negative triangles 1074: dt=0.0335, 330 negative triangles 1075: dt=0.0335, 324 negative triangles 1076: dt=0.0335, 321 negative triangles 1077: dt=0.0335, 326 negative triangles 1078: dt=0.0335, 324 negative triangles 1079: dt=0.0335, 323 negative triangles 1080: dt=0.0335, 323 negative triangles 1081: dt=0.0335, 324 negative triangles 1082: dt=0.0335, 321 negative triangles 1083: dt=0.0335, 323 negative triangles 1084: dt=0.0319, 326 negative triangles 1085: dt=0.0319, 323 negative triangles 1086: dt=0.0319, 320 negative triangles 1087: dt=0.0319, 318 negative triangles 1088: dt=0.0319, 316 negative triangles 1089: dt=0.0319, 318 negative triangles 1090: dt=0.0319, 320 negative triangles 1091: dt=0.0319, 316 negative triangles 1092: dt=0.0319, 321 negative triangles 1093: dt=0.0319, 320 negative triangles 1094: dt=0.0303, 315 negative triangles 1095: dt=0.0303, 320 negative triangles 1096: dt=0.0303, 320 negative triangles 1097: dt=0.0303, 322 negative triangles 1098: dt=0.0303, 323 negative triangles 1099: dt=0.0303, 320 negative triangles 1100: dt=0.0303, 321 negative triangles 1101: dt=0.0303, 323 negative triangles 1102: dt=0.0303, 323 negative triangles 1103: dt=0.0303, 325 negative triangles 1104: dt=0.0287, 322 negative triangles 1105: dt=0.0287, 325 negative triangles 1106: dt=0.0287, 326 negative triangles 1107: dt=0.0287, 322 negative triangles 1108: dt=0.0287, 323 negative triangles 1109: dt=0.0287, 327 negative triangles 1110: dt=0.0287, 327 negative triangles 1111: dt=0.0287, 324 negative triangles 1112: dt=0.0287, 325 negative triangles 1113: dt=0.0287, 323 negative triangles 1114: dt=0.0273, 325 negative triangles 1115: dt=0.0273, 328 negative triangles 1116: dt=0.0273, 321 negative triangles 1117: dt=0.0273, 323 negative triangles 1118: dt=0.0273, 322 negative triangles 1119: dt=0.0273, 324 negative triangles 1120: dt=0.0273, 320 negative triangles 1121: dt=0.0273, 324 negative triangles 1122: dt=0.0273, 314 negative triangles 1123: dt=0.0273, 322 negative triangles 1124: dt=0.0259, 320 negative triangles 1125: dt=0.0259, 316 negative triangles 1126: dt=0.0259, 319 negative triangles 1127: dt=0.0259, 319 negative triangles 1128: dt=0.0259, 321 negative triangles 1129: dt=0.0259, 322 negative triangles 1130: dt=0.0259, 317 negative triangles 1131: dt=0.0259, 317 negative triangles 1132: dt=0.0259, 317 negative triangles 1133: dt=0.0259, 324 negative triangles 1134: dt=0.0246, 322 negative triangles 1135: dt=0.0246, 316 negative triangles 1136: dt=0.0246, 314 negative triangles 1137: dt=0.0246, 313 negative triangles 1138: dt=0.0246, 315 negative triangles 1139: dt=0.0246, 316 negative triangles 1140: dt=0.0246, 319 negative triangles 1141: dt=0.0246, 323 negative triangles 1142: dt=0.0246, 326 negative triangles 1143: dt=0.0246, 322 negative triangles 1144: dt=0.0234, 322 negative triangles 1145: dt=0.0234, 327 negative triangles 1146: dt=0.0234, 324 negative triangles 1147: dt=0.0234, 324 negative triangles 1148: dt=0.0234, 327 negative triangles 1149: dt=0.0234, 324 negative triangles 1150: dt=0.0234, 325 negative triangles 1151: dt=0.0234, 329 negative triangles 1152: dt=0.0234, 330 negative triangles 1153: dt=0.0234, 325 negative triangles 1154: dt=0.0222, 326 negative triangles 1155: dt=0.0222, 326 negative triangles 1156: dt=0.0222, 326 negative triangles 1157: dt=0.0222, 326 negative triangles 1158: dt=0.0222, 325 negative triangles 1159: dt=0.0222, 324 negative triangles 1160: dt=0.0222, 326 negative triangles 1161: dt=0.0222, 329 negative triangles 1162: dt=0.0222, 326 negative triangles 1163: dt=0.0222, 326 negative triangles 1164: dt=0.0211, 324 negative triangles 1165: dt=0.0211, 327 negative triangles 1166: dt=0.0211, 329 negative triangles 1167: dt=0.0211, 332 negative triangles 1168: dt=0.0211, 335 negative triangles 1169: dt=0.0211, 332 negative triangles 1170: dt=0.0211, 329 negative triangles 1171: dt=0.0211, 331 negative triangles 1172: dt=0.0211, 331 negative triangles 1173: dt=0.0211, 329 negative triangles 1174: dt=0.0201, 329 negative triangles 1175: dt=0.0201, 326 negative triangles 1176: dt=0.0201, 325 negative triangles 1177: dt=0.0201, 327 negative triangles 1178: dt=0.0201, 328 negative triangles 1179: dt=0.0201, 330 negative triangles 1180: dt=0.0201, 328 negative triangles 1181: dt=0.0201, 325 negative triangles 1182: dt=0.0201, 325 negative triangles 1183: dt=0.0201, 328 negative triangles 1184: dt=0.0191, 330 negative triangles 1185: dt=0.0191, 330 negative triangles 1186: dt=0.0191, 327 negative triangles 1187: dt=0.0191, 332 negative triangles 1188: dt=0.0191, 331 negative triangles 1189: dt=0.0191, 329 negative triangles 1190: dt=0.0191, 331 negative triangles 1191: dt=0.0191, 332 negative triangles 1192: dt=0.0191, 332 negative triangles 1193: dt=0.0191, 327 negative triangles 1194: dt=0.0181, 330 negative triangles 1195: dt=0.0181, 330 negative triangles 1196: dt=0.0181, 327 negative triangles 1197: dt=0.0181, 325 negative triangles 1198: dt=0.0181, 325 negative triangles 1199: dt=0.0181, 328 negative triangles 1200: dt=0.0181, 328 negative triangles 1201: dt=0.0181, 329 negative triangles 1202: dt=0.0181, 327 negative triangles 1203: dt=0.0181, 325 negative triangles 1204: dt=0.0172, 322 negative triangles 1205: dt=0.0172, 320 negative triangles 1206: dt=0.0172, 322 negative triangles 1207: dt=0.0172, 321 negative triangles 1208: dt=0.0172, 331 negative triangles 1209: dt=0.0172, 322 negative triangles 1210: dt=0.0172, 323 negative triangles 1211: dt=0.0172, 324 negative triangles 1212: dt=0.0172, 320 negative triangles 1213: dt=0.0172, 320 negative triangles 1214: dt=0.0164, 324 negative triangles 1215: dt=0.0164, 322 negative triangles 1216: dt=0.0164, 323 negative triangles 1217: dt=0.0164, 328 negative triangles 1218: dt=0.0164, 327 negative triangles 1219: dt=0.0164, 324 negative triangles 1220: dt=0.0164, 328 negative triangles 1221: dt=0.0164, 323 negative triangles 1222: dt=0.0164, 328 negative triangles 1223: dt=0.0164, 334 negative triangles 1224: dt=0.0155, 327 negative triangles 1225: dt=0.0155, 329 negative triangles 1226: dt=0.0155, 332 negative triangles 1227: dt=0.0155, 333 negative triangles 1228: dt=0.0155, 328 negative triangles 1229: dt=0.0155, 327 negative triangles 1230: dt=0.0155, 327 negative triangles 1231: dt=0.0155, 328 negative triangles 1232: dt=0.0155, 330 negative triangles 1233: dt=0.0155, 329 negative triangles 1234: dt=0.0148, 330 negative triangles 1235: dt=0.0148, 326 negative triangles 1236: dt=0.0148, 333 negative triangles 1237: dt=0.0148, 328 negative triangles 1238: dt=0.0148, 330 negative triangles 1239: dt=0.0148, 325 negative triangles 1240: dt=0.0148, 331 negative triangles 1241: dt=0.0148, 330 negative triangles 1242: dt=0.0148, 323 negative triangles 1243: dt=0.0148, 322 negative triangles 1244: dt=0.0140, 322 negative triangles 1245: dt=0.0140, 323 negative triangles 1246: dt=0.0140, 325 negative triangles 1247: dt=0.0140, 326 negative triangles 1248: dt=0.0140, 323 negative triangles 1249: dt=0.0140, 323 negative triangles 1250: dt=0.0140, 325 negative triangles 1251: 328 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1146 hours FSRUNTIME@ mris_sphere 0.1146 hours 4 threads #VMPC# mris_sphere VmPeak 768940 mris_sphere done PIDs (291982 291985) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Fri Jan 6 19:04:27 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Fri Jan 6 19:04:27 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 292068 of (292068 292071) to complete... Waiting for PID 292071 of (292068 292071) to complete... mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.0 7.3.0 reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=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=0.0682 min MRISrigidBodyAlignGlobal() done 0.07 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 0.0529 hours 4 threads mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.0 7.3.0 reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=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 = 5.421 curvature mean = 0.040, std = 0.809 curvature mean = 0.014, std = 0.883 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.50, -12.00, -6.50) sse = 188026.5, elapsed since starting=0.0667 min MRISrigidBodyAlignGlobal() done 0.07 min curvature mean = 0.020, std = 0.835 curvature mean = 0.005, std = 0.958 curvature mean = 0.019, std = 0.847 curvature mean = 0.002, std = 0.984 curvature mean = 0.018, std = 0.850 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.032, std = 0.864 curvature mean = 0.040, std = 0.239 curvature mean = 0.025, std = 0.124 curvature mean = 0.035, std = 0.300 curvature mean = 0.015, std = 0.194 curvature mean = 0.034, std = 0.327 curvature mean = 0.009, std = 0.259 curvature mean = 0.034, std = 0.338 curvature mean = 0.004, std = 0.346 MRISregister() return, current seed 0 -01: dt=0.0000, 431 negative triangles VmPeak 768972 113: dt=0.9900, 431 negative triangles expanding nbhd size to 1 114: dt=0.9900, 453 negative triangles 115: dt=0.9900, 426 negative triangles 116: dt=0.9900, 423 negative triangles 117: dt=0.9900, 421 negative triangles 118: dt=0.9900, 425 negative triangles 119: dt=0.9900, 422 negative triangles 120: dt=0.9900, 421 negative triangles 121: dt=0.9900, 414 negative triangles 122: dt=0.9900, 416 negative triangles 123: dt=0.9900, 418 negative triangles 124: dt=0.9900, 417 negative triangles 125: dt=0.9900, 414 negative triangles 126: dt=0.9900, 413 negative triangles 127: dt=0.9900, 410 negative triangles 128: dt=0.9900, 412 negative triangles 129: dt=0.9900, 409 negative triangles 130: dt=0.9900, 412 negative triangles 131: dt=0.9900, 409 negative triangles 132: dt=0.9900, 407 negative triangles 133: dt=0.9900, 404 negative triangles 134: dt=0.9900, 405 negative triangles 135: dt=0.9900, 402 negative triangles 136: dt=0.9900, 401 negative triangles 137: dt=0.9900, 402 negative triangles 138: dt=0.9900, 397 negative triangles 139: dt=0.9900, 395 negative triangles 140: dt=0.9900, 396 negative triangles 141: dt=0.9900, 395 negative triangles 142: dt=0.9900, 392 negative triangles 143: dt=0.9900, 394 negative triangles 144: dt=0.9900, 390 negative triangles 145: dt=0.9900, 390 negative triangles 146: dt=0.9900, 388 negative triangles 147: dt=0.9900, 387 negative triangles 148: dt=0.9900, 395 negative triangles 149: dt=0.9900, 390 negative triangles 150: dt=0.9900, 389 negative triangles 151: dt=0.9900, 390 negative triangles 152: dt=0.9900, 396 negative triangles 153: dt=0.9900, 392 negative triangles 154: dt=0.9900, 388 negative triangles 155: dt=0.9900, 392 negative triangles 156: dt=0.9900, 389 negative triangles 157: dt=0.9405, 392 negative triangles 158: dt=0.9405, 393 negative triangles 159: dt=0.9405, 393 negative triangles 160: dt=0.9405, 399 negative triangles 161: dt=0.9405, 395 negative triangles 162: dt=0.9405, 395 negative triangles 163: dt=0.9405, 397 negative triangles 164: dt=0.9405, 394 negative triangles 165: dt=0.9405, 394 negative triangles 166: dt=0.9405, 390 negative triangles 167: dt=0.8935, 394 negative triangles 168: dt=0.8935, 395 negative triangles 169: dt=0.8935, 392 negative triangles 170: dt=0.8935, 396 negative triangles 171: dt=0.8935, 392 negative triangles 172: dt=0.8935, 391 negative triangles 173: dt=0.8935, 392 negative triangles 174: dt=0.8935, 389 negative triangles 175: dt=0.8935, 387 negative triangles 176: dt=0.8935, 394 negative triangles 177: dt=0.8488, 399 negative triangles 178: dt=0.8488, 395 negative triangles 179: dt=0.8488, 396 negative triangles 180: dt=0.8488, 394 negative triangles 181: dt=0.8488, 396 negative triangles 182: dt=0.8488, 397 negative triangles 183: dt=0.8488, 396 negative triangles 184: dt=0.8488, 389 negative triangles 185: dt=0.8488, 394 negative triangles 186: dt=0.8488, 391 negative triangles 187: dt=0.8064, 389 negative triangles 188: dt=0.8064, 387 negative triangles 189: dt=0.8064, 390 negative triangles 190: dt=0.8064, 386 negative triangles 191: dt=0.8064, 390 negative triangles 192: dt=0.8064, 390 negative triangles 193: dt=0.8064, 398 negative triangles 194: dt=0.8064, 390 negative triangles 195: dt=0.8064, 389 negative triangles 196: dt=0.8064, 385 negative triangles 197: dt=0.8064, 388 negative triangles 198: dt=0.8064, 390 negative triangles 199: dt=0.8064, 384 negative triangles 200: dt=0.8064, 387 negative triangles 201: dt=0.8064, 384 negative triangles 202: dt=0.8064, 392 negative triangles 203: dt=0.8064, 384 negative triangles 204: dt=0.8064, 380 negative triangles 205: dt=0.8064, 388 negative triangles 206: dt=0.8064, 384 negative triangles 207: dt=0.8064, 386 negative triangles 208: dt=0.8064, 385 negative triangles 209: dt=0.8064, 383 negative triangles 210: dt=0.8064, 380 negative triangles 211: dt=0.8064, 381 negative triangles 212: dt=0.8064, 386 negative triangles 213: dt=0.8064, 377 negative triangles 214: dt=0.8064, 382 negative triangles 215: dt=0.8064, 381 negative triangles 216: dt=0.8064, 381 negative triangles 217: dt=0.8064, 380 negative triangles 218: dt=0.8064, 380 negative triangles 219: dt=0.8064, 379 negative triangles 220: dt=0.8064, 380 negative triangles 221: dt=0.8064, 377 negative triangles 222: dt=0.8064, 381 negative triangles 223: dt=0.7660, 379 negative triangles 224: dt=0.7660, 379 negative triangles 225: dt=0.7660, 379 negative triangles 226: dt=0.7660, 377 negative triangles 227: dt=0.7660, 379 negative triangles 228: dt=0.7660, 380 negative triangles 229: dt=0.7660, 382 negative triangles 230: dt=0.7660, 380 negative triangles 231: dt=0.7660, 383 negative triangles 232: dt=0.7660, 381 negative triangles 233: dt=0.7277, 381 negative triangles 234: dt=0.7277, 379 negative triangles 235: dt=0.7277, 382 negative triangles 236: dt=0.7277, 377 negative triangles 237: dt=0.7277, 379 negative triangles 238: dt=0.7277, 368 negative triangles 239: dt=0.7277, 373 negative triangles 240: dt=0.7277, 372 negative triangles 241: dt=0.7277, 373 negative triangles 242: dt=0.7277, 374 negative triangles 243: dt=0.7277, 372 negative triangles 244: dt=0.7277, 374 negative triangles 245: dt=0.7277, 375 negative triangles 246: dt=0.7277, 375 negative triangles 247: dt=0.7277, 372 negative triangles 248: dt=0.6914, 371 negative triangles 249: dt=0.6914, 375 negative triangles 250: dt=0.6914, 373 negative triangles 251: dt=0.6914, 372 negative triangles 252: dt=0.6914, 370 negative triangles 253: dt=0.6914, 372 negative triangles 254: dt=0.6914, 375 negative triangles 255: dt=0.6914, 376 negative triangles 256: dt=0.6914, 371 negative triangles 257: dt=0.6914, 376 negative triangles 258: dt=0.6568, 371 negative triangles 259: dt=0.6568, 371 negative triangles 260: dt=0.6568, 374 negative triangles 261: dt=0.6568, 375 negative triangles 262: dt=0.6568, 372 negative triangles 263: dt=0.6568, 372 negative triangles 264: dt=0.6568, 376 negative triangles 265: dt=0.6568, 371 negative triangles 266: dt=0.6568, 378 negative triangles 267: dt=0.6568, 373 negative triangles 268: dt=0.6239, 371 negative triangles 269: dt=0.6239, 371 negative triangles 270: dt=0.6239, 371 negative triangles 271: dt=0.6239, 372 negative triangles 272: dt=0.6239, 372 negative triangles 273: dt=0.6239, 371 negative triangles 274: dt=0.6239, 371 negative triangles 275: dt=0.6239, 372 negative triangles 276: dt=0.6239, 376 negative triangles 277: dt=0.6239, 375 negative triangles 278: dt=0.5927, 371 negative triangles 279: dt=0.5927, 375 negative triangles 280: dt=0.5927, 373 negative triangles 281: dt=0.5927, 376 negative triangles 282: dt=0.5927, 374 negative triangles 283: dt=0.5927, 374 negative triangles 284: dt=0.5927, 372 negative triangles 285: dt=0.5927, 376 negative triangles 286: dt=0.5927, 375 negative triangles 287: dt=0.5927, 376 negative triangles 288: dt=0.5631, 373 negative triangles 289: dt=0.5631, 377 negative triangles 290: dt=0.5631, 372 negative triangles 291: dt=0.5631, 374 negative triangles 292: dt=0.5631, 370 negative triangles 293: dt=0.5631, 373 negative triangles 294: dt=0.5631, 371 negative triangles 295: dt=0.5631, 366 negative triangles 296: dt=0.5631, 370 negative triangles 297: dt=0.5631, 370 negative triangles 298: dt=0.5631, 374 negative triangles 299: dt=0.5631, 371 negative triangles 300: dt=0.5631, 369 negative triangles 301: dt=0.5631, 378 negative triangles 302: dt=0.5631, 378 negative triangles 303: dt=0.5631, 373 negative triangles 304: dt=0.5631, 371 negative triangles 305: dt=0.5350, 371 negative triangles 306: dt=0.5350, 376 negative triangles 307: dt=0.5350, 372 negative triangles 308: dt=0.5350, 373 negative triangles 309: dt=0.5350, 373 negative triangles 310: dt=0.5350, 376 negative triangles 311: dt=0.5350, 367 negative triangles 312: dt=0.5350, 369 negative triangles 313: dt=0.5350, 374 negative triangles 314: dt=0.5350, 380 negative triangles 315: dt=0.5082, 375 negative triangles 316: dt=0.5082, 374 negative triangles 317: dt=0.5082, 376 negative triangles 318: dt=0.5082, 374 negative triangles 319: dt=0.5082, 369 negative triangles 320: dt=0.5082, 371 negative triangles 321: dt=0.5082, 374 negative triangles 322: dt=0.5082, 371 negative triangles 323: dt=0.5082, 367 negative triangles 324: dt=0.5082, 373 negative triangles 325: dt=0.4828, 371 negative triangles 326: dt=0.4828, 372 negative triangles 327: dt=0.4828, 375 negative triangles 328: dt=0.4828, 370 negative triangles 329: dt=0.4828, 373 negative triangles 330: dt=0.4828, 374 negative triangles 331: dt=0.4828, 371 negative triangles 332: dt=0.4828, 373 negative triangles 333: dt=0.4828, 374 negative triangles 334: dt=0.4828, 370 negative triangles 335: dt=0.4587, 367 negative triangles 336: dt=0.4587, 367 negative triangles 337: dt=0.4587, 373 negative triangles 338: dt=0.4587, 370 negative triangles 339: dt=0.4587, 367 negative triangles 340: dt=0.4587, 371 negative triangles 341: dt=0.4587, 369 negative triangles 342: dt=0.4587, 371 negative triangles 343: dt=0.4587, 369 negative triangles 344: dt=0.4587, 363 negative triangles 345: dt=0.4587, 375 negative triangles 346: dt=0.4587, 373 negative triangles 347: dt=0.4587, 371 negative triangles 348: dt=0.4587, 370 negative triangles 349: dt=0.4587, 363 negative triangles 350: dt=0.4587, 368 negative triangles 351: dt=0.4587, 367 negative triangles 352: dt=0.4587, 365 negative triangles 353: dt=0.4587, 367 negative triangles 354: dt=0.4357, 367 negative triangles 355: dt=0.4357, 367 negative triangles 356: dt=0.4357, 366 negative triangles 357: dt=0.4357, 363 negative triangles 358: dt=0.4357, 366 negative triangles 359: dt=0.4357, 367 negative triangles 360: dt=0.4357, 369 negative triangles 361: dt=0.4357, 367 negative triangles 362: dt=0.4357, 373 negative triangles 363: dt=0.4357, 364 negative triangles 364: dt=0.4139, 369 negative triangles 365: dt=0.4139, 368 negative triangles 366: dt=0.4139, 367 negative triangles 367: dt=0.4139, 366 negative triangles 368: dt=0.4139, 370 negative triangles 369: dt=0.4139, 372 negative triangles 370: dt=0.4139, 366 negative triangles 371: dt=0.4139, 367 negative triangles 372: dt=0.4139, 363 negative triangles 373: dt=0.4139, 365 negative triangles 374: dt=0.3932, 369 negative triangles 375: dt=0.3932, 364 negative triangles 376: dt=0.3932, 365 negative triangles 377: dt=0.3932, 372 negative triangles 378: dt=0.3932, 372 negative triangles 379: dt=0.3932, 370 negative triangles 380: dt=0.3932, 372 negative triangles 381: dt=0.3932, 372 negative triangles 382: dt=0.3932, 370 negative triangles 383: dt=0.3932, 370 negative triangles 384: dt=0.3736, 370 negative triangles 385: dt=0.3736, 366 negative triangles 386: dt=0.3736, 372 negative triangles 387: dt=0.3736, 370 negative triangles 388: dt=0.3736, 367 negative triangles 389: dt=0.3736, 374 negative triangles 390: dt=0.3736, 366 negative triangles 391: dt=0.3736, 372 negative triangles 392: dt=0.3736, 367 negative triangles 393: dt=0.3736, 364 negative triangles 394: dt=0.3736, 357 negative triangles 395: dt=0.3736, 367 negative triangles 396: dt=0.3736, 360 negative triangles 397: dt=0.3736, 364 negative triangles 398: dt=0.3736, 364 negative triangles 399: dt=0.3736, 360 negative triangles 400: dt=0.3736, 368 negative triangles 401: dt=0.3736, 366 negative triangles 402: dt=0.3736, 369 negative triangles 403: dt=0.3736, 370 negative triangles 404: dt=0.3549, 370 negative triangles 405: dt=0.3549, 362 negative triangles 406: dt=0.3549, 364 negative triangles 407: dt=0.3549, 360 negative triangles 408: dt=0.3549, 364 negative triangles 409: dt=0.3549, 360 negative triangles 410: dt=0.3549, 366 negative triangles 411: dt=0.3549, 369 negative triangles 412: dt=0.3549, 373 negative triangles 413: dt=0.3549, 373 negative triangles 414: dt=0.3372, 367 negative triangles 415: dt=0.3372, 363 negative triangles 416: dt=0.3372, 360 negative triangles 417: dt=0.3372, 363 negative triangles 418: dt=0.3372, 361 negative triangles 419: dt=0.3372, 368 negative triangles 420: dt=0.3372, 371 negative triangles 421: dt=0.3372, 367 negative triangles 422: dt=0.3372, 364 negative triangles 423: dt=0.3372, 366 negative triangles 424: dt=0.3203, 372 negative triangles 425: dt=0.3203, 368 negative triangles 426: dt=0.3203, 365 negative triangles 427: dt=0.3203, 369 negative triangles 428: dt=0.3203, 373 negative triangles 429: dt=0.3203, 370 negative triangles 430: dt=0.3203, 368 negative triangles 431: dt=0.3203, 369 negative triangles 432: dt=0.3203, 372 negative triangles 433: dt=0.3203, 364 negative triangles 434: dt=0.3043, 369 negative triangles 435: dt=0.3043, 375 negative triangles 436: dt=0.3043, 370 negative triangles 437: dt=0.3043, 367 negative triangles 438: dt=0.3043, 375 negative triangles 439: dt=0.3043, 369 negative triangles 440: dt=0.3043, 369 negative triangles 441: dt=0.3043, 371 negative triangles 442: dt=0.3043, 369 negative triangles 443: dt=0.3043, 370 negative triangles 444: dt=0.2891, 366 negative triangles 445: dt=0.2891, 364 negative triangles 446: dt=0.2891, 367 negative triangles 447: dt=0.2891, 362 negative triangles 448: dt=0.2891, 364 negative triangles 449: dt=0.2891, 368 negative triangles 450: dt=0.2891, 368 negative triangles 451: dt=0.2891, 364 negative triangles 452: dt=0.2891, 368 negative triangles 453: dt=0.2891, 364 negative triangles 454: dt=0.2746, 363 negative triangles 455: dt=0.2746, 365 negative triangles 456: dt=0.2746, 370 negative triangles 457: dt=0.2746, 364 negative triangles 458: dt=0.2746, 366 negative triangles 459: dt=0.2746, 365 negative triangles 460: dt=0.2746, 364 negative triangles 461: dt=0.2746, 365 negative triangles 462: dt=0.2746, 366 negative triangles 463: dt=0.2746, 369 negative triangles 464: dt=0.2609, 365 negative triangles 465: dt=0.2609, 364 negative triangles 466: dt=0.2609, 363 negative triangles 467: dt=0.2609, 370 negative triangles 468: dt=0.2609, 366 negative triangles 469: dt=0.2609, 363 negative triangles 470: dt=0.2609, 365 negative triangles 471: dt=0.2609, 366 negative triangles 472: dt=0.2609, 371 negative triangles 473: dt=0.2609, 359 negative triangles 474: dt=0.2478, 367 negative triangles 475: dt=0.2478, 368 negative triangles 476: dt=0.2478, 369 negative triangles 477: dt=0.2478, 367 negative triangles 478: dt=0.2478, 366 negative triangles 479: dt=0.2478, 367 negative triangles 480: dt=0.2478, 365 negative triangles 481: dt=0.2478, 362 negative triangles 482: dt=0.2478, 380 negative triangles 483: dt=0.2478, 365 negative triangles 484: dt=0.2354, 371 negative triangles 485: dt=0.2354, 362 negative triangles 486: dt=0.2354, 364 negative triangles 487: dt=0.2354, 362 negative triangles 488: dt=0.2354, 368 negative triangles 489: dt=0.2354, 368 negative triangles 490: dt=0.2354, 363 negative triangles 491: dt=0.2354, 362 negative triangles 492: dt=0.2354, 360 negative triangles 493: dt=0.2354, 359 negative triangles 494: dt=0.2237, 360 negative triangles 495: dt=0.2237, 362 negative triangles 496: dt=0.2237, 377 negative triangles 497: dt=0.2237, 367 negative triangles 498: dt=0.2237, 368 negative triangles 499: dt=0.2237, 364 negative triangles 500: dt=0.2237, 360 negative triangles 501: dt=0.2237, 362 negative triangles 502: dt=0.2237, 364 negative triangles 503: dt=0.2237, 366 negative triangles 504: dt=0.2125, 364 negative triangles 505: dt=0.2125, 364 negative triangles 506: dt=0.2125, 366 negative triangles 507: dt=0.2125, 360 negative triangles 508: dt=0.2125, 361 negative triangles 509: dt=0.2125, 363 negative triangles 510: dt=0.2125, 366 negative triangles 511: dt=0.2125, 369 negative triangles 512: dt=0.2125, 369 negative triangles 513: dt=0.2125, 366 negative triangles 514: dt=0.2019, 365 negative triangles 515: dt=0.2019, 366 negative triangles 516: dt=0.2019, 363 negative triangles 517: dt=0.2019, 358 negative triangles 518: dt=0.2019, 357 negative triangles 519: dt=0.2019, 367 negative triangles 520: dt=0.2019, 361 negative triangles 521: dt=0.2019, 360 negative triangles 522: dt=0.2019, 365 negative triangles 523: dt=0.2019, 365 negative triangles 524: dt=0.1918, 367 negative triangles 525: dt=0.1918, 363 negative triangles 526: dt=0.1918, 369 negative triangles 527: dt=0.1918, 361 negative triangles 528: dt=0.1918, 363 negative triangles 529: dt=0.1918, 358 negative triangles 530: dt=0.1918, 360 negative triangles 531: dt=0.1918, 356 negative triangles 532: dt=0.1918, 357 negative triangles 533: dt=0.1918, 357 negative triangles 534: dt=0.1918, 369 negative triangles 535: dt=0.1918, 368 negative triangles 536: dt=0.1918, 374 negative triangles 537: dt=0.1918, 373 negative triangles 538: dt=0.1918, 366 negative triangles 539: dt=0.1918, 362 negative triangles 540: dt=0.1918, 367 negative triangles 541: dt=0.1822, 361 negative triangles 542: dt=0.1822, 365 negative triangles 543: dt=0.1822, 367 negative triangles 544: dt=0.1822, 362 negative triangles 545: dt=0.1822, 361 negative triangles 546: dt=0.1822, 360 negative triangles 547: dt=0.1822, 359 negative triangles 548: dt=0.1822, 365 negative triangles 549: dt=0.1822, 363 negative triangles 550: dt=0.1822, 360 negative triangles 551: dt=0.1731, 365 negative triangles 552: dt=0.1731, 368 negative triangles 553: dt=0.1731, 372 negative triangles 554: dt=0.1731, 367 negative triangles 555: dt=0.1731, 362 negative triangles 556: dt=0.1731, 361 negative triangles 557: dt=0.1731, 361 negative triangles 558: dt=0.1731, 357 negative triangles 559: dt=0.1731, 365 negative triangles 560: dt=0.1731, 358 negative triangles 561: dt=0.1644, 359 negative triangles 562: dt=0.1644, 358 negative triangles 563: dt=0.1644, 360 negative triangles 564: dt=0.1644, 357 negative triangles 565: dt=0.1644, 356 negative triangles 566: dt=0.1644, 358 negative triangles 567: dt=0.1644, 361 negative triangles 568: dt=0.1644, 366 negative triangles 569: dt=0.1644, 360 negative triangles 570: dt=0.1644, 370 negative triangles 571: dt=0.1562, 363 negative triangles 572: dt=0.1562, 369 negative triangles 573: dt=0.1562, 370 negative triangles 574: dt=0.1562, 365 negative triangles 575: dt=0.1562, 360 negative triangles 576: dt=0.1562, 364 negative triangles 577: dt=0.1562, 361 negative triangles 578: dt=0.1562, 358 negative triangles 579: dt=0.1562, 358 negative triangles 580: dt=0.1562, 362 negative triangles 581: dt=0.1484, 365 negative triangles 582: dt=0.1484, 372 negative triangles 583: dt=0.1484, 371 negative triangles 584: dt=0.1484, 372 negative triangles 585: dt=0.1484, 368 negative triangles 586: dt=0.1484, 362 negative triangles 587: dt=0.1484, 365 negative triangles 588: dt=0.1484, 361 negative triangles 589: dt=0.1484, 369 negative triangles 590: dt=0.1484, 364 negative triangles 591: dt=0.1410, 365 negative triangles 592: dt=0.1410, 359 negative triangles 593: dt=0.1410, 366 negative triangles 594: dt=0.1410, 367 negative triangles 595: dt=0.1410, 362 negative triangles 596: dt=0.1410, 364 negative triangles 597: dt=0.1410, 371 negative triangles 598: dt=0.1410, 370 negative triangles 599: dt=0.1410, 365 negative triangles 600: dt=0.1410, 361 negative triangles 601: dt=0.1339, 358 negative triangles 602: dt=0.1339, 357 negative triangles 603: dt=0.1339, 366 negative triangles 604: dt=0.1339, 364 negative triangles 605: dt=0.1339, 362 negative triangles 606: dt=0.1339, 364 negative triangles 607: dt=0.1339, 366 negative triangles 608: dt=0.1339, 370 negative triangles 609: dt=0.1339, 364 negative triangles 610: dt=0.1339, 355 negative triangles 611: dt=0.1339, 359 negative triangles 612: dt=0.1339, 360 negative triangles 613: dt=0.1339, 362 negative triangles 614: dt=0.1339, 366 negative triangles 615: dt=0.1339, 357 negative triangles 616: dt=0.1339, 359 negative triangles 617: dt=0.1339, 363 negative triangles 618: dt=0.1339, 364 negative triangles 619: dt=0.1339, 367 negative triangles 620: dt=0.1272, 365 negative triangles 621: dt=0.1272, 368 negative triangles 622: dt=0.1272, 367 negative triangles 623: dt=0.1272, 369 negative triangles 624: dt=0.1272, 369 negative triangles 625: dt=0.1272, 369 negative triangles 626: dt=0.1272, 372 negative triangles 627: dt=0.1272, 363 negative triangles 628: dt=0.1272, 362 negative triangles 629: dt=0.1272, 364 negative triangles 630: dt=0.1209, 364 negative triangles 631: dt=0.1209, 362 negative triangles 632: dt=0.1209, 360 negative triangles 633: dt=0.1209, 367 negative triangles 634: dt=0.1209, 365 negative triangles 635: dt=0.1209, 365 negative triangles 636: dt=0.1209, 358 negative triangles 637: dt=0.1209, 358 negative triangles 638: dt=0.1209, 359 negative triangles 639: dt=0.1209, 362 negative triangles 640: dt=0.1148, 364 negative triangles 641: dt=0.1148, 366 negative triangles 642: dt=0.1148, 362 negative triangles 643: dt=0.1148, 366 negative triangles 644: dt=0.1148, 359 negative triangles 645: dt=0.1148, 366 negative triangles 646: dt=0.1148, 365 negative triangles 647: dt=0.1148, 371 negative triangles 648: dt=0.1148, 367 negative triangles 649: dt=0.1148, 370 negative triangles 650: dt=0.1091, 375 negative triangles 651: dt=0.1091, 364 negative triangles 652: dt=0.1091, 363 negative triangles 653: dt=0.1091, 363 negative triangles 654: dt=0.1091, 367 negative triangles 655: dt=0.1091, 366 negative triangles 656: dt=0.1091, 368 negative triangles 657: dt=0.1091, 361 negative triangles 658: dt=0.1091, 361 negative triangles 659: dt=0.1091, 362 negative triangles 660: dt=0.1036, 359 negative triangles 661: dt=0.1036, 361 negative triangles 662: dt=0.1036, 359 negative triangles 663: dt=0.1036, 363 negative triangles 664: dt=0.1036, 363 negative triangles 665: dt=0.1036, 363 negative triangles 666: dt=0.1036, 362 negative triangles 667: dt=0.1036, 369 negative triangles 668: dt=0.1036, 365 negative triangles 669: dt=0.1036, 364 negative triangles 670: dt=0.0984, 364 negative triangles 671: dt=0.0984, 368 negative triangles 672: dt=0.0984, 375 negative triangles 673: dt=0.0984, 379 negative triangles 674: dt=0.0984, 371 negative triangles 675: dt=0.0984, 376 negative triangles 676: dt=0.0984, 369 negative triangles 677: dt=0.0984, 371 negative triangles 678: dt=0.0984, 381 negative triangles 679: dt=0.0984, 375 negative triangles 680: dt=0.0935, 372 negative triangles 681: dt=0.0935, 371 negative triangles 682: dt=0.0935, 374 negative triangles 683: dt=0.0935, 369 negative triangles 684: dt=0.0935, 372 negative triangles 685: dt=0.0935, 367 negative triangles 686: dt=0.0935, 371 negative triangles 687: dt=0.0935, 378 negative triangles 688: dt=0.0935, 366 negative triangles 689: dt=0.0935, 366 negative triangles 690: dt=0.0888, 366 negative triangles 691: dt=0.0888, 362 negative triangles 692: dt=0.0888, 369 negative triangles 693: dt=0.0888, 362 negative triangles 694: dt=0.0888, 369 negative triangles 695: dt=0.0888, 365 negative triangles 696: dt=0.0888, 367 negative triangles 697: dt=0.0888, 371 negative triangles 698: dt=0.0888, 373 negative triangles 699: dt=0.0888, 371 negative triangles 700: dt=0.0844, 367 negative triangles 701: dt=0.0844, 371 negative triangles 702: dt=0.0844, 368 negative triangles 703: dt=0.0844, 369 negative triangles 704: dt=0.0844, 370 negative triangles 705: dt=0.0844, 373 negative triangles 706: dt=0.0844, 369 negative triangles 707: dt=0.0844, 373 negative triangles 708: dt=0.0844, 374 negative triangles 709: dt=0.0844, 371 negative triangles 710: dt=0.0802, 369 negative triangles 711: dt=0.0802, 369 negative triangles 712: dt=0.0802, 366 negative triangles 713: dt=0.0802, 374 negative triangles 714: dt=0.0802, 368 negative triangles 715: dt=0.0802, 372 negative triangles 716: dt=0.0802, 371 negative triangles 717: dt=0.0802, 376 negative triangles 718: dt=0.0802, 375 negative triangles 719: dt=0.0802, 381 negative triangles 720: dt=0.0762, 378 negative triangles 721: dt=0.0762, 374 negative triangles 722: dt=0.0762, 375 negative triangles 723: dt=0.0762, 369 negative triangles 724: dt=0.0762, 364 negative triangles 725: dt=0.0762, 368 negative triangles 726: dt=0.0762, 366 negative triangles 727: dt=0.0762, 363 negative triangles 728: dt=0.0762, 365 negative triangles 729: dt=0.0762, 363 negative triangles 730: dt=0.0724, 365 negative triangles 731: dt=0.0724, 368 negative triangles 732: dt=0.0724, 363 negative triangles 733: dt=0.0724, 369 negative triangles 734: dt=0.0724, 372 negative triangles 735: dt=0.0724, 371 negative triangles 736: dt=0.0724, 374 negative triangles 737: dt=0.0724, 368 negative triangles 738: dt=0.0724, 368 negative triangles 739: dt=0.0724, 368 negative triangles 740: dt=0.0687, 375 negative triangles 741: dt=0.0687, 366 negative triangles 742: dt=0.0687, 368 negative triangles 743: dt=0.0687, 368 negative triangles 744: dt=0.0687, 371 negative triangles 745: dt=0.0687, 369 negative triangles 746: dt=0.0687, 371 negative triangles 747: dt=0.0687, 371 negative triangles 748: dt=0.0687, 366 negative triangles 749: dt=0.0687, 365 negative triangles 750: dt=0.0653, 366 negative triangles 751: dt=0.0653, 365 negative triangles 752: dt=0.0653, 368 negative triangles 753: dt=0.0653, 367 negative triangles 754: dt=0.0653, 368 negative triangles 755: dt=0.0653, 364 negative triangles 756: dt=0.0653, 371 negative triangles 757: dt=0.0653, 366 negative triangles 758: dt=0.0653, 371 negative triangles 759: dt=0.0653, 368 negative triangles 760: dt=0.0620, 364 negative triangles 761: dt=0.0620, 367 negative triangles 762: dt=0.0620, 364 negative triangles 763: dt=0.0620, 369 negative triangles 764: dt=0.0620, 368 negative triangles 765: dt=0.0620, 368 negative triangles 766: dt=0.0620, 367 negative triangles 767: dt=0.0620, 363 negative triangles 768: dt=0.0620, 366 negative triangles 769: dt=0.0620, 361 negative triangles 770: dt=0.0589, 367 negative triangles 771: dt=0.0589, 365 negative triangles 772: dt=0.0589, 364 negative triangles 773: dt=0.0589, 363 negative triangles 774: dt=0.0589, 365 negative triangles 775: dt=0.0589, 367 negative triangles 776: dt=0.0589, 366 negative triangles 777: dt=0.0589, 365 negative triangles 778: dt=0.0589, 363 negative triangles 779: dt=0.0589, 364 negative triangles 780: dt=0.0560, 369 negative triangles 781: dt=0.0560, 363 negative triangles 782: dt=0.0560, 369 negative triangles 783: dt=0.0560, 371 negative triangles 784: dt=0.0560, 366 negative triangles 785: dt=0.0560, 371 negative triangles 786: dt=0.0560, 371 negative triangles 787: dt=0.0560, 375 negative triangles 788: dt=0.0560, 374 negative triangles 789: dt=0.0560, 373 negative triangles 790: dt=0.0532, 374 negative triangles 791: dt=0.0532, 374 negative triangles 792: dt=0.0532, 376 negative triangles 793: dt=0.0532, 379 negative triangles 794: dt=0.0532, 375 negative triangles 795: dt=0.0532, 375 negative triangles 796: dt=0.0532, 366 negative triangles 797: dt=0.0532, 366 negative triangles 798: dt=0.0532, 371 negative triangles 799: dt=0.0532, 369 negative triangles 800: dt=0.0505, 371 negative triangles 801: dt=0.0505, 362 negative triangles 802: dt=0.0505, 369 negative triangles 803: dt=0.0505, 366 negative triangles 804: dt=0.0505, 365 negative triangles 805: dt=0.0505, 362 negative triangles 806: dt=0.0505, 361 negative triangles 807: dt=0.0505, 361 negative triangles 808: dt=0.0505, 361 negative triangles 809: dt=0.0505, 364 negative triangles 810: dt=0.0480, 358 negative triangles 811: dt=0.0480, 359 negative triangles 812: dt=0.0480, 357 negative triangles 813: dt=0.0480, 360 negative triangles 814: dt=0.0480, 357 negative triangles 815: dt=0.0480, 358 negative triangles 816: dt=0.0480, 361 negative triangles 817: dt=0.0480, 364 negative triangles 818: dt=0.0480, 359 negative triangles 819: dt=0.0480, 361 negative triangles 820: dt=0.0456, 363 negative triangles 821: dt=0.0456, 363 negative triangles 822: dt=0.0456, 362 negative triangles 823: dt=0.0456, 365 negative triangles 824: dt=0.0456, 367 negative triangles 825: dt=0.0456, 371 negative triangles 826: dt=0.0456, 366 negative triangles 827: dt=0.0456, 372 negative triangles 828: dt=0.0456, 365 negative triangles 829: dt=0.0456, 365 negative triangles 830: dt=0.0433, 361 negative triangles 831: dt=0.0433, 366 negative triangles 832: dt=0.0433, 366 negative triangles 833: dt=0.0433, 373 negative triangles 834: dt=0.0433, 373 negative triangles 835: dt=0.0433, 374 negative triangles 836: dt=0.0433, 378 negative triangles 837: dt=0.0433, 376 negative triangles 838: dt=0.0433, 374 negative triangles 839: dt=0.0433, 375 negative triangles 840: dt=0.0412, 377 negative triangles 841: dt=0.0412, 374 negative triangles 842: dt=0.0412, 376 negative triangles 843: dt=0.0412, 374 negative triangles 844: dt=0.0412, 370 negative triangles 845: dt=0.0412, 373 negative triangles 846: dt=0.0412, 372 negative triangles 847: dt=0.0412, 381 negative triangles 848: dt=0.0412, 375 negative triangles 849: dt=0.0412, 380 negative triangles 850: dt=0.0391, 381 negative triangles 851: dt=0.0391, 375 negative triangles 852: dt=0.0391, 377 negative triangles 853: dt=0.0391, 377 negative triangles 854: dt=0.0391, 380 negative triangles 855: dt=0.0391, 379 negative triangles 856: dt=0.0391, 369 negative triangles 857: dt=0.0391, 367 negative triangles 858: dt=0.0391, 373 negative triangles 859: dt=0.0391, 371 negative triangles 860: dt=0.0371, 367 negative triangles 861: dt=0.0371, 366 negative triangles 862: dt=0.0371, 367 negative triangles 863: dt=0.0371, 366 negative triangles 864: dt=0.0371, 366 negative triangles 865: dt=0.0371, 367 negative triangles 866: dt=0.0371, 367 negative triangles 867: dt=0.0371, 369 negative triangles 868: dt=0.0371, 367 negative triangles 869: dt=0.0371, 365 negative triangles 870: dt=0.0353, 366 negative triangles 871: dt=0.0353, 368 negative triangles 872: dt=0.0353, 363 negative triangles 873: dt=0.0353, 361 negative triangles 874: dt=0.0353, 361 negative triangles 875: dt=0.0353, 358 negative triangles 876: dt=0.0353, 359 negative triangles 877: dt=0.0353, 363 negative triangles 878: dt=0.0353, 360 negative triangles 879: dt=0.0353, 360 negative triangles 880: dt=0.0335, 358 negative triangles 881: dt=0.0335, 362 negative triangles 882: dt=0.0335, 365 negative triangles 883: dt=0.0335, 360 negative triangles 884: dt=0.0335, 365 negative triangles 885: dt=0.0335, 357 negative triangles 886: dt=0.0335, 363 negative triangles 887: dt=0.0335, 365 negative triangles 888: dt=0.0335, 362 negative triangles 889: dt=0.0335, 358 negative triangles 890: dt=0.0319, 359 negative triangles 891: dt=0.0319, 363 negative triangles 892: dt=0.0319, 361 negative triangles 893: dt=0.0319, 361 negative triangles 894: dt=0.0319, 356 negative triangles 895: dt=0.0319, 356 negative triangles 896: dt=0.0319, 359 negative triangles 897: dt=0.0319, 361 negative triangles 898: dt=0.0319, 361 negative triangles 899: dt=0.0319, 363 negative triangles 900: dt=0.0303, 359 negative triangles 901: dt=0.0303, 361 negative triangles 902: dt=0.0303, 361 negative triangles 903: dt=0.0303, 360 negative triangles 904: dt=0.0303, 361 negative triangles 905: dt=0.0303, 353 negative triangles 906: dt=0.0303, 357 negative triangles 907: dt=0.0303, 356 negative triangles 908: dt=0.0303, 358 negative triangles 909: dt=0.0303, 358 negative triangles 910: dt=0.0303, 356 negative triangles 911: dt=0.0303, 357 negative triangles 912: dt=0.0303, 357 negative triangles 913: dt=0.0303, 358 negative triangles 914: dt=0.0303, 356 negative triangles 915: dt=0.0287, 354 negative triangles 916: dt=0.0287, 354 negative triangles 917: dt=0.0287, 355 negative triangles 918: dt=0.0287, 355 negative triangles 919: dt=0.0287, 355 negative triangles 920: dt=0.0287, 354 negative triangles 921: dt=0.0287, 357 negative triangles 922: dt=0.0287, 353 negative triangles 923: dt=0.0287, 355 negative triangles 924: dt=0.0287, 355 negative triangles 925: dt=0.0273, 362 negative triangles 926: dt=0.0273, 367 negative triangles 927: dt=0.0273, 368 negative triangles 928: dt=0.0273, 367 negative triangles 929: dt=0.0273, 364 negative triangles 930: dt=0.0273, 370 negative triangles 931: dt=0.0273, 369 negative triangles 932: dt=0.0273, 369 negative triangles 933: dt=0.0273, 362 negative triangles 934: dt=0.0273, 365 negative triangles 935: dt=0.0259, 363 negative triangles 936: dt=0.0259, 364 negative triangles 937: dt=0.0259, 363 negative triangles 938: dt=0.0259, 364 negative triangles 939: dt=0.0259, 359 negative triangles 940: dt=0.0259, 359 negative triangles 941: dt=0.0259, 358 negative triangles 942: dt=0.0259, 366 negative triangles 943: dt=0.0259, 365 negative triangles 944: dt=0.0259, 363 negative triangles 945: dt=0.0246, 362 negative triangles 946: dt=0.0246, 363 negative triangles 947: dt=0.0246, 364 negative triangles 948: dt=0.0246, 364 negative triangles 949: dt=0.0246, 365 negative triangles 950: dt=0.0246, 363 negative triangles 951: dt=0.0246, 362 negative triangles 952: dt=0.0246, 364 negative triangles 953: dt=0.0246, 364 negative triangles 954: dt=0.0246, 363 negative triangles 955: dt=0.0234, 364 negative triangles 956: dt=0.0234, 366 negative triangles 957: dt=0.0234, 365 negative triangles 958: dt=0.0234, 366 negative triangles 959: dt=0.0234, 366 negative triangles 960: dt=0.0234, 365 negative triangles 961: dt=0.0234, 367 negative triangles 962: dt=0.0234, 366 negative triangles 963: dt=0.0234, 366 negative triangles 964: dt=0.0234, 364 negative triangles 965: dt=0.0222, 366 negative triangles 966: dt=0.0222, 367 negative triangles 967: dt=0.0222, 368 negative triangles 968: dt=0.0222, 368 negative triangles 969: dt=0.0222, 371 negative triangles 970: dt=0.0222, 374 negative triangles 971: dt=0.0222, 373 negative triangles 972: dt=0.0222, 371 negative triangles 973: dt=0.0222, 370 negative triangles 974: dt=0.0222, 365 negative triangles 975: dt=0.0211, 362 negative triangles 976: dt=0.0211, 361 negative triangles 977: dt=0.0211, 361 negative triangles 978: dt=0.0211, 361 negative triangles 979: dt=0.0211, 364 negative triangles 980: dt=0.0211, 366 negative triangles 981: dt=0.0211, 368 negative triangles 982: dt=0.0211, 374 negative triangles 983: dt=0.0211, 373 negative triangles 984: dt=0.0211, 374 negative triangles 985: dt=0.0201, 372 negative triangles 986: dt=0.0201, 370 negative triangles 987: dt=0.0201, 372 negative triangles 988: dt=0.0201, 373 negative triangles 989: dt=0.0201, 374 negative triangles 990: dt=0.0201, 375 negative triangles 991: dt=0.0201, 377 negative triangles 992: dt=0.0201, 378 negative triangles 993: dt=0.0201, 372 negative triangles 994: dt=0.0201, 374 negative triangles 995: dt=0.0191, 371 negative triangles 996: dt=0.0191, 368 negative triangles 997: dt=0.0191, 367 negative triangles 998: dt=0.0191, 363 negative triangles 999: dt=0.0191, 366 negative triangles 1000: dt=0.0191, 373 negative triangles 1001: dt=0.0191, 369 negative triangles 1002: dt=0.0191, 369 negative triangles 1003: dt=0.0191, 368 negative triangles 1004: dt=0.0191, 368 negative triangles 1005: dt=0.0181, 367 negative triangles 1006: dt=0.0181, 371 negative triangles 1007: dt=0.0181, 373 negative triangles 1008: dt=0.0181, 375 negative triangles 1009: dt=0.0181, 375 negative triangles 1010: dt=0.0181, 373 negative triangles 1011: dt=0.0181, 373 negative triangles 1012: dt=0.0181, 371 negative triangles 1013: dt=0.0181, 374 negative triangles 1014: dt=0.0181, 371 negative triangles 1015: dt=0.0172, 376 negative triangles 1016: dt=0.0172, 374 negative triangles 1017: dt=0.0172, 373 negative triangles 1018: dt=0.0172, 370 negative triangles 1019: dt=0.0172, 369 negative triangles 1020: dt=0.0172, 372 negative triangles 1021: dt=0.0172, 369 negative triangles 1022: dt=0.0172, 370 negative triangles 1023: dt=0.0172, 375 negative triangles 1024: dt=0.0172, 370 negative triangles 1025: dt=0.0164, 373 negative triangles 1026: dt=0.0164, 375 negative triangles 1027: dt=0.0164, 371 negative triangles 1028: dt=0.0164, 369 negative triangles 1029: dt=0.0164, 370 negative triangles 1030: dt=0.0164, 369 negative triangles 1031: dt=0.0164, 372 negative triangles 1032: dt=0.0164, 366 negative triangles 1033: dt=0.0164, 367 negative triangles 1034: dt=0.0164, 373 negative triangles 1035: dt=0.0155, 371 negative triangles 1036: dt=0.0155, 370 negative triangles 1037: dt=0.0155, 370 negative triangles 1038: dt=0.0155, 369 negative triangles 1039: dt=0.0155, 371 negative triangles 1040: dt=0.0155, 368 negative triangles 1041: dt=0.0155, 366 negative triangles 1042: dt=0.0155, 365 negative triangles 1043: dt=0.0155, 367 negative triangles 1044: dt=0.0155, 371 negative triangles 1045: dt=0.0148, 374 negative triangles 1046: dt=0.0148, 373 negative triangles 1047: dt=0.0148, 367 negative triangles 1048: dt=0.0148, 365 negative triangles 1049: dt=0.0148, 362 negative triangles 1050: dt=0.0148, 356 negative triangles 1051: dt=0.0148, 363 negative triangles 1052: dt=0.0148, 363 negative triangles 1053: dt=0.0148, 364 negative triangles 1054: dt=0.0148, 368 negative triangles 1055: dt=0.0140, 365 negative triangles 1056: dt=0.0140, 365 negative triangles 1057: dt=0.0140, 362 negative triangles 1058: dt=0.0140, 360 negative triangles 1059: dt=0.0140, 363 negative triangles 1060: dt=0.0140, 365 negative triangles 1061: dt=0.0140, 370 negative triangles 1062: dt=0.0140, 371 negative triangles 1063: dt=0.0140, 366 negative triangles 1064: dt=0.0140, 368 negative triangles 1065: dt=0.0133, 367 negative triangles 1066: dt=0.0133, 368 negative triangles 1067: dt=0.0133, 363 negative triangles 1068: dt=0.0133, 367 negative triangles 1069: dt=0.0133, 361 negative triangles 1070: dt=0.0133, 364 negative triangles 1071: dt=0.0133, 367 negative triangles 1072: dt=0.0133, 364 negative triangles 1073: dt=0.0133, 365 negative triangles 1074: dt=0.0133, 356 negative triangles 1075: dt=0.0127, 360 negative triangles 1076: dt=0.0127, 357 negative triangles 1077: dt=0.0127, 363 negative triangles 1078: dt=0.0127, 365 negative triangles 1079: dt=0.0127, 365 negative triangles 1080: dt=0.0127, 368 negative triangles 1081: dt=0.0127, 366 negative triangles 1082: dt=0.0127, 361 negative triangles 1083: dt=0.0127, 359 negative triangles 1084: dt=0.0127, 361 negative triangles 1085: dt=0.0120, 353 negative triangles 1086: dt=0.0120, 362 negative triangles 1087: dt=0.0120, 364 negative triangles 1088: dt=0.0120, 371 negative triangles 1089: dt=0.0120, 371 negative triangles 1090: dt=0.0120, 373 negative triangles 1091: dt=0.0120, 374 negative triangles 1092: dt=0.0120, 374 negative triangles 1093: dt=0.0120, 374 negative triangles 1094: dt=0.0120, 372 negative triangles 1095: dt=0.0114, 370 negative triangles 1096: dt=0.0114, 369 negative triangles 1097: dt=0.0114, 369 negative triangles 1098: dt=0.0114, 366 negative triangles 1099: dt=0.0114, 368 negative triangles 1100: dt=0.0114, 367 negative triangles 1101: dt=0.0114, 370 negative triangles 1102: dt=0.0114, 372 negative triangles 1103: dt=0.0114, 365 negative triangles 1104: dt=0.0114, 362 negative triangles 1105: dt=0.0108, 364 negative triangles 1106: dt=0.0108, 360 negative triangles 1107: dt=0.0108, 363 negative triangles 1108: dt=0.0108, 366 negative triangles 1109: dt=0.0108, 368 negative triangles 1110: dt=0.0108, 366 negative triangles 1111: dt=0.0108, 363 negative triangles 1112: dt=0.0108, 364 negative triangles writing registered surface to ../surf/rh.sphere.reg... 1113: dt=0.0108, 364 negative triangles 1114: 367 negative triangles registration took 0.08 hours #VMPC# mris_register VmPeak 768972 FSRUNTIME@ mris_register 0.0797 hours 4 threads PIDs (292068 292071) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri Jan 6 19:09:14 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Jan 6 19:09:14 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 292134 of (292134 292137) to complete... Waiting for PID 292137 of (292134 292137) 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 (292134 292137) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri Jan 6 19:09:14 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Fri Jan 6 19:09:14 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 292186 of (292186 292189) to complete... Waiting for PID 292189 of (292186 292189) to complete... mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (292186 292189) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri Jan 6 19:09:15 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 New_patient_test3_bugfix lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Fri Jan 6 19:09:15 CET 2023 /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 New_patient_test3_bugfix rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 292238 of (292238 292241) to complete... Waiting for PID 292241 of (292238 292241) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 New_patient_test3_bugfix lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.0 7.3.0 reading atlas from /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 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 New_patient_test3_bugfix rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.0 7.3.0 reading atlas from /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 896 labels changed using aseg relabeling using gibbs priors... 000: 2402 changed, 112444 examined... 001: 528 changed, 10406 examined... 002: 150 changed, 2986 examined... 003: 47 changed, 903 examined... 004: 20 changed, 298 examined... 005: 8 changed, 126 examined... 006: 2 changed, 50 examined... 007: 3 changed, 10 examined... 008: 2 changed, 12 examined... 009: 0 changed, 10 examined... 194 labels changed using aseg 000: 71 total segments, 24 labels (128 vertices) changed 001: 47 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1557 vertices marked for relabeling... 1557 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 6 seconds. PIDs (292238 292241) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Fri Jan 6 19:09:22 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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 0.0346 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 0.0237 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 0.0127 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 0.0081 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 1.55 minutes #VMPC# mris_place_surfaces VmPeak 1963028 mris_place_surface done #-------------------------------------------- #@# WhiteSurfs rh Fri Jan 6 19:11:18 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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: 99 intersecting step 1 with no progress (num=102, old_num=99) 001: 102 intersecting step 2 with no progress (num=105, old_num=102) 002: 105 intersecting step 3 with no progress (num=105, old_num=105) 003: 105 intersecting step 4 with no progress (num=108, old_num=105) 004: 108 intersecting 005: 107 intersecting step 1 with no progress (num=110, old_num=107) 006: 110 intersecting 007: 108 intersecting step 1 with no progress (num=117, old_num=108) 008: 117 intersecting 009: 115 intersecting step 1 with no progress (num=117, old_num=115) 010: 117 intersecting step 2 with no progress (num=124, old_num=117) 011: 124 intersecting step 3 with no progress (num=132, old_num=124) 012: 132 intersecting step 4 with no progress (num=132, old_num=132) 013: 132 intersecting 014: 121 intersecting step 1 with no progress (num=124, old_num=121) 015: 124 intersecting 016: 113 intersecting 017: 106 intersecting step 1 with no progress (num=112, old_num=106) 018: 112 intersecting step 2 with no progress (num=113, old_num=112) 019: 113 intersecting 020: 112 intersecting step 1 with no progress (num=113, old_num=112) 021: 113 intersecting step 2 with no progress (num=120, old_num=113) 022: 120 intersecting step 3 with no progress (num=124, old_num=120) 023: 124 intersecting step 4 with no progress (num=132, old_num=124) 024: 132 intersecting step 5 with no progress (num=153, old_num=132) 025: 153 intersecting step 6 with no progress (num=165, old_num=153) 026: 165 intersecting step 7 with no progress (num=167, old_num=165) 027: 167 intersecting 028: 152 intersecting step 1 with no progress (num=156, old_num=152) 029: 156 intersecting step 2 with no progress (num=175, old_num=156) 030: 175 intersecting 031: 172 intersecting 032: 155 intersecting step 1 with no progress (num=156, old_num=155) 033: 156 intersecting 034: 155 intersecting step 1 with no progress (num=159, old_num=155) 035: 159 intersecting step 2 with no progress (num=169, old_num=159) 036: 169 intersecting step 3 with no progress (num=171, old_num=169) 037: 171 intersecting 038: 160 intersecting 039: 153 intersecting step 1 with no progress (num=153, old_num=153) 040: 153 intersecting 041: 152 intersecting step 1 with no progress (num=161, old_num=152) 042: 161 intersecting 043: 156 intersecting 044: 152 intersecting step 1 with no progress (num=152, old_num=152) 045: 152 intersecting step 2 with no progress (num=154, old_num=152) 046: 154 intersecting step 3 with no progress (num=156, old_num=154) 047: 156 intersecting step 4 with no progress (num=157, old_num=156) 048: 157 intersecting 049: 155 intersecting 050: 150 intersecting step 1 with no progress (num=152, old_num=150) 051: 152 intersecting step 2 with no progress (num=158, old_num=152) 052: 158 intersecting 053: 153 intersecting 054: 147 intersecting step 1 with no progress (num=150, old_num=147) 055: 150 intersecting step 2 with no progress (num=150, old_num=150) 056: 150 intersecting 057: 149 intersecting step 1 with no progress (num=154, old_num=149) 058: 154 intersecting step 2 with no progress (num=155, old_num=154) 059: 155 intersecting 060: 148 intersecting step 1 with no progress (num=154, old_num=148) 061: 154 intersecting step 2 with no progress (num=168, old_num=154) 062: 168 intersecting 063: 165 intersecting step 1 with no progress (num=166, old_num=165) 064: 166 intersecting 065: 154 intersecting 066: 149 intersecting step 1 with no progress (num=149, old_num=149) 067: 149 intersecting step 2 with no progress (num=153, old_num=149) 068: 153 intersecting step 3 with no progress (num=159, old_num=153) 069: 159 intersecting 070: 143 intersecting step 1 with no progress (num=155, old_num=143) 071: 155 intersecting 072: 148 intersecting step 1 with no progress (num=150, old_num=148) 073: 150 intersecting 074: 146 intersecting step 1 with no progress (num=158, old_num=146) 075: 158 intersecting 076: 157 intersecting step 1 with no progress (num=157, old_num=157) 077: 157 intersecting step 2 with no progress (num=170, old_num=157) 078: 170 intersecting 079: 166 intersecting step 1 with no progress (num=171, old_num=166) 080: 171 intersecting step 2 with no progress (num=180, old_num=171) 081: 180 intersecting step 3 with no progress (num=187, old_num=180) 082: 187 intersecting step 4 with no progress (num=199, old_num=187) 083: 199 intersecting step 5 with no progress (num=199, old_num=199) 084: 199 intersecting step 6 with no progress (num=199, old_num=199) 085: 199 intersecting 086: 198 intersecting step 1 with no progress (num=198, old_num=198) 087: 198 intersecting 088: 197 intersecting 089: 196 intersecting step 1 with no progress (num=196, old_num=196) 090: 196 intersecting step 2 with no progress (num=196, old_num=196) 091: 196 intersecting step 3 with no progress (num=196, old_num=196) 092: 196 intersecting step 4 with no progress (num=196, old_num=196) 093: 196 intersecting step 5 with no progress (num=196, old_num=196) 094: 196 intersecting step 6 with no progress (num=196, old_num=196) 095: 196 intersecting step 7 with no progress (num=196, old_num=196) 096: 196 intersecting step 8 with no progress (num=196, old_num=196) 097: 196 intersecting step 9 with no progress (num=196, old_num=196) 098: 196 intersecting step 10 with no progress (num=196, old_num=196) 099: 196 intersecting step 11 with no progress (num=196, old_num=196) 100: 196 intersecting step 12 with no progress (num=196, old_num=196) 101: 196 intersecting terminating search with 99 intersecting Area 224884 0.33535 0.11903 0.000000 2.0430 Corner 674652 60.00000 14.57273 0.000068 179.9998 Edge 337326 0.89119 0.20026 0.000331 3.6792 Hinge 337326 11.97857 14.72392 0.000013 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 7600/112444 vertices (104844 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 528 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56222: xyz = (12.5079,-15.7543,70.3104) oxyz = (12.5079,-15.7543,70.3104) wxzy = (12.5079,-15.7543,70.3104) pxyz = (0,0,0) CBVO Creating mask 112444 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=2 had to be increased for 476 vertices, nripped=8128 mean border=91.0, 449 (449) missing vertices, mean dist 0.2 [0.9 (%28.1)->0.6 (%71.9))] %56 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0334 min Finding expansion regions mean absolute distance = 0.67 +- 1.10 3096 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=1805232.5, rms=4.488 001: dt: 0.5000, sse=1398333.8, rms=2.989 (33.397%) 002: dt: 0.5000, sse=1260136.8, rms=2.325 (22.225%) 003: dt: 0.5000, sse=1226089.5, rms=2.209 (4.957%) rms = 2.0914/2.2095, sse=1227765.4/1226089.5, time step reduction 1 of 3 to 0.250 0 1 0 004: dt: 0.5000, sse=1227765.4, rms=2.091 (5.345%) 005: dt: 0.2500, sse=505372.8, rms=1.739 (16.844%) rms = 1.6446/1.7391, sse=1157628.2/505372.8, time step reduction 2 of 3 to 0.125 0 1 0 006: dt: 0.2500, sse=1157628.2, rms=1.645 (5.436%) rms = 1.6003/1.6446, sse=1157369.0/1157628.2, time step reduction 3 of 3 to 0.062 0 0 1 007: dt: 0.1250, sse=1157369.0, rms=1.600 (2.689%) maximum number of reductions reached, breaking from loop positioning took 0.3 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=1 had to be increased for 390 vertices, nripped=8128 mean border=92.4, 380 (187) missing vertices, mean dist -0.2 [0.5 (%61.9)->0.3 (%38.1))] %72 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0229 min Finding expansion regions mean absolute distance = 0.39 +- 0.71 2854 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=1284380.5, rms=2.895 008: dt: 0.5000, sse=1200242.0, rms=2.003 (30.817%) rms = 1.7597/2.0032, sse=1200787.2/1200242.0, time step reduction 1 of 3 to 0.250 0 1 0 009: dt: 0.5000, sse=1200787.2, rms=1.760 (12.155%) 010: dt: 0.2500, sse=1171289.1, rms=1.463 (16.832%) 011: dt: 0.2500, sse=1167890.0, rms=1.388 (5.136%) rms = 1.3729/1.3883, sse=1173417.6/1167890.0, time step reduction 2 of 3 to 0.125 0 1 1 012: dt: 0.2500, sse=1173417.6, rms=1.373 (1.108%) rms = 1.3474/1.3729, sse=1159859.9/1173417.6, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=1159859.9, rms=1.347 (1.862%) 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 389 vertices, nripped=8128 mean border=93.2, 430 (132) 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 +- 0.49 3020 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=1213060.9, rms=2.105 rms = 1.6600/2.1050, sse=1218047.7/1213060.8, time step reduction 1 of 3 to 0.250 0 1 0 014: dt: 0.5000, sse=1218047.6, rms=1.660 (21.139%) 015: dt: 0.2500, sse=1195290.1, rms=1.351 (18.633%) 016: dt: 0.2500, sse=1187045.1, rms=1.284 (4.924%) rms = 1.2701/1.2842, sse=1196399.2/1187045.1, time step reduction 2 of 3 to 0.125 0 1 1 017: dt: 0.2500, sse=1196399.1, rms=1.270 (1.101%) rms = 1.2210/1.2701, sse=1183506.2/1196399.2, time step reduction 3 of 3 to 0.062 0 0 1 018: dt: 0.1250, sse=1183506.1, rms=1.221 (3.861%) 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 = 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 411 vertices, nripped=8128 mean border=93.5, 524 (113) missing vertices, mean dist -0.0 [0.3 (%51.6)->0.2 (%48.4))] %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 2748 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=1191881.0, rms=1.407 019: dt: 0.5000, sse=1152166.9, rms=1.337 (4.943%) rms = 1.3777/1.3372, sse=1176423.9/1152166.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=577092.9, rms=1.124 (15.978%) rms = 1.1159/1.1236, sse=1074775.8/577093.0, time step reduction 2 of 3 to 0.125 0 1 1 021: dt: 0.2500, sse=1074775.9, rms=1.116 (0.682%) rms = 1.0283/1.1159, sse=1168521.3/1074775.8, time step reduction 3 of 3 to 0.062 0 1 0 022: dt: 0.1250, sse=1168521.2, rms=1.028 (7.854%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 76 intersecting step 1 with no progress (num=82, old_num=76) 001: 82 intersecting step 2 with no progress (num=88, old_num=82) 002: 88 intersecting 003: 65 intersecting step 1 with no progress (num=72, old_num=65) 004: 72 intersecting step 2 with no progress (num=80, old_num=72) 005: 80 intersecting 006: 68 intersecting step 1 with no progress (num=81, old_num=68) 007: 81 intersecting 008: 75 intersecting step 1 with no progress (num=86, old_num=75) 009: 86 intersecting 010: 79 intersecting step 1 with no progress (num=80, old_num=79) 011: 80 intersecting 012: 79 intersecting step 1 with no progress (num=85, old_num=79) 013: 85 intersecting 014: 82 intersecting step 1 with no progress (num=85, old_num=82) 015: 85 intersecting 016: 76 intersecting step 1 with no progress (num=85, old_num=76) 017: 85 intersecting 018: 82 intersecting step 1 with no progress (num=89, old_num=82) 019: 89 intersecting 020: 81 intersecting step 1 with no progress (num=85, old_num=81) 021: 85 intersecting 022: 83 intersecting 023: 80 intersecting step 1 with no progress (num=81, old_num=80) 024: 81 intersecting step 2 with no progress (num=88, old_num=81) 025: 88 intersecting 026: 84 intersecting 027: 83 intersecting step 1 with no progress (num=84, old_num=83) 028: 84 intersecting step 2 with no progress (num=90, old_num=84) 029: 90 intersecting step 3 with no progress (num=92, old_num=90) 030: 92 intersecting step 4 with no progress (num=92, old_num=92) 031: 92 intersecting step 5 with no progress (num=92, old_num=92) 032: 92 intersecting step 6 with no progress (num=92, old_num=92) 033: 92 intersecting step 7 with no progress (num=92, old_num=92) 034: 92 intersecting step 8 with no progress (num=92, old_num=92) 035: 92 intersecting step 9 with no progress (num=92, old_num=92) 036: 92 intersecting step 10 with no progress (num=92, old_num=92) 037: 92 intersecting step 11 with no progress (num=92, old_num=92) 038: 92 intersecting step 12 with no progress (num=92, old_num=92) 039: 92 intersecting step 13 with no progress (num=92, old_num=92) 040: 92 intersecting step 14 with no progress (num=92, old_num=92) 041: 92 intersecting step 15 with no progress (num=92, old_num=92) 042: 92 intersecting step 16 with no progress (num=92, old_num=92) terminating search with 65 intersecting Writing output to ../surf/rh.white #ET# mris_place_surface 1.80 minutes #VMPC# mris_place_surfaces VmPeak 2145996 mris_place_surface done #-------------------------------------------- #@# T1PialSurf lh Fri Jan 6 19:14:47 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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 0.0280 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 0.0086 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 0.0051 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 2.20 minutes #VMPC# mris_place_surfaces VmPeak 1462548 mris_place_surface done #-------------------------------------------- #@# T1PialSurf rh Fri Jan 6 19:17:22 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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: 65 intersecting step 1 with no progress (num=72, old_num=65) 001: 72 intersecting step 2 with no progress (num=80, old_num=72) 002: 80 intersecting 003: 68 intersecting step 1 with no progress (num=81, old_num=68) 004: 81 intersecting 005: 75 intersecting step 1 with no progress (num=86, old_num=75) 006: 86 intersecting 007: 79 intersecting step 1 with no progress (num=80, old_num=79) 008: 80 intersecting 009: 79 intersecting step 1 with no progress (num=85, old_num=79) 010: 85 intersecting 011: 82 intersecting step 1 with no progress (num=85, old_num=82) 012: 85 intersecting 013: 76 intersecting step 1 with no progress (num=85, old_num=76) 014: 85 intersecting 015: 82 intersecting step 1 with no progress (num=89, old_num=82) 016: 89 intersecting 017: 81 intersecting step 1 with no progress (num=85, old_num=81) 018: 85 intersecting 019: 83 intersecting 020: 80 intersecting step 1 with no progress (num=81, old_num=80) 021: 81 intersecting step 2 with no progress (num=88, old_num=81) 022: 88 intersecting 023: 84 intersecting 024: 83 intersecting step 1 with no progress (num=84, old_num=83) 025: 84 intersecting step 2 with no progress (num=90, old_num=84) 026: 90 intersecting step 3 with no progress (num=92, old_num=90) 027: 92 intersecting step 4 with no progress (num=92, old_num=92) 028: 92 intersecting step 5 with no progress (num=92, old_num=92) 029: 92 intersecting step 6 with no progress (num=92, old_num=92) 030: 92 intersecting step 7 with no progress (num=92, old_num=92) 031: 92 intersecting step 8 with no progress (num=92, old_num=92) 032: 92 intersecting step 9 with no progress (num=92, old_num=92) 033: 92 intersecting step 10 with no progress (num=92, old_num=92) 034: 92 intersecting step 11 with no progress (num=92, old_num=92) 035: 92 intersecting step 12 with no progress (num=92, old_num=92) 036: 92 intersecting step 13 with no progress (num=92, old_num=92) 037: 92 intersecting step 14 with no progress (num=92, old_num=92) 038: 92 intersecting step 15 with no progress (num=92, old_num=92) 039: 92 intersecting step 16 with no progress (num=92, old_num=92) terminating search with 65 intersecting Area 224884 0.33872 0.13498 0.000000 2.9368 Corner 674652 60.00000 16.08352 0.003161 179.9903 Edge 337326 0.89799 0.22414 0.000053 5.5128 Hinge 337326 12.03740 14.80629 0.000064 179.9854 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 6547/112444 vertices (105897 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 56222: xyz = (12.5148,-15.7668,70.3197) oxyz = (12.5148,-15.7668,70.3197) wxzy = (12.5148,-15.7668,70.3197) pxyz = (12.5148,-15.7668,70.3197) CBVO Creating mask 112444 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=2 had to be increased for 565 vertices, nripped=6547 mean border=71.4, 465 (465) missing vertices, mean dist 1.4 [2.7 (%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 0.0274 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=11480660.0, rms=23.171 001: dt: 0.5000, sse=8407320.0, rms=19.777 (14.646%) 002: dt: 0.5000, sse=6193771.0, rms=16.915 (14.472%) 003: dt: 0.5000, sse=4760029.0, rms=14.766 (12.703%) 004: dt: 0.5000, sse=3866710.2, rms=13.251 (10.262%) 005: dt: 0.5000, sse=3277171.2, rms=12.147 (8.335%) 006: dt: 0.5000, sse=2843396.2, rms=11.264 (7.268%) 007: dt: 0.5000, sse=2489585.8, rms=10.487 (6.893%) 008: dt: 0.5000, sse=2147017.5, rms=9.676 (7.735%) 009: dt: 0.5000, sse=1836288.1, rms=8.876 (8.272%) 010: dt: 0.5000, sse=1558295.1, rms=8.092 (8.827%) 011: dt: 0.5000, sse=1359950.8, rms=7.482 (7.548%) 012: dt: 0.5000, sse=1216275.0, rms=7.004 (6.385%) 013: dt: 0.5000, sse=1126796.0, rms=6.687 (4.525%) 014: dt: 0.5000, sse=1060093.8, rms=6.438 (3.719%) 015: dt: 0.5000, sse=1014581.6, rms=6.262 (2.732%) 016: dt: 0.5000, sse=980355.1, rms=6.125 (2.194%) 017: dt: 0.5000, sse=958268.7, rms=6.033 (1.495%) 018: dt: 0.5000, sse=944015.2, rms=5.971 (1.031%) 019: dt: 0.5000, sse=931510.2, rms=5.917 (0.916%) rms = 5.8693/5.9165, sse=920884.2/931510.3, time step reduction 1 of 3 to 0.250 0 0 1 020: dt: 0.5000, sse=920884.2, rms=5.869 (0.798%) 021: dt: 0.2500, sse=788768.8, rms=5.292 (9.837%) 022: dt: 0.2500, sse=754194.9, rms=5.131 (3.036%) rms = 5.1202/5.1312, sse=752399.0/754195.0, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=752399.0, rms=5.120 (0.215%) 024: dt: 0.1250, sse=700444.6, rms=4.869 (4.905%) 025: dt: 0.1250, sse=687823.6, rms=4.806 (1.302%) rms = 4.7897/4.8056, sse=684820.5/687823.6, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=684820.5, rms=4.790 (0.331%) 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=1 had to be increased for 13931 vertices, nripped=6547 mean border=69.9, 7901 (139) 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=954590.3, rms=5.798 rms = 6.0405/5.7981, sse=1014557.1/954590.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=870586.9, rms=5.442 (6.142%) 028: dt: 0.2500, sse=840536.8, rms=5.308 (2.465%) rms = 5.4418/5.3079, sse=870515.7/840536.7, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 029: dt: 0.1250, sse=822650.8, rms=5.226 (1.534%) 030: dt: 0.1250, sse=807994.2, rms=5.158 (1.311%) rms = 5.1311/5.1579, sse=802173.3/807994.2, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=802173.3, rms=5.131 (0.519%) 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 14383 vertices, nripped=6547 mean border=69.4, 7884 (111) missing vertices, mean dist 0.2 [0.3 (%31.2)->0.6 (%68.8))] %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=858336.8, rms=5.386 rms = 6.1338/5.3857, sse=1037536.1/858336.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=830091.4, rms=5.260 (2.327%) rms = 5.4162/5.2604, sse=864434.9/830091.4, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 5.2417/5.2604, sse=825998.1/830091.4, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=825998.1, rms=5.242 (0.356%) 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=112444 Gdiag_no=-1 vno start=0, stop=112444 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 10224 vertices, nripped=6547 mean border=68.9, 12650 (105) missing vertices, mean dist 0.1 [0.3 (%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=850620.0, rms=5.351 rms = 5.5247/5.3513, sse=885116.5/850620.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=807543.4, rms=5.160 (3.576%) 035: dt: 0.2500, sse=770760.9, rms=5.000 (3.108%) rms = 4.9740/4.9996, sse=763973.0/770761.0, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=763973.0, rms=4.974 (0.511%) 037: dt: 0.1250, sse=699491.0, rms=4.656 (6.392%) 038: dt: 0.1250, sse=675950.1, rms=4.537 (2.553%) 039: dt: 0.1250, sse=664657.0, rms=4.479 (1.272%) rms = 4.4481/4.4795, sse=658458.4/664657.0, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=658458.4, rms=4.448 (0.700%) 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=109, old_num=43) 001: 109 intersecting 002: 102 intersecting step 1 with no progress (num=110, old_num=102) 003: 110 intersecting 004: 96 intersecting step 1 with no progress (num=117, old_num=96) 005: 117 intersecting step 2 with no progress (num=127, old_num=117) 006: 127 intersecting 007: 116 intersecting 008: 111 intersecting step 1 with no progress (num=117, old_num=111) 009: 117 intersecting 010: 104 intersecting step 1 with no progress (num=109, old_num=104) 011: 109 intersecting 012: 101 intersecting step 1 with no progress (num=101, old_num=101) 013: 101 intersecting step 2 with no progress (num=101, old_num=101) 014: 101 intersecting step 3 with no progress (num=101, old_num=101) 015: 101 intersecting step 4 with no progress (num=101, old_num=101) 016: 101 intersecting step 5 with no progress (num=101, old_num=101) 017: 101 intersecting step 6 with no progress (num=101, old_num=101) 018: 101 intersecting step 7 with no progress (num=101, old_num=101) 019: 101 intersecting step 8 with no progress (num=101, old_num=101) 020: 101 intersecting step 9 with no progress (num=101, old_num=101) 021: 101 intersecting step 10 with no progress (num=101, old_num=101) 022: 101 intersecting step 11 with no progress (num=101, old_num=101) 023: 101 intersecting step 12 with no progress (num=101, old_num=101) 024: 101 intersecting step 13 with no progress (num=101, old_num=101) 025: 101 intersecting step 14 with no progress (num=101, old_num=101) 026: 101 intersecting step 15 with no progress (num=101, old_num=101) 027: 101 intersecting step 16 with no progress (num=101, old_num=101) terminating search with 43 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.35 minutes #VMPC# mris_place_surfaces VmPeak 1522988 mris_place_surface done #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Fri Jan 6 19:20:27 CET 2023 bbregister --s New_patient_test3_bugfix --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz --lta /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask tmp /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483 Log file is /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.log Fri Jan 6 19:20:27 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts /usr/local/freesurfer/bin/bbregister --s New_patient_test3_bugfix --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz --lta /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask bbregister 7.3.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii mri_convert /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii reading from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii... mri_coreg --s New_patient_test3_bugfix --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --regdat /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/reg.init.dat --reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts cmdline mri_coreg --s New_patient_test3_bugfix --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --regdat /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/reg.init.dat --reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii INFO: This is an unsigined short. Reading in ref /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 73.1 sec To check run: tkregisterfv --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --targ /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/brainmask.mgz --reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/mri_coreg.lta --s New_patient_test3_bugfix --surfs mri_coreg done mri_segreg --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --init-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/reg.init.dat --out-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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 7.3.0 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mri_segreg --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --init-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/reg.init.dat --out-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii regfile /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/reg.init.dat subject New_patient_test3_bugfix dof 6 outregfile /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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 1673989746 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 1.041823 1 -25.0 -25.0 25.0 1.005023 2 -25.0 25.0 -25.0 1.011816 3 -25.0 25.0 25.0 1.026199 4 25.0 -25.0 -25.0 0.990029 5 25.0 -25.0 25.0 0.997787 6 25.0 25.0 -25.0 1.000416 7 25.0 25.0 25.0 0.963764 REL: 8 0.115550 8.036856 1.004607 rel = 0.11502 Initial costs ---------------- Number of surface hits 2112 WM Intensity 238.3321 +/- 33.8180 Ctx Intensity 332.5030 +/- 75.9229 Pct Contrast 31.0639 +/- 23.6178 Cost 0.1155 RelCost 0.1150 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9961 0.9961 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9940 0.9940 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9836 0.9836 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9144 0.9144 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8276 0.8276 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.7590 0.7590 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.6144 0.6144 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5420 0.5420 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1155 0.1155 0.0 Brute Force -------------------------- Min cost was 0.115550 Number of iterations 729 Search time 0.809988 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 = 0.115550 5 -0.618 0.000 0.000 0.000 0.000 0.000 0.0927221172 7 -0.574 0.000 0.000 0.000 0.000 0.000 0.0926302775 8 -0.582 0.000 0.000 0.000 0.000 0.000 0.0925595024 9 -0.593 0.000 0.000 0.000 0.000 0.000 0.0925335651 10 -0.590 0.000 0.000 0.000 0.000 0.000 0.0925325768 11 -0.591 0.000 0.000 0.000 0.000 0.000 0.0925319627 21 -0.591 -0.001 0.000 0.000 0.000 0.000 0.0925296649 22 -0.591 -0.004 0.000 0.000 0.000 0.000 0.0925255286 31 -0.591 -0.004 -0.618 0.000 0.000 0.000 0.0890026764 33 -0.591 -0.004 -0.364 0.000 0.000 0.000 0.0867975710 34 -0.591 -0.004 -0.381 0.000 0.000 0.000 0.0866369510 35 -0.591 -0.004 -0.434 0.000 0.000 0.000 0.0861436813 38 -0.591 -0.004 -0.442 0.000 0.000 0.000 0.0860682409 39 -0.591 -0.004 -0.446 0.000 0.000 0.000 0.0860628167 40 -0.591 -0.004 -0.445 0.000 0.000 0.000 0.0860617598 51 -0.591 -0.004 -0.445 -0.001 0.000 0.000 0.0860617153 61 -0.591 -0.004 -0.445 -0.001 -0.086 0.000 0.0856186095 64 -0.591 -0.004 -0.445 -0.001 -0.088 0.000 0.0855954843 65 -0.591 -0.004 -0.445 -0.001 -0.110 0.000 0.0854655654 67 -0.591 -0.004 -0.445 -0.001 -0.106 0.000 0.0854555762 79 -0.591 -0.004 -0.445 -0.001 -0.106 0.002 0.0854333717 81 -0.591 -0.004 -0.445 -0.001 -0.106 0.006 0.0854230627 powell nthiter 1: fret = 0.085423 94 -0.560 -0.004 -0.445 -0.001 -0.106 0.006 0.0852654835 95 -0.561 -0.004 -0.445 -0.001 -0.106 0.006 0.0852614508 96 -0.567 -0.004 -0.445 -0.001 -0.106 0.006 0.0852587122 98 -0.564 -0.004 -0.445 -0.001 -0.106 0.006 0.0852548150 99 -0.563 -0.004 -0.445 -0.001 -0.106 0.006 0.0852543816 107 -0.563 -0.007 -0.445 -0.001 -0.106 0.006 0.0852333099 110 -0.563 -0.018 -0.445 -0.001 -0.106 0.006 0.0852246453 111 -0.563 -0.014 -0.445 -0.001 -0.106 0.006 0.0852177106 120 -0.563 -0.014 -0.272 -0.001 -0.106 0.006 0.0852075668 129 -0.563 -0.014 -0.274 -0.001 -0.106 0.006 0.0852069300 137 -0.563 -0.014 -0.274 0.070 -0.106 0.006 0.0850292781 138 -0.563 -0.014 -0.274 0.064 -0.106 0.006 0.0849843606 139 -0.563 -0.014 -0.274 0.042 -0.106 0.006 0.0848704254 141 -0.563 -0.014 -0.274 0.046 -0.106 0.006 0.0848617879 142 -0.563 -0.014 -0.274 0.047 -0.106 0.006 0.0848608631 154 -0.563 -0.014 -0.274 0.047 -0.140 0.006 0.0848534782 155 -0.563 -0.014 -0.274 0.047 -0.129 0.006 0.0847211521 156 -0.563 -0.014 -0.274 0.047 -0.123 0.006 0.0847003634 172 -0.563 -0.014 -0.274 0.047 -0.123 0.000 0.0846924281 174 -0.563 -0.014 -0.274 0.047 -0.123 0.002 0.0846870520 powell nthiter 2: fret = 0.084687 188 -0.555 -0.014 -0.274 0.047 -0.123 0.002 0.0846412504 189 -0.554 -0.014 -0.274 0.047 -0.123 0.002 0.0846403923 197 -0.554 0.038 -0.274 0.047 -0.123 0.002 0.0842479848 200 -0.554 0.035 -0.274 0.047 -0.123 0.002 0.0842453719 211 -0.554 0.035 -0.276 0.047 -0.123 0.002 0.0842422994 212 -0.554 0.035 -0.281 0.047 -0.123 0.002 0.0842411340 214 -0.554 0.035 -0.279 0.047 -0.123 0.002 0.0842398710 223 -0.554 0.035 -0.279 0.081 -0.123 0.002 0.0840283530 226 -0.554 0.035 -0.279 0.094 -0.123 0.002 0.0840179075 227 -0.554 0.035 -0.279 0.089 -0.123 0.002 0.0840091531 237 -0.554 0.035 -0.279 0.089 -0.126 0.002 0.0839983032 242 -0.554 0.035 -0.279 0.089 -0.129 0.002 0.0839938723 254 -0.554 0.035 -0.279 0.089 -0.129 -0.010 0.0839360025 255 -0.554 0.035 -0.279 0.089 -0.129 -0.008 0.0839350417 258 -0.544 0.084 -0.283 0.130 -0.135 -0.018 0.0838439287 261 -0.529 0.164 -0.290 0.198 -0.144 -0.034 0.0833377216 266 -0.530 0.156 -0.290 0.192 -0.143 -0.032 0.0832492965 267 -0.531 0.154 -0.289 0.189 -0.143 -0.032 0.0832460380 268 -0.531 0.154 -0.289 0.190 -0.143 -0.032 0.0832451213 269 -0.531 0.154 -0.289 0.190 -0.143 -0.032 0.0832449719 powell nthiter 3: fret = 0.083245 282 -0.518 0.154 -0.289 0.190 -0.143 -0.032 0.0832050811 284 -0.522 0.154 -0.289 0.190 -0.143 -0.032 0.0831940878 296 -0.522 0.154 -0.289 0.190 -0.143 -0.039 0.0831219621 298 -0.522 0.154 -0.289 0.190 -0.143 -0.038 0.0831216481 307 -0.522 0.154 -0.250 0.190 -0.143 -0.038 0.0830096859 308 -0.522 0.154 -0.246 0.190 -0.143 -0.038 0.0829996810 309 -0.522 0.154 -0.117 0.190 -0.143 -0.038 0.0827258074 311 -0.522 0.154 -0.166 0.190 -0.143 -0.038 0.0825783513 312 -0.522 0.154 -0.165 0.190 -0.143 -0.038 0.0825738857 313 -0.522 0.154 -0.153 0.190 -0.143 -0.038 0.0825470102 314 -0.522 0.154 -0.139 0.190 -0.143 -0.038 0.0825464291 315 -0.522 0.154 -0.146 0.190 -0.143 -0.038 0.0825401316 326 -0.522 0.154 -0.146 0.211 -0.143 -0.038 0.0822803281 327 -0.522 0.154 -0.146 0.213 -0.143 -0.038 0.0822704476 329 -0.522 0.154 -0.146 0.216 -0.143 -0.038 0.0822627155 330 -0.522 0.154 -0.146 0.217 -0.143 -0.038 0.0822626535 339 -0.522 0.154 -0.146 0.217 -0.136 -0.038 0.0822624700 341 -0.522 0.154 -0.146 0.217 -0.139 -0.038 0.0822614694 343 -0.522 0.154 -0.146 0.217 -0.140 -0.038 0.0822607909 344 -0.522 0.154 -0.146 0.217 -0.141 -0.038 0.0822607620 350 -0.518 0.173 -0.147 0.233 -0.144 -0.042 0.0820819926 354 -0.519 0.171 -0.147 0.231 -0.143 -0.042 0.0820792394 356 -0.519 0.171 -0.147 0.231 -0.143 -0.042 0.0820790702 358 -0.519 0.171 -0.147 0.231 -0.143 -0.042 0.0820789781 powell nthiter 4: fret = 0.082079 374 -0.518 0.171 -0.147 0.231 -0.143 -0.042 0.0820786364 383 -0.518 0.171 -0.147 0.231 -0.143 -0.050 0.0819760881 384 -0.518 0.171 -0.147 0.231 -0.143 -0.051 0.0819722384 385 -0.518 0.171 -0.147 0.231 -0.143 -0.052 0.0819705820 396 -0.518 0.171 -0.166 0.231 -0.143 -0.052 0.0819536065 397 -0.518 0.171 -0.161 0.231 -0.143 -0.052 0.0819469827 398 -0.518 0.171 -0.160 0.231 -0.143 -0.052 0.0819466977 407 -0.518 0.171 -0.160 0.275 -0.143 -0.052 0.0819227708 408 -0.518 0.171 -0.160 0.255 -0.143 -0.052 0.0816002374 410 -0.518 0.171 -0.160 0.256 -0.143 -0.052 0.0815993638 420 -0.518 0.171 -0.160 0.256 -0.121 -0.052 0.0814411811 421 -0.518 0.171 -0.160 0.256 -0.117 -0.052 0.0814312799 422 -0.518 0.171 -0.160 0.256 -0.111 -0.052 0.0813959201 423 -0.518 0.171 -0.160 0.256 -0.101 -0.052 0.0812854142 426 -0.518 0.171 -0.160 0.256 -0.100 -0.052 0.0812828569 435 -0.518 0.171 -0.160 0.256 -0.100 -0.052 0.0812823904 436 -0.517 0.174 -0.160 0.258 -0.100 -0.053 0.0812645023 442 -0.517 0.174 -0.160 0.258 -0.100 -0.053 0.0812640654 446 -0.517 0.174 -0.160 0.258 -0.100 -0.053 0.0812636209 powell nthiter 5: fret = 0.081264 457 -0.531 0.174 -0.160 0.258 -0.100 -0.053 0.0810666390 458 -0.534 0.174 -0.160 0.258 -0.100 -0.053 0.0810564759 471 -0.534 0.174 -0.160 0.258 -0.100 -0.056 0.0810494078 472 -0.534 0.174 -0.160 0.258 -0.100 -0.055 0.0810473323 485 -0.534 0.174 -0.161 0.258 -0.100 -0.055 0.0810417530 486 -0.534 0.174 -0.165 0.258 -0.100 -0.055 0.0810332222 499 -0.534 0.174 -0.165 0.267 -0.100 -0.055 0.0809623346 510 -0.534 0.174 -0.165 0.267 -0.098 -0.055 0.0809459010 514 -0.534 0.174 -0.165 0.267 -0.097 -0.055 0.0809451922 521 -0.535 0.169 -0.164 0.263 -0.096 -0.054 0.0809278937 522 -0.535 0.170 -0.164 0.263 -0.096 -0.054 0.0809236882 523 -0.535 0.171 -0.164 0.264 -0.096 -0.054 0.0809197092 524 -0.535 0.172 -0.164 0.265 -0.096 -0.055 0.0809168060 527 -0.535 0.172 -0.164 0.265 -0.096 -0.055 0.0809161427 528 -0.535 0.172 -0.164 0.265 -0.096 -0.054 0.0809159525 powell nthiter 6: fret = 0.080916 541 -0.538 0.172 -0.164 0.265 -0.096 -0.054 0.0809125172 543 -0.537 0.172 -0.164 0.265 -0.096 -0.054 0.0809115595 554 -0.537 0.172 -0.164 0.265 -0.096 -0.059 0.0808748443 555 -0.537 0.172 -0.164 0.265 -0.096 -0.058 0.0808737591 567 -0.537 0.172 -0.174 0.265 -0.096 -0.058 0.0808451937 568 -0.537 0.172 -0.173 0.265 -0.096 -0.058 0.0808398244 569 -0.537 0.172 -0.171 0.265 -0.096 -0.058 0.0808371072 580 -0.537 0.172 -0.171 0.269 -0.096 -0.058 0.0808195811 591 -0.537 0.172 -0.171 0.269 -0.093 -0.058 0.0807952030 592 -0.537 0.172 -0.171 0.269 -0.088 -0.058 0.0807877715 593 -0.537 0.172 -0.171 0.269 -0.089 -0.058 0.0807827192 594 -0.537 0.172 -0.171 0.269 -0.090 -0.058 0.0807820484 602 -0.538 0.166 -0.170 0.264 -0.090 -0.057 0.0807378126 604 -0.538 0.167 -0.171 0.265 -0.090 -0.057 0.0807316504 606 -0.538 0.167 -0.171 0.266 -0.090 -0.057 0.0807301307 607 -0.538 0.168 -0.171 0.266 -0.090 -0.057 0.0807292564 608 -0.538 0.168 -0.171 0.266 -0.090 -0.057 0.0807282954 612 -0.540 0.164 -0.177 0.267 -0.083 -0.060 0.0805745474 615 -0.545 0.157 -0.187 0.268 -0.072 -0.065 0.0804526957 616 -0.546 0.156 -0.190 0.268 -0.069 -0.066 0.0804461441 621 -0.546 0.156 -0.190 0.268 -0.070 -0.066 0.0804460980 625 -0.546 0.156 -0.190 0.268 -0.070 -0.066 0.0804458929 627 -0.546 0.156 -0.190 0.268 -0.070 -0.066 0.0804458034 powell nthiter 7: fret = 0.080446 638 -0.554 0.156 -0.190 0.268 -0.070 -0.066 0.0804032029 640 -0.553 0.156 -0.190 0.268 -0.070 -0.066 0.0804016001 652 -0.553 0.156 -0.190 0.268 -0.070 -0.074 0.0803994261 653 -0.553 0.156 -0.190 0.268 -0.070 -0.070 0.0803781514 663 -0.553 0.156 -0.191 0.268 -0.070 -0.070 0.0803627209 665 -0.553 0.156 -0.202 0.268 -0.070 -0.070 0.0802798097 666 -0.553 0.156 -0.201 0.268 -0.070 -0.070 0.0802794578 677 -0.553 0.156 -0.201 0.266 -0.070 -0.070 0.0802753488 688 -0.553 0.156 -0.201 0.266 -0.069 -0.070 0.0802733959 691 -0.555 0.152 -0.207 0.267 -0.062 -0.073 0.0802498749 698 -0.555 0.152 -0.207 0.266 -0.062 -0.073 0.0802495835 699 -0.555 0.152 -0.207 0.266 -0.062 -0.073 0.0802495333 powell nthiter 8: fret = 0.080250 715 -0.556 0.152 -0.207 0.266 -0.062 -0.073 0.0802492046 738 -0.556 0.152 -0.210 0.266 -0.062 -0.073 0.0802398583 739 -0.556 0.152 -0.211 0.266 -0.062 -0.073 0.0802386830 750 -0.556 0.152 -0.211 0.265 -0.062 -0.073 0.0802344085 763 -0.559 0.148 -0.217 0.265 -0.056 -0.075 0.0802249116 767 -0.558 0.150 -0.215 0.265 -0.058 -0.074 0.0802224587 769 -0.558 0.149 -0.215 0.265 -0.058 -0.075 0.0802223417 775 -0.561 0.147 -0.224 0.264 -0.053 -0.076 0.0802049033 778 -0.565 0.142 -0.237 0.261 -0.046 -0.080 0.0801957654 779 -0.565 0.143 -0.236 0.262 -0.047 -0.079 0.0801943993 781 -0.563 0.144 -0.231 0.262 -0.049 -0.078 0.0801941130 783 -0.564 0.144 -0.233 0.262 -0.048 -0.079 0.0801930513 792 -0.564 0.144 -0.233 0.262 -0.048 -0.079 0.0801928365 powell nthiter 9: fret = 0.080193 814 -0.564 0.144 -0.233 0.262 -0.048 -0.077 0.0801861832 825 -0.564 0.144 -0.228 0.262 -0.048 -0.077 0.0801843265 827 -0.564 0.144 -0.230 0.262 -0.048 -0.077 0.0801802481 852 -0.567 0.141 -0.239 0.261 -0.043 -0.079 0.0801765706 856 -0.566 0.142 -0.235 0.261 -0.045 -0.078 0.0801758958 860 -0.566 0.142 -0.236 0.261 -0.045 -0.078 0.0801757209 861 -0.566 0.142 -0.236 0.261 -0.045 -0.078 0.0801756257 powell nthiter 10: fret = 0.080176 878 -0.567 0.142 -0.236 0.261 -0.045 -0.078 0.0801744131 889 -0.567 0.142 -0.236 0.261 -0.045 -0.077 0.0801733980 900 -0.567 0.142 -0.234 0.261 -0.045 -0.077 0.0801706230 912 -0.567 0.142 -0.234 0.260 -0.045 -0.077 0.0801691987 921 -0.567 0.142 -0.234 0.260 -0.046 -0.077 0.0801690062 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 1.068861 1 -25.0 -25.0 25.0 1.026634 2 -25.0 25.0 -25.0 1.027798 3 -25.0 25.0 25.0 1.044711 4 25.0 -25.0 -25.0 1.011490 5 25.0 -25.0 25.0 1.017702 6 25.0 25.0 -25.0 0.986409 7 25.0 25.0 25.0 0.984615 REL: 8 0.080169 8.168221 1.021028 rel = 0.078518 Number of iterations 10 Min cost was 0.080169 Number of FunctionCalls 937 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.040863 sec Parameters at optimum (transmm) -0.56698 0.14186 -0.23365 Parameters at optimum (rotdeg) 0.26021 -0.04628 -0.07726 Final costs ---------------- Number of surface hits 2112 WM Intensity 237.6294 +/- 32.9988 Ctx Intensity 333.8140 +/- 73.1351 Pct Contrast 31.8218 +/- 23.8217 Cost 0.0802 RelCost 0.1150 Reg at min cost was 0.00438 0.99997 0.00690 0.27071; 0.99641 -0.00495 0.08448 -0.17888; -0.08451 -0.00651 0.99640 -0.54983; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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 -0.00141 0.00000 0.00069 0.56715; -0.00039 0.00132 0.00453 -0.14216; -0.00453 -0.00079 -0.00040 0.23443; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.749523 Computing change in rh position Surface-RMS-Diff-mm 0.676320 0.088424 0.863788 mri_segreg done mri_segreg --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --init-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/bbr.pass1.dat --out-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 7.3.0 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/scripts mri_segreg --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii --init-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/bbr.pass1.dat --out-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/template.nii regfile /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/tmp.bbregister.292483/bbr.pass1.dat subject New_patient_test3_bugfix dof 6 outregfile /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 1673836619 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00438 0.99997 0.00690 0.27071; 0.99641 -0.00495 0.08448 -0.17888; -0.08451 -0.00651 0.99640 -0.54983; 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 1.030601 1 -25.0 -25.0 25.0 1.016391 2 -25.0 25.0 -25.0 1.011956 3 -25.0 25.0 25.0 1.006787 4 25.0 -25.0 -25.0 0.998209 5 25.0 -25.0 25.0 1.024787 6 25.0 25.0 -25.0 1.006223 7 25.0 25.0 25.0 1.006626 REL: 8 0.083815 8.101581 1.012698 rel = 0.0827645 Initial costs ---------------- Number of surface hits 212274 WM Intensity 236.5507 +/- 31.3948 Ctx Intensity 337.1428 +/- 73.3573 Pct Contrast 33.2041 +/- 23.9649 Cost 0.0838 RelCost 0.0828 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0850 0.0850 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0850 0.0850 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0846 0.0846 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0840 0.0840 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0838 0.0838 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.0834 0.0834 0.0 48 -0.1000 -0.1000 0.0000 0.1000 0.0000 -0.1000 0.0828 0.0828 0.0 243 0.0000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0815 0.0815 0.0 264 0.0000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0808 0.0808 0.0 Brute Force -------------------------- Min cost was 0.080822 Number of iterations 729 Search time 0.812059 sec Parameters at best (transmm, rotdeg) 0.000 -0.100 -0.100 0.100 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -0.1 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 = 0.084911 7 0.151 -0.100 -0.100 0.100 0.000 -0.100 0.0843589921 8 0.145 -0.100 -0.100 0.100 0.000 -0.100 0.0843534858 10 0.140 -0.100 -0.100 0.100 0.000 -0.100 0.0843523912 12 0.141 -0.100 -0.100 0.100 0.000 -0.100 0.0843523702 20 0.141 -0.045 -0.100 0.100 0.000 -0.100 0.0842690461 21 0.141 -0.050 -0.100 0.100 0.000 -0.100 0.0842568009 22 0.141 -0.064 -0.100 0.100 0.000 -0.100 0.0842370214 32 0.141 -0.064 -0.122 0.100 0.000 -0.100 0.0841297234 35 0.141 -0.064 -0.136 0.100 0.000 -0.100 0.0841015930 42 0.141 -0.064 -0.136 -0.518 0.000 -0.100 0.0833880406 44 0.141 -0.064 -0.136 -0.232 0.000 -0.100 0.0816508003 47 0.141 -0.064 -0.136 -0.196 0.000 -0.100 0.0815975554 48 0.141 -0.064 -0.136 -0.184 0.000 -0.100 0.0815972559 49 0.141 -0.064 -0.136 -0.190 0.000 -0.100 0.0815963024 58 0.141 -0.064 -0.136 -0.190 -0.066 -0.100 0.0811868019 59 0.141 -0.064 -0.136 -0.190 -0.132 -0.100 0.0811754423 60 0.141 -0.064 -0.136 -0.190 -0.101 -0.100 0.0811028687 62 0.141 -0.064 -0.136 -0.190 -0.105 -0.100 0.0811018112 64 0.141 -0.064 -0.136 -0.190 -0.104 -0.100 0.0811015582 72 0.141 -0.064 -0.136 -0.190 -0.104 0.020 0.0809134488 76 0.141 -0.064 -0.136 -0.190 -0.104 0.033 0.0809082366 78 0.141 -0.064 -0.136 -0.190 -0.104 0.042 0.0809023210 79 0.141 -0.064 -0.136 -0.190 -0.104 0.041 0.0809016551 powell nthiter 1: fret = 0.080902 88 0.225 -0.064 -0.136 -0.190 -0.104 0.041 0.0808641471 92 0.241 -0.064 -0.136 -0.190 -0.104 0.041 0.0808476279 94 0.238 -0.064 -0.136 -0.190 -0.104 0.041 0.0808475990 96 0.239 -0.064 -0.136 -0.190 -0.104 0.041 0.0808472851 97 0.240 -0.064 -0.136 -0.190 -0.104 0.041 0.0808471950 104 0.240 -0.128 -0.136 -0.190 -0.104 0.041 0.0808310398 108 0.240 -0.158 -0.136 -0.190 -0.104 0.041 0.0808020153 111 0.240 -0.160 -0.136 -0.190 -0.104 0.041 0.0808018157 120 0.240 -0.160 -0.116 -0.190 -0.104 0.041 0.0807987700 123 0.240 -0.160 -0.113 -0.190 -0.104 0.041 0.0807985612 132 0.240 -0.160 -0.113 -0.328 -0.104 0.041 0.0802661565 133 0.240 -0.160 -0.113 -0.338 -0.104 0.041 0.0802542515 135 0.240 -0.160 -0.113 -0.350 -0.104 0.041 0.0802475176 137 0.240 -0.160 -0.113 -0.348 -0.104 0.041 0.0802468939 146 0.240 -0.160 -0.113 -0.348 -0.112 0.041 0.0802216075 147 0.240 -0.160 -0.113 -0.348 -0.152 0.041 0.0801058272 149 0.240 -0.160 -0.113 -0.348 -0.235 0.041 0.0800603231 150 0.240 -0.160 -0.113 -0.348 -0.208 0.041 0.0800019525 151 0.240 -0.160 -0.113 -0.348 -0.199 0.041 0.0800009514 152 0.240 -0.160 -0.113 -0.348 -0.203 0.041 0.0799995154 161 0.240 -0.160 -0.113 -0.348 -0.203 -0.002 0.0799982070 162 0.240 -0.160 -0.113 -0.348 -0.203 0.019 0.0799928769 164 0.240 -0.160 -0.113 -0.348 -0.203 0.027 0.0799887098 166 0.240 -0.160 -0.113 -0.348 -0.203 0.029 0.0799881653 168 0.240 -0.160 -0.113 -0.348 -0.203 0.030 0.0799880435 169 0.240 -0.160 -0.113 -0.348 -0.203 0.031 0.0799880096 177 0.278 -0.197 -0.104 -0.409 -0.240 0.028 0.0798676634 178 0.293 -0.212 -0.101 -0.433 -0.255 0.026 0.0798665288 181 0.299 -0.218 -0.099 -0.444 -0.262 0.026 0.0798624010 185 0.299 -0.218 -0.099 -0.444 -0.262 0.026 0.0798623514 powell nthiter 2: fret = 0.079862 193 0.302 -0.218 -0.099 -0.444 -0.262 0.026 0.0798574677 194 0.328 -0.218 -0.099 -0.444 -0.262 0.026 0.0798461052 196 0.319 -0.218 -0.099 -0.444 -0.262 0.026 0.0798425756 197 0.320 -0.218 -0.099 -0.444 -0.262 0.026 0.0798424953 205 0.320 -0.286 -0.099 -0.444 -0.262 0.026 0.0798259178 206 0.320 -0.255 -0.099 -0.444 -0.262 0.026 0.0797733143 208 0.320 -0.260 -0.099 -0.444 -0.262 0.026 0.0797708453 211 0.320 -0.259 -0.099 -0.444 -0.262 0.026 0.0797708236 220 0.320 -0.259 -0.077 -0.444 -0.262 0.026 0.0797213035 221 0.320 -0.259 -0.063 -0.444 -0.262 0.026 0.0797134616 230 0.320 -0.259 -0.063 -0.444 -0.262 -0.041 0.0794927348 232 0.320 -0.259 -0.063 -0.444 -0.262 -0.030 0.0794781945 245 0.320 -0.259 -0.063 -0.444 -0.255 -0.030 0.0794764573 254 0.314 -0.253 -0.064 -0.433 -0.249 -0.029 0.0794684022 256 0.314 -0.253 -0.064 -0.434 -0.249 -0.029 0.0794683220 257 0.314 -0.253 -0.064 -0.434 -0.250 -0.029 0.0794682921 powell nthiter 3: fret = 0.079468 270 0.309 -0.253 -0.064 -0.434 -0.250 -0.029 0.0794655834 271 0.306 -0.253 -0.064 -0.434 -0.250 -0.029 0.0794650916 281 0.306 -0.273 -0.064 -0.434 -0.250 -0.029 0.0794096908 282 0.306 -0.277 -0.064 -0.434 -0.250 -0.029 0.0794066378 294 0.306 -0.277 -0.070 -0.434 -0.250 -0.029 0.0794026279 303 0.306 -0.277 -0.070 -0.434 -0.250 -0.052 0.0794013826 304 0.306 -0.277 -0.070 -0.434 -0.250 -0.041 0.0793877863 305 0.306 -0.277 -0.070 -0.434 -0.250 -0.040 0.0793877457 324 0.302 -0.274 -0.071 -0.428 -0.246 -0.040 0.0793874065 325 0.304 -0.275 -0.071 -0.430 -0.247 -0.040 0.0793865071 329 0.293 -0.297 -0.077 -0.426 -0.245 -0.051 0.0793538301 334 0.287 -0.310 -0.081 -0.424 -0.243 -0.058 0.0793475664 336 0.289 -0.307 -0.080 -0.424 -0.243 -0.056 0.0793475279 337 0.288 -0.308 -0.080 -0.424 -0.243 -0.057 0.0793473148 powell nthiter 4: fret = 0.079347 350 0.286 -0.308 -0.080 -0.424 -0.243 -0.057 0.0793468923 352 0.287 -0.308 -0.080 -0.424 -0.243 -0.057 0.0793468871 360 0.292 -0.313 -0.079 -0.433 -0.249 -0.057 0.0793434467 362 0.292 -0.313 -0.079 -0.433 -0.249 -0.057 0.0793434342 378 0.292 -0.313 -0.077 -0.433 -0.249 -0.057 0.0793427250 381 0.292 -0.313 -0.072 -0.433 -0.249 -0.057 0.0793418355 390 0.292 -0.313 -0.072 -0.433 -0.249 -0.073 0.0793286811 392 0.292 -0.313 -0.072 -0.433 -0.249 -0.070 0.0793275668 393 0.292 -0.313 -0.072 -0.433 -0.249 -0.069 0.0793274462 394 0.292 -0.313 -0.072 -0.433 -0.249 -0.068 0.0793272988 408 0.292 -0.313 -0.072 -0.433 -0.248 -0.068 0.0793270294 416 0.290 -0.317 -0.073 -0.432 -0.247 -0.069 0.0793260577 powell nthiter 5: fret = 0.079326 440 0.295 -0.321 -0.072 -0.439 -0.252 -0.070 0.0793250449 442 0.293 -0.320 -0.072 -0.437 -0.250 -0.070 0.0793248625 444 0.293 -0.320 -0.072 -0.437 -0.250 -0.070 0.0793248548 457 0.293 -0.320 -0.070 -0.437 -0.250 -0.070 0.0793241522 458 0.293 -0.320 -0.067 -0.437 -0.250 -0.070 0.0793241353 461 0.293 -0.320 -0.068 -0.437 -0.250 -0.070 0.0793239655 470 0.293 -0.320 -0.068 -0.437 -0.250 -0.072 0.0793236703 472 0.293 -0.320 -0.068 -0.437 -0.250 -0.071 0.0793236670 483 0.293 -0.320 -0.068 -0.437 -0.249 -0.071 0.0793234442 484 0.293 -0.320 -0.068 -0.437 -0.248 -0.071 0.0793234301 493 0.291 -0.324 -0.070 -0.436 -0.248 -0.072 0.0793221512 500 0.292 -0.330 -0.066 -0.440 -0.248 -0.076 0.0793210325 powell nthiter 6: fret = 0.079322 542 0.294 -0.326 -0.068 -0.440 -0.250 -0.075 0.0793207475 557 0.294 -0.326 -0.068 -0.440 -0.249 -0.075 0.0793205105 565 0.292 -0.329 -0.069 -0.439 -0.248 -0.076 0.0793197485 569 0.292 -0.329 -0.069 -0.439 -0.248 -0.076 0.0793196865 574 0.292 -0.335 -0.068 -0.442 -0.249 -0.081 0.0793179521 581 0.293 -0.336 -0.068 -0.443 -0.249 -0.081 0.0793178956 589 0.293 -0.336 -0.068 -0.443 -0.249 -0.081 0.0793178839 591 0.293 -0.336 -0.068 -0.443 -0.249 -0.081 0.0793178801 powell nthiter 7: fret = 0.079318 601 0.294 -0.336 -0.068 -0.443 -0.249 -0.081 0.0793178348 658 0.294 -0.336 -0.068 -0.443 -0.249 -0.081 0.0793178200 powell nthiter 8: fret = 0.079318 734 0.294 -0.336 -0.068 -0.443 -0.249 -0.081 0.0793178185 powell nthiter 9: fret = 0.079318 Powell done niters = 9 Computing relative cost 0 -25.0 -25.0 -25.0 1.030433 1 -25.0 -25.0 25.0 1.016508 2 -25.0 25.0 -25.0 1.014427 3 -25.0 25.0 25.0 1.011112 4 25.0 -25.0 -25.0 0.999258 5 25.0 -25.0 25.0 1.022956 6 25.0 25.0 -25.0 1.007405 7 25.0 25.0 25.0 1.003827 REL: 8 0.079318 8.105926 1.013241 rel = 0.0782813 Number of iterations 9 Min cost was 0.079318 Number of FunctionCalls 807 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 21.756615 sec Parameters at optimum (transmm) 0.29358 -0.33616 -0.06842 Parameters at optimum (rotdeg) -0.44263 -0.24919 -0.08107 Final costs ---------------- Number of surface hits 212273 WM Intensity 236.0213 +/- 31.4592 Ctx Intensity 335.9931 +/- 71.8559 Pct Contrast 33.2116 +/- 23.3705 Cost 0.0793 RelCost 0.0828 Reg at min cost was 0.00619 0.99998 0.00270 0.56642; 0.99572 -0.00641 0.09217 -0.51967; -0.09219 -0.00212 0.99574 -0.61566; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat, type = 14 Original Reg 0.00438 0.99997 0.00690 0.27071; 0.99641 -0.00495 0.08448 -0.17888; -0.08451 -0.00651 0.99640 -0.54983; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00181 -0.00001 0.00420 -0.29571; 0.00069 0.00147 -0.00769 0.34079; 0.00768 -0.00439 0.00066 0.06583; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.290687 Computing change in rh position Surface-RMS-Diff-mm 0.384619 0.174777 0.856403 mri_segreg done MinCost: 0.079318 236.021279 335.993106 33.211589 tkregister2_cmdl --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz --reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat --noedit --ltaout /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz reg file /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 7.3.0 Diagnostic Level -1 ---- Input registration matrix -------- 0.00619 0.99998 0.00270 0.56642; 0.99572 -0.00641 0.09217 -0.51967; -0.09219 -0.00212 0.99574 -0.61566; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 -------- 0.00619 0.99998 0.00270 0.56642; 0.99572 -0.00641 0.09217 -0.51967; -0.09219 -0.00212 0.99574 -0.61566; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = New_patient_test3_bugfix RegMat --------------------------- 0.00619 0.99998 0.00270 0.56642; 0.99572 -0.00641 0.09217 -0.51967; -0.09219 -0.00212 0.99574 -0.61566; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Fri Jan 6 19:20:27 CET 2023 Ended at Fri Jan 6 19:22:10 CET 2023 BBR-Run-Time-Sec 103 bbregister Done To check results, run: tkregisterfv --mov /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz --reg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.lta --surfs --sd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training cp /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.auto.lta /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.lta mri_convert -odt float -at /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.lta -rl /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.prenorm.mgz reading from /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/orig.mgz... INFO: Applying transformation from file /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99996 0.00738 0.00583 0.56039; -0.00736 0.99996 -0.00463 -0.61453; -0.00586 0.00458 0.99997 0.71085; 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 0 932 1000, flo=0, fhi=0.999, dest_type=3 writing to /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.prenorm.mgz... mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/aseg.presurf.mgz -surface /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/lh.white identity.nofile -surface /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/surf/rh.white identity.nofile /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.prenorm.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 47621 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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.prenorm.mgz... writing normalized volume to /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 1019248 mri_normalize done mri_mask -transfer 255 -keep_mask_deletion_edits /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.norm.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/brain.finalsurfs.mgz /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri/T2.mgz...done. #-------------------------------------------- #@# MMPialSurf lh Fri Jan 6 19:22:32 CET 2023 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/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 7.3.0 7.3.0 cd /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training/New_patient_test3_bugfix/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/20xx_Projects/2028_TractographyRespeech/03_Data/01_Training 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=0.0217966 Creating white distance volumes t=0.382711 (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=0.770368 (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 = 1.21856 Starting loop over 115656 vertices vno = 0, t = 1.21856 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 New_patient_test3_bugfix exited with ERRORS at Fri Jan 6 19:24:15 CET 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting