Tue Feb 11 18:14:07 CST 2025 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data /Applications/freesurfer/8.0.0/bin/recon-all -i /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii -s sub-01 -all subjid sub-01 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data FREESURFER_HOME /Applications/freesurfer/8.0.0 Actual FREESURFER_HOME /Applications/freesurfer/8.0.0 build-stamp.txt: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 65535 memorylocked unlimited maxproc 10666 PhysMem: 105G used (5750M wired, 31G compressor), 22G unused. ######################################## program versions used dev (freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a) dev ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:07-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:07-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:07-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:08-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:09-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:09-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:09-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:09-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:09-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:09-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:10-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:11-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:11-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:11-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:11-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:11-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:11-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 dev ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 dev ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:12-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:13-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:13-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:13-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 mris_convert -all-info ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:13-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:13-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:13-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:14-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:14-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:14-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:14-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:14-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:14-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:15-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:15-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:15-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:15-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:15-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:15-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:16-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:17-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:17-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:17-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:17-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:17-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:17-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:18-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:18-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:18-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:18-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 mri_motion_correct.fsl dev mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2025/02/12-00:14:18-GMT BuildTime: Feb 5 2025 04:40:27 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a User: yanez-ramos.mariaguadalupe Machine: r5523400.mayo.edu Platform: Darwin PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0 ####################################### GCADIR /Applications/freesurfer/8.0.0/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 /Applications/freesurfer/8.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01 \n mri_convert /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig/001.mgz \n mri_convert /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=2) reading from /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Feb 11 18:14:19 CST 2025 Found 1 runs /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/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. \n cp /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig/001.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz \n \n mri_info /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz \n rawavg.mgz ======================================== Volume information for /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 181 x 217 x 181 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 217.000 dof: 1 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 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 = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -90.0000 0.0000 1.0000 0.0000 -126.0000 0.0000 0.0000 1.0000 -72.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 0.0000 0.0000 90.0000 0.0000 1.0000 0.0000 126.0000 0.0000 0.0000 1.0000 72.0000 0.0000 0.0000 0.0000 1.0000 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01 \n mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --conform \n mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --conform reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) volume geometry: valid : 0 extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) shears : ( 0.0000, 0.0000, 0.0000) file : /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 49785.6 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz... \n mri_add_xform_to_header -c /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/talairach.xfm /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz \n INFO: extension is mgz \n mri_info /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz \n orig.mgz ======================================== Volume information for /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz type: MGH intent: MRI (0) 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 = 0.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -17.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 18.5000 talairach xfm : /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.5000 0.0000 0.0000 1.0000 -145.5000 0.0000 -1.0000 0.0000 146.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.5000 -0.0000 -0.0000 -1.0000 146.5000 -0.0000 1.0000 -0.0000 145.5000 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz --trg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg2orig.lta dev --inlta: identity.nofile input LTA transform. --src: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg.mgz src image (geometry). --trg: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz trg image (geometry). --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg2orig.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/rawavg2orig.lta... lta_convert successful. \n mri_synthstrip --threads 1 -i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthstrip.mgz \n Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthstrip.mgz If you use SynthStrip in your analysis, please cite: ---------------------------------------------------- SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://doi.org/10.1016/j.neuroimage.2022.119474 Website: https://synthstrip.io \n mri_synthseg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthseg.rca.mgz --threads 1 --vol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/stats/synthseg.vol.csv --keepgeom --addctab --cpu \n SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread addctab True predicting 1/1 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 325s 325s/step Reslicing to have same geom as the input [1. 1. 1.] segmentation saved in: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthseg.rca.mgz volumes saved in: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/stats/synthseg.vol.csv #@# mri_synthseg vmpeak None If you use this tool in a publication, please cite: SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl, A.V. Dalca, J.E. Iglesias Medical Image Analysis, 2023. Tue Feb 11 18:21:36 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01 /Applications/freesurfer/8.0.0/bin/fs-synthmorph-reg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthstrip.mgz --t /Applications/freesurfer/8.0.0/average/mni305.cor.stripped.mgz --affine-only --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305 --threads 1 -rwxr-xr-x 1 root wheel 30890 Feb 5 03:56 /Applications/freesurfer/8.0.0/bin/fs-synthmorph-reg freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 15822 Tue Feb 11 18:21:36 CST 2025 \n\n mri_synthmorph -m affine -t /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthstrip.mgz /Applications/freesurfer/8.0.0/average/mni305.cor.stripped.mgz -j 1 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305 ~/Documents/GitLabMayo/visual_connectivity/data/sub-01 ~/Documents/GitLabMayo/visual_connectivity/data/sub-01 lta_convert --invert --inlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/aff.lta --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta dev --invert: will invert transform. --inlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/aff.lta input LTA transform. --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta output LTA. LTA read, type : 1 1.08684 0.08641 0.04272 -2.30560; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta... lta_convert successful. \n\n To check affine registration tkregisterfv --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthstrip.mgz --targ /Applications/freesurfer/8.0.0/average/mni305.cor.stripped.mgz --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.mni305/aff.lta AffineOnly specified, so exiting now Started at Tue Feb 11 18:21:36 CST 2025 Ended at Tue Feb 11 18:22:27 CST 2025 Fs-Synthmorph-Reg-Run-Time-Sec 51 Fs-Synthmorph-Reg-Run-Time-Min 0.85 Fs-Synthmorph-Reg-Run-Time-Hours 0.01 fs-synthmorph-reg Done dev --ltavox2vox: output LTA as VOX_TO_VOX transform. --inlta: synthmorph.mni305/aff.lta input LTA transform. --outlta: talairach.xfm.lta output LTA. LTA read, type : 1 1.08684 0.08641 0.04272 -2.30560; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file talairach.xfm.lta... lta_convert successful. dev --inlta: talairach.xfm.lta input LTA transform. --outmni: talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.08684 0.08641 0.04272 -2.30562; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. \n fs-synthmorph-reg --s sub-01 --threads 1 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --test \n Tue Feb 11 18:22:28 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01 /Applications/freesurfer/8.0.0/bin/fs-synthmorph-reg --s sub-01 --threads 1 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --test -rwxr-xr-x 1 root wheel 30890 Feb 5 03:56 /Applications/freesurfer/8.0.0/bin/fs-synthmorph-reg freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 16010 mri_mask -bb 3 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz cropping npad = 3 DoAbs = 0 Computing bounding box, npad = 3, 3, 3, 3, 3, 3 35 35 16 180 187 223 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done. lta_convert --inlta identity.nofile --src /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --trg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta dev --inlta: identity.nofile input LTA transform. --src: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz src image (geometry). --trg: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz trg image (geometry). --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta... lta_convert successful. Tue Feb 11 18:22:28 CST 2025 \n\n mri_synthmorph -m affine -t /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io Tue Feb 11 18:23:27 CST 2025 \n\n mri_concatenate_lta -invert1 -invertout /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta invert the first LTA before applying it invert the output LTA Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Inverting output LTA Writing combined LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta... mri_concatenate_lta successful. \n\n mri_concatenate_lta -invert2 /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert the second LTA before applying it Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta... mri_concatenate_lta successful. \n\n lta_convert --invert --inlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta dev --invert: will invert transform. --inlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta input LTA transform. --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta output LTA. LTA read, type : 1 0.87815 -0.06784 -0.04863 2.87647; 0.03993 0.91526 0.09739 1.04553; -0.00669 0.01654 0.78237 3.06534; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta... lta_convert successful. \n\n lta_convert --inlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta --outmni /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm dev --inlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta input LTA transform. --outmni: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm output MNI/XFM matrix. LTA read, type : 1 1.13544 0.08307 0.06023 -3.53753; -0.05069 1.09134 -0.13900 -0.56914; 0.01077 -0.02236 1.28161 -3.93619; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. \n\n To check affine registration tkregisterfv --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz --targ /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta \n\n mri_synthmorph -m deform -t /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz -i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io \n\nmri_warp_convert --inras /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz --insrcgeom /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --outm3z /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz --vg-thresh 1e-5 --lta1-inv /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta --lta2 /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta dev --inras: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz input RAS warp. --insrcgeom: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz atlas/source image (used for geometry). --outm3z: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz output M3Z. Setting vg_isEqual_Threshold to 0.000010 Applying LTAs to the GCAM GCAMwrite(/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [193 x 229 x 193] [INFO] Warpfield::convert(): gcam image [256 x 256 x 256] [INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193] [INFO] Warpfield::convert(): total out of range voxel count: 0 [INFO] niiWrite(): MGZ_INTENT_WARPMAP => NIFTI_INTENT_DISPVECT, intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [INFO] niiWrite(): convert displacement from 0 to 3 mri_warp_convert successful. \n\nmri_ca_register -invert-and-save /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading gcam [INFO] niiRead(): intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 Computing inverse of GCAM Filling inverse of GCAM Allocating inv_gcam...(256, 256, 256) Saving inverse to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz GCAMwrite(/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [256 x 256 x 256] [INFO] Warpfield::convert(): gcam image [193 x 229 x 193] [INFO] Warpfield::convert(): gcam atlas [256 x 256 x 256] [INFO] Warpfield::convert(): total out of range voxel count: 0 [INFO] niiWrite(): MGZ_INTENT_WARPMAP => NIFTI_INTENT_DISPVECT, intent_code = 1006, dimensions = {5, 256, 256, 256, 1, 3, 1, 1} [INFO] niiWrite(): convert displacement from 0 to 3 mri_vol2vol --regheader --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz --targ /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz targvol /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739857877 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 13.50000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -20.00000; 0.00000 1.00000 0.00000 -20.00000; 0.00000 0.00000 1.00000 -2.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert -rt nearest /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz -at /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz mri_convert -rt nearest /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz -at /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... INFO: Applying transformation from file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... Applying morph_3d ... [INFO] niiRead(): intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 morphing to atlas with resample type 0 writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz... mri_diff --po /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz mri_diff --po /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz diffcount 4338064 Volumes differ in pixel data maxdiff 108.62528229 at 64 177 128 0 tkmeditfv -f /Applications/freesurfer/8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -aux /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz Started at Tue Feb 11 18:22:28 CST 2025 Ended at Tue Feb 11 18:40:42 CST 2025 Fs-Synthmorph-Reg-Run-Time-Sec 1094 Fs-Synthmorph-Reg-Run-Time-Min 18.23 Fs-Synthmorph-Reg-Run-Time-Hours 0.30 fs-synthmorph-reg Done #-------------------------------------------- #@# Nu Intensity Correction Tue Feb 11 18:40:42 CST 2025 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 \n /usr/bin/bc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri /Applications/freesurfer/8.0.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 FreeSurferEnv.csh dev Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 Tue Feb 11 18:40:43 CST 2025 tmpdir is ./tmp.mri_nu_correct.mni.16672 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.16672/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.16672/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.16672/ones.mgz dev cwd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.16672/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.16672/ones.mgz sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe input ./tmp.mri_nu_correct.mni.16672/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.16672/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.16672/ones.mgz Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16672/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16672/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16672/input.mean.dat dev cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16672/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16672/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16672/input.mean.dat sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.16672/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.16672/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16672/ones.mgz --i ./tmp.mri_nu_correct.mni.16672/nu0.mgz --sum ./tmp.mri_nu_correct.mni.16672/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16672/output.mean.dat dev cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16672/ones.mgz --i ./tmp.mri_nu_correct.mni.16672/nu0.mgz --sum ./tmp.mri_nu_correct.mni.16672/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16672/output.mean.dat sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.16672/ones.mgz Loading ./tmp.mri_nu_correct.mni.16672/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.16672/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.16672/nu0.mgz ./tmp.mri_nu_correct.mni.16672/nu0.mgz mul 1.13345000013348604136 Packing Done packing Unpacking Saving result to './tmp.mri_nu_correct.mni.16672/nu0.mgz' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 0 mri_convert ./tmp.mri_nu_correct.mni.16672/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.16672/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.16672/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 1 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 5, i2 = 71 #mri_make_uchar# mapping 12 167 to 3 110 : b -5.59015 m 0.691738 : thresh 8.08131 maxsat 376.718 : nzero 13848606 nsat 0 Tue Feb 11 18:41:28 CST 2025 mri_nu_correct.mni done \n mri_add_xform_to_header -c /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/talairach.xfm nu.mgz nu.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Feb 11 18:41:28 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri \n mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz \n 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 1.08684 0.08641 0.04272 -2.30562; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 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 = 22 Starting OpenSpline(): npoints = 22 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 68 (68), valley at 32 (32) csf peak at 10, setting threshold to 48 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 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 0 minutes and 45 seconds. #-------------------------------------- \n#@# MCADura Segmentation Tue Feb 11 18:42:13 CST 2025 mri_mcadura_seg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/mca-dura.mgz --threads 1 --synthmorphdir /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm Tue Feb 11 18:42:14 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri /Applications/freesurfer/8.0.0/bin/mri_mcadura_seg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/mca-dura.mgz --threads 1 --synthmorphdir /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root wheel 13384 Feb 5 03:54 /Applications/freesurfer/8.0.0/bin/mri_mcadura_seg freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 16925 ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925 ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri mri_vol2vol --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /Applications/freesurfer/8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/mcadura.prior.lh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67021; 0.05069 -1.09134 0.13900 4.76448; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /Applications/freesurfer/8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/mcadura.prior.lh.nii.gz regfile /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739471082 Final tkRAS-to-tkRAS Matrix is: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67021; 0.05069 -1.09134 0.13900 4.76448; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.13544 -0.06023 0.08307 235.10382; 0.05069 0.13900 1.09134 -54.23622; -0.01077 -1.28161 -0.02236 266.45721; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/mcadura.prior.lh.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/lh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 5557 voxels in mask (pct= 0.03) MRIcropToFoV(): thresh=0.001 FoV = (80,80,80) nhits=5557 centroid = (161.479,159.884,163.755) min = (134,139,147) max = (181,177,179) delta = (48,39,33) Region 121 120 124 80 80 80 121 120 124 80 80 80 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/lh.crop.nii.gz...done. mri_vol2vol --regheader --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/lh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.lh.crop.nii.gz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/lh.crop.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.lh.crop.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1740107388 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -33.00000; 0.00000 1.00000 0.00000 36.00000; 0.00000 0.00000 1.00000 -32.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 121.00000; 0.00000 1.00000 0.00000 120.00000; 0.00000 0.00000 1.00000 124.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_sclimbic_seg --model /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.lh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.mgz /Applications/freesurfer/8.0.0/python/scripts/mri_sclimbic_seg --model /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.lh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.ctab Loaded population stats /Applications/freesurfer/8.0.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 Loaded input image from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.lh.crop.nii.gz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 2s 2s/step Wrote segmentation to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.mgz done mri_vol2vol --regheader --interp nearest --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.mgz --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.uncropped.mgz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.uncropped.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739514172 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 33.00000; 0.00000 1.00000 0.00000 -36.00000; 0.00000 0.00000 1.00000 32.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -121.00000; 0.00000 1.00000 0.00000 -120.00000; 0.00000 0.00000 1.00000 -124.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /Applications/freesurfer/8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/mcadura.prior.rh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67021; 0.05069 -1.09134 0.13900 4.76448; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /Applications/freesurfer/8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/mcadura.prior.rh.nii.gz regfile /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739802396 Final tkRAS-to-tkRAS Matrix is: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67021; 0.05069 -1.09134 0.13900 4.76448; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.13544 -0.06023 0.08307 235.10382; 0.05069 0.13900 1.09134 -54.23622; -0.01077 -1.28161 -0.02236 266.45721; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/mcadura.prior.rh.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/rh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 5881 voxels in mask (pct= 0.04) MRIcropToFoV(): thresh=0.001 FoV = (80,80,80) nhits=5881 centroid = (92.2088,160.456,168.074) min = (73,139,151) max = (115,177,187) delta = (43,39,37) Region 52 120 128 80 80 80 52 120 128 80 80 80 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/rh.crop.nii.gz...done. mri_vol2vol --regheader --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/rh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.nii.gz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/rh.crop.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739416476 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 36.00000; 0.00000 1.00000 0.00000 40.00000; 0.00000 0.00000 1.00000 -32.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 52.00000; 0.00000 1.00000 0.00000 120.00000; 0.00000 0.00000 1.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.nii.gz --left-right-reverse-pix /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.lrrev.nii.gz mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.nii.gz --left-right-reverse-pix /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.lrrev.nii.gz reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.nii.gz... WARNING: applying left-right reversal to the input pixels without changing geometry. This will likely make the volume geometry WRONG, so make sure you know what you are doing. Reversing pixels for the columns TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.lrrev.nii.gz... mri_sclimbic_seg --model /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.lrrev.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.lrrev.mgz /Applications/freesurfer/8.0.0/python/scripts/mri_sclimbic_seg --model /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.lrrev.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.lrrev.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.ctab Loaded population stats /Applications/freesurfer/8.0.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /Applications/freesurfer/8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 Loaded input image from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/invol.rh.crop.lrrev.nii.gz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 2s 2s/step Wrote segmentation to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.lrrev.mgz done mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.lrrev.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.mgz --left-right-swap-label-table /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.index /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.rh.index --left-right-reverse-pix mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.lrrev.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.mgz --left-right-swap-label-table /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.lh.index /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/dumca.rh.index --left-right-reverse-pix reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.lrrev.mgz... Performing left-right swap of labels MRIlrswapSeg(): nswaps 423 WARNING: applying left-right reversal to the input pixels without changing geometry. This will likely make the volume geometry WRONG, so make sure you know what you are doing. Reversing pixels for the columns TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.mgz... mri_vol2vol --regheader --interp nearest --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.mgz --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.uncropped.mgz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.uncropped.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739940085 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -36.00000; 0.00000 1.00000 0.00000 -40.00000; 0.00000 0.00000 1.00000 32.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -52.00000; 0.00000 1.00000 0.00000 -120.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_concat /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.lh.uncropped.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.mri_mcadura_seg.16925/seg.rh.uncropped.mgz --sum --ctab /Applications/freesurfer/8.0.0/models/mca-dura.ctab --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/mca-dura.mgz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing sum across frames Writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/mca-dura.mgz fsvglrun freeview -neuro-view --hide-3d-slices --view coronal /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/mca-dura.mgz:isosurface=1:outline=1 Started at Tue Feb 11 18:42:14 CST 2025 Ended at Tue Feb 11 18:42:45 CST 2025 mri_mcadura_seg-Run-Time-Sec 31 mri_mcadura_seg Done #-------------------------------------- \n#@# VSinus Segmentation Tue Feb 11 18:42:45 CST 2025 mri_vsinus_seg --s sub-01 --rca-synthseg --threads 1 --synthmorphdir /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm Tue Feb 11 18:42:45 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri /Applications/freesurfer/8.0.0/bin/mri_vsinus_seg --s sub-01 --rca-synthseg --threads 1 --synthmorphdir /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root wheel 20960 Feb 5 03:54 /Applications/freesurfer/8.0.0/bin/mri_vsinus_seg freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 17127 mri_vol2vol --mov /Applications/freesurfer/8.0.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz --lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz Matrix from LTA: -1.13544 -0.08307 -0.06023 3.80928; 0.01077 -0.02236 1.28161 1.67023; 0.05069 -1.09134 0.13900 4.76447; 0.00000 0.00000 0.00000 1.00000; /Applications/freesurfer/8.0.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz movvol /Applications/freesurfer/8.0.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz regfile /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1740007251 Final tkRAS-to-tkRAS Matrix is: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67024; 0.05069 -1.09134 0.13900 4.76447; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.13544 -0.06023 0.08307 235.10379; 0.05069 0.13900 1.09134 -54.23622; -0.01077 -1.28161 -0.02236 266.45721; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop 0 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz threshold mask volume at 0.001 cropping npad = 0 DoAbs = 0 Found 75867 voxels in mask (pct= 0.45) Computing bounding box, npad = 0, 0, 0, 0, 0, 0 60 67 46 121 107 104 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz...done. mri_binarize --crop-around-ras /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz nolta cras /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz 0 144 144 144 Getting cras from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz final ras2vox matrix -1.00000 -0.00000 -0.00000 128.50000; -0.00000 -0.00000 -1.00000 146.50000; -0.00000 1.00000 -0.00000 145.50000; -0.00000 -0.00000 -0.00000 1.00000; -------------------------- ostr LIA (144 144 144) (144 144 144) rasCenter 8 -47.5 26 crsCenter 120.5 120.5 98 MRIcropAroundCRS() vol size 256 256 256 center 120.5 120.5 98 fov 144 144 144 limits 50 193 50 193 27 170 using MRIextractRegion() mri_sclimbic_seg --model /Applications/freesurfer/8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.no-sp.ctab --keep_ac --conform --percentile 99.9 --vmp --output-base vsinus --logfile mri_vsinus_seg.log --fov 144 --threads 1 --no-cite-sclimbic --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz /Applications/freesurfer/8.0.0/python/scripts/mri_sclimbic_seg --model /Applications/freesurfer/8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.no-sp.ctab --keep_ac --conform --percentile 99.9 --vmp --output-base vsinus --logfile mri_vsinus_seg.log --fov 144 --threads 1 --no-cite-sclimbic --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.no-sp.ctab Loaded population stats /Applications/freesurfer/8.0.0/models/sclimbic.volstats.csv nb_labels 6 inshape (144, 144, 144) features 24 (None, 144, 144, 144, 1) Loading weights from /Applications/freesurfer/8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /Applications/freesurfer/8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 Segmenting image 1/1 Loaded input image from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 13s 13s/step Wrote segmentation to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz done mri_binarize --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthseg.rca.mgz --match 3 42 --inv --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/ctxsegmask.mgz dev cwd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri cmdline mri_binarize --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthseg.rca.mgz --match 3 42 --inv --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/ctxsegmask.mgz sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe input /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthseg.rca.mgz frame 0 nErode3d 0 nErode2d 0 output /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/ctxsegmask.mgz Binarizing based on matching values nMatch 2 0 3 1 42 binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 408451 values in range Counting number of voxels in first frame Found 408451 voxels in final mask Writing output to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/ctxsegmask.mgz Count: 408451 408451.000000 16777216 2.434558 mri_binarize done mri_vol2vol --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --interp nearest --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz --regheader movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1740222851 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -6.00000; 0.00000 1.00000 0.00000 29.00000; 0.00000 0.00000 1.00000 -6.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -50.00000; 0.00000 1.00000 0.00000 -50.00000; 0.00000 0.00000 1.00000 -27.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/tmp.vsinus/ctxsegmask.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz...done. mri_segstats --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --seg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz --sum /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/stats/vsinus.stats --subject sub-01 --etiv dev cwd cmdline mri_segstats --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz --seg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz --sum /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/stats/vsinus.stats --subject sub-01 --etiv sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1404246 mm^3 (det: 1.387296 ) Loading /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz Using embedded color table (and excluding seg 0) Loading /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 6 segmentations Computing statistics for each segmentation Reporting on 5 segmentations Using PrintSegStat mri_segstats done fsvglrun freeview --hide-3d-slices --view coronal -neuro-view /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz:lock=1 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz:isosurface=1:outline=1 Started at Tue Feb 11 18:42:45 CST 2025 Ended at Tue Feb 11 18:43:04 CST 2025 Mri_Vsinus_Seg-Run-Time-Sec 19 Mri_Vsinus_Seg-Run-Time-Min 0.32 Mri_Vsinus_Seg-Run-Time-Hours 0.01 mri_vsinus_seg Done \n mri_mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/T1.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/synthstrip.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/brainmask.mgz \n DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/brainmask.mgz...done. #------------------------------------- #@# EM Registration Tue Feb 11 18:43:05 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri \n mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /Applications/freesurfer/8.0.0/average/RB_all_2020-01-02.gca transforms/talairach.lta \n setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/Applications/freesurfer/8.0.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 0 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=9.0 skull bounding box = (57, 77, 48) --> (184, 193, 220) finding center of left hemi white matter using (99, 116, 134) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (83,102,113) --> (114, 130,155) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 110 +- 3.6 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 initial log_p = -4.547 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.305016 @ (-10.526, -10.526, -10.526) max log p = -4.046669 @ (5.263, -5.263, -5.263) max log p = -4.026153 @ (2.632, -2.632, -2.632) max log p = -3.957917 @ (1.316, 1.316, -1.316) max log p = -3.940705 @ (-0.658, 0.658, 0.658) max log p = -3.940705 @ (0.000, 0.000, 0.000) max log p = -3.940705 @ (0.000, 0.000, 0.000) max log p = -3.940705 @ (0.000, 0.000, 0.000) Found translation: (-2.0, -16.4, -19.1): log p = -3.941 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.921, old_max_log_p =-3.941 (thresh=-3.9) 1.00000 0.00000 0.00000 -1.97369; 0.00000 1.15000 0.00000 -36.80802; 0.00000 0.00000 1.00000 -19.07895; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 22 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.921, old_max_log_p =-3.921 (thresh=-3.9) 1.00000 0.00000 0.00000 -1.97369; 0.00000 1.15000 0.00000 -36.80802; 0.00000 0.00000 1.00000 -19.07895; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 22 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.815, old_max_log_p =-3.921 (thresh=-3.9) 1.05426 0.07429 -0.03883 -10.50928; -0.05824 1.10518 0.00898 -28.32996; 0.03727 0.00315 1.01706 -28.10434; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.815, old_max_log_p =-3.815 (thresh=-3.8) 1.05426 0.07429 -0.03883 -10.50928; -0.05824 1.10518 0.00898 -28.32996; 0.03727 0.00315 1.01706 -28.10434; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.783, old_max_log_p =-3.815 (thresh=-3.8) 1.05470 0.06526 -0.03897 -9.29100; -0.04912 1.10186 0.01693 -29.53570; 0.03770 -0.00588 1.01576 -25.79817; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 19 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.777, old_max_log_p =-3.783 (thresh=-3.8) 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 19 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.777, old_max_log_p =-3.777 (thresh=-3.8) 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 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 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 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: 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.777 (old=-4.547) transform before final EM align: 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 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 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 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: 011: -log(p) = 4.1 tol 0.000000 final transform: 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 0 FSRUNTIME@ mri_em_register 0.0452 hours 1 threads registration took 2 minutes and 43 seconds. #-------------------------------------- #@# CA Normalize Tue Feb 11 18:45:48 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri \n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/8.0.0/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz \n writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/Applications/freesurfer/8.0.0/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=9.0 skull bounding box = (57, 77, 48) --> (184, 193, 220) finding center of left hemi white matter using (99, 116, 134) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (83,102,113) --> (114, 130,155) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 110 +- 3.6 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 using 246437 sample points... INFO: compute sample coordinates transform 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01289; 0.03774 -0.00589 1.01695 -25.95194; 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 (120, 78, 47) --> (188, 186, 212) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 1 of 141 (0.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (62, 77, 48) --> (128, 185, 213) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 8 of 7139 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (122, 153, 68) --> (168, 196, 122) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 169 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (79, 152, 68) --> (122, 193, 125) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 127 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (107, 148, 104) --> (140, 211, 134) Brain_Stem: limiting intensities to 95.0 --> 132.0 0 of 683 (0.0%) samples deleted using 8259 total control points for intensity normalization... bias field = 0.964 +- 0.078 11 of 8250 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (120, 78, 47) --> (188, 186, 212) Left_Cerebral_White_Matter: limiting intensities to 113.0 --> 132.0 165 of 197 (83.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (62, 77, 48) --> (128, 185, 213) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 7258 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (122, 153, 68) --> (168, 196, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 197 (10.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (79, 152, 68) --> (122, 193, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 144 (13.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (107, 148, 104) --> (140, 211, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 62 of 715 (8.7%) samples deleted using 8511 total control points for intensity normalization... bias field = 1.038 +- 0.057 43 of 8210 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (120, 78, 47) --> (188, 186, 212) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 108 of 249 (43.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (62, 77, 48) --> (128, 185, 213) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 11 of 7278 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (122, 153, 68) --> (168, 196, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 169 of 211 (80.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (79, 152, 68) --> (122, 193, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 78 of 152 (51.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (107, 148, 104) --> (140, 211, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 474 of 732 (64.8%) samples deleted using 8622 total control points for intensity normalization... bias field = 1.045 +- 0.044 52 of 7711 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 24 seconds. #-------------------------------------- \n#@# EntoWM Segmentation Tue Feb 11 18:46:11 CST 2025 mri_entowm_seg --s sub-01 --conform --threads 1 mri_sclimbic_seg --no-cite-sclimbic --model /Applications/freesurfer/8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /Applications/freesurfer/8.0.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-01 --conform --threads 1 /Applications/freesurfer/8.0.0/python/scripts/mri_sclimbic_seg --no-cite-sclimbic --model /Applications/freesurfer/8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /Applications/freesurfer/8.0.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-01 --conform --threads 1 Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /Applications/freesurfer/8.0.0/models/entowm.ctab Loaded population stats /Applications/freesurfer/8.0.0/models/sclimbic.volstats.csv nb_labels 5 inshape (160, 160, 160) features 24 (None, 160, 160, 160, 1) Loading weights from /Applications/freesurfer/8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /Applications/freesurfer/8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 Using subject directory /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data Computed eTIV from talairach Segmenting subject sub-01 1/1 Loaded input image from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/nu.mgz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 18s 18s/step Wrote segmentation to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/entowm.mgz Wrote volume stats to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/stats/entowm.stats done Started at Tue Feb 11 18:46:12 CST 2025 Started at Tue Feb 11 18:46:12 CST 2025 Ended at Tue Feb 11 18:46:32 CST 2025 Ended at Tue Feb 11 18:46:32 CST 2025 mri_entowm_seg-Run-Time-Sec 20 mri_entowm_seg-Run-Time-Sec 20 mri_entowm_seg-Run-Time-Min 0.40 mri_entowm_seg-Run-Time-Min 0.40 mri_entowm_seg-Run-Time-Hours 0.01 mri_entowm_seg-Run-Time-Hours 0.01 mri_entowm_seg Done mri_entowm_seg Done 1 3006 665 680.5787 wm-lh-entorhinal 2 3201 262 272.3829 wm-lh-gyrus-ambiens 3 4006 1069 1100.2047 wm-rh-entorhinal 4 4201 301 317.9394 wm-rh-gyrus-ambiens #-------------------------------------- #@# CC Seg Tue Feb 11 18:46:32 CST 2025 \n seg2cc --s sub-01 \n Tue Feb 11 18:46:33 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri /Applications/freesurfer/8.0.0/bin/seg2cc --s sub-01 freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a FreeSurferEnv.csh dev Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri IsConformed yes Tue Feb 11 18:46:33 CST 2025 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta sub-01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as transforms/cc_up.lta reading aseg from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/aseg.auto_noCCseg.mgz reading norm from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/norm.mgz 24999 voxels in left wm, 31272 in right wm, xrange [125, 134] searching rotation angles z=[-6 8], y=[-10 4] searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 global minimum found at slice 129.0, rotations (-2.81, 1.05) final transformation (x=129.0, yr=-2.811, zr=1.049): 0.99863 -0.01831 -0.04903 8.07287; 0.01829 0.99983 -0.00090 -1.21811; 0.04904 0.00000 0.99880 -12.16479; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 min_x_fornix = 127 min_x_fornix = 139 min_x_fornix = 139 min_x_fornix = 138 min_x_fornix = 122 cc center is found at 127 127 134 eigenvectors: -0.00546 0.00222 0.99998; 0.19925 -0.97994 0.00326; 0.97993 0.19926 0.00491; writing aseg with callosum to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.2 minutes #VMPC# mri_cc VmPeak 0 mri_cc done Tue Feb 11 18:46:42 CST 2025 ~/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri Started at Tue Feb 11 18:46:33 CST 2025 Ended at Tue Feb 11 18:46:42 CST 2025 Seg2cc-Run-Time-Sec 9 Seg2cc-Run-Time-Hours 0.00 seg2cc Done #-------------------------------------- #@# Merge ASeg Tue Feb 11 18:46:42 CST 2025 \n cp aseg.auto.mgz aseg.presurf.mgz \n #-------------------------------------------- #@# Intensity Normalization2 Tue Feb 11 18:46:42 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri \n mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz \n 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 aseg read with width 256 (src width 256) normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 2900 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 71 (71), valley at 39 (39) csf peak at 15, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 71 (71), valley at 39 (39) csf peak at 15, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 0 minutes and 57 seconds. #-------------------------------------------- #@# Mask BFS Tue Feb 11 18:47:40 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 DoAbs = 0 Found 1367035 voxels in mask (pct= 8.15) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. \n mri_mask -oval 1 -invert brain.finalsurfs.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/mca-dura.mgz brain.finalsurfs.mgz \n setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 16776792 Resetting threshold to 0.5 DoAbs = 0 Found 16776792 voxels in mask (pct=100.00) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. \n mri_mask -oval 1 -invert brain.finalsurfs.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/vsinus.mgz brain.finalsurfs.mgz \n setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 16773202 Resetting threshold to 0.5 DoAbs = 0 Found 16773202 voxels in mask (pct= 99.98) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. \n mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 2 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz \n mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 2 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz Fixing entowm 2 255 255 MRIfixEntoWM(): 255 255 Level=2 MRIfixEntoWM(): nchanged = 563 \n mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz \n mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz supposed to be reproducible but seed not set LabelAmygalaCortalJunction((): nhits = 3149 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 564 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Tue Feb 11 18:47:43 CST 2025 \n AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz \n \n mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz \n 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 MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 262987, nonwhite = 16263757, ambig = 250472, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (103.0): 103.3 +- 5.8 [79.0 --> 125.0] CCS GM (71.0) : 68.3 +- 12.1 [30.0 --> 95.0] white_mean 103.267 white_sigma 5.79131 gray_mean 68.2591 gray_sigma 12.1096 setting bottom of white matter range wm_low to 80.4 setting top of gray matter range gray_hi to 92.5 wm_low 80.3687 wm_hi 125 gray_low 30 gray_hi 92.4783 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=80.3687, wm_hi=125, gray_hi=92.4783 white = 338365, nonwhite = 16293461, ambig = 145390, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 80.3687 wm_hi 125 gray_low 30 gray_hi 92.4783 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 92.4783, wm_low = 80.3687 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=92.4783, wmlow=80.3687 137903 voxels processed (0.82%) 64799 voxels white (0.39%) 73104 voxels non-white (0.44%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=75.3687, gray_hi=92.4783, wsize=13 222525 voxels tested (1.33%) 53114 voxels changed (0.32%) 44114 multi-scale searches (0.26%) Recovering bright white MRIrecoverBrightWhite() wm_low 80.3687 wm_hi 125 slack 5.79131 pct_thresh 0.33 intensity_thresh 130.791 nvox_thresh 8.58 538 voxels tested (0.00%) 438 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=75.3687, hithr=92.4783 smoothing input volume with sigma = 0.250 100453 voxels tested (0.60%) 16322 voxels changed (0.10%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 2959 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1606 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 11077 filled MRIfindBrightNonWM(): 1767 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 0.4 minutes writing output to wm.seg.mgz... \n mri_edit_wm_with_aseg -keep-in -fix-ento-wm entowm.mgz 3 255 255 -fix-acj aseg.presurf.mgz 255 255 -fill-seg-wm -fix-scm-ha 1 wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz \n mri_edit_wm_with_aseg -keep-in -fix-ento-wm entowm.mgz 3 255 255 -fix-acj aseg.presurf.mgz 255 255 -fill-seg-wm -fix-scm-ha 1 wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... supposed to be reproducible but seed not set auto filling took 0.22 minutes Fixing entowm 3 255 255 LabelAmygalaCortalJunction((): nhits = 3149 Fixing ACJ 255 255 FixSCM HA 1 reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 13809 additional wm voxels added 0 additional wm voxels added SEG EDIT: 198592 voxels turned on, 50193 voxels turned off. Dilating 1 voxels in 3d propagating editing to output volume from wm.seg.mgz MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 2297 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 564 writing edited volume to wm.asegedit.mgz.... \n mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz \n Iteration Number : 1 pass 1 (xy+): 78 found - 78 modified | TOTAL: 78 pass 2 (xy+): 0 found - 78 modified | TOTAL: 78 pass 1 (xy-): 54 found - 54 modified | TOTAL: 132 pass 2 (xy-): 0 found - 54 modified | TOTAL: 132 pass 1 (yz+): 59 found - 59 modified | TOTAL: 191 pass 2 (yz+): 0 found - 59 modified | TOTAL: 191 pass 1 (yz-): 91 found - 91 modified | TOTAL: 282 pass 2 (yz-): 0 found - 91 modified | TOTAL: 282 pass 1 (xz+): 55 found - 55 modified | TOTAL: 337 pass 2 (xz+): 0 found - 55 modified | TOTAL: 337 pass 1 (xz-): 69 found - 69 modified | TOTAL: 406 pass 2 (xz-): 0 found - 69 modified | TOTAL: 406 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 24 found - 24 modified | TOTAL: 42 pass 2 (+++): 0 found - 24 modified | TOTAL: 42 pass 1 (+++): 25 found - 25 modified | TOTAL: 67 pass 2 (+++): 0 found - 25 modified | TOTAL: 67 pass 1 (+++): 14 found - 14 modified | TOTAL: 81 pass 2 (+++): 0 found - 14 modified | TOTAL: 81 Iteration Number : 1 pass 1 (++): 67 found - 67 modified | TOTAL: 67 pass 2 (++): 0 found - 67 modified | TOTAL: 67 pass 1 (+-): 62 found - 62 modified | TOTAL: 129 pass 2 (+-): 0 found - 62 modified | TOTAL: 129 pass 1 (--): 97 found - 97 modified | TOTAL: 226 pass 2 (--): 0 found - 97 modified | TOTAL: 226 pass 1 (-+): 65 found - 65 modified | TOTAL: 291 pass 2 (-+): 0 found - 65 modified | TOTAL: 291 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 6 found - 6 modified | TOTAL: 12 pass 2 (xy-): 0 found - 6 modified | TOTAL: 12 pass 1 (yz+): 3 found - 3 modified | TOTAL: 15 pass 2 (yz+): 0 found - 3 modified | TOTAL: 15 pass 1 (yz-): 7 found - 7 modified | TOTAL: 22 pass 2 (yz-): 0 found - 7 modified | TOTAL: 22 pass 1 (xz+): 9 found - 9 modified | TOTAL: 31 pass 2 (xz+): 0 found - 9 modified | TOTAL: 31 pass 1 (xz-): 7 found - 7 modified | TOTAL: 38 pass 2 (xz-): 0 found - 7 modified | TOTAL: 38 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 2 found - 2 modified | TOTAL: 7 pass 2 (+-): 0 found - 2 modified | TOTAL: 7 pass 1 (--): 1 found - 1 modified | TOTAL: 8 pass 2 (--): 0 found - 1 modified | TOTAL: 8 pass 1 (-+): 2 found - 2 modified | TOTAL: 10 pass 2 (-+): 0 found - 2 modified | TOTAL: 10 Iteration Number : 3 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+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 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 = 837 (out of 448118: 0.186781) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done Fixing entowm in wm.mgz \n mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 3 255 255 wm.mgz wm.mgz \n mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 3 255 255 wm.mgz wm.mgz Fixing entowm 3 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 2297 Fixing ACJ in wm.mgz \n mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 wm.mgz wm.mgz \n mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 wm.mgz wm.mgz supposed to be reproducible but seed not set LabelAmygalaCortalJunction((): nhits = 3149 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 564 #-------------------------------------------- #@# Fill Tue Feb 11 18:48:39 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri \n mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /Applications/freesurfer/8.0.0/SubCorticalMassLUT.txt wm.mgz filled.mgz \n 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... done. searching for cutting planes...voxel to talairach voxel transform 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01288; 0.03774 -0.00589 1.01695 -25.95193; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.05470 0.06526 -0.03897 -9.29100; -0.04894 1.09799 0.01687 -29.01288; 0.03774 -0.00589 1.01695 -25.95193; 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] = 752 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (130, 114, 146), TAL = (-2.0, 18.0, 14.0) talairach voxel to voxel transform 0.94421 -0.05592 0.03711 8.11317; 0.04262 0.90815 -0.01343 26.39561; -0.03480 0.00733 0.98188 25.37125; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (130, 114, 146) --> (-2.0, 18.0, 14.0) done. filling took 0.3 minutes talairach cc position changed to (-2.00, 18.00, 14.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(16.00, 18.00, 14.00) SRC: (112.91, 132.74, 165.66) search lh wm seed point around talairach space (-20.00, 18.00, 14.00), SRC: (146.90, 134.27, 164.41) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Tue Feb 11 18:49:00 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz \n Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 7 found - 7 modified | TOTAL: 12 pass 2 (xy-): 0 found - 7 modified | TOTAL: 12 pass 1 (yz+): 5 found - 5 modified | TOTAL: 17 pass 2 (yz+): 0 found - 5 modified | TOTAL: 17 pass 1 (yz-): 3 found - 3 modified | TOTAL: 20 pass 2 (yz-): 0 found - 3 modified | TOTAL: 20 pass 1 (xz+): 0 found - 0 modified | TOTAL: 20 pass 1 (xz-): 1 found - 1 modified | TOTAL: 21 pass 2 (xz-): 0 found - 1 modified | TOTAL: 21 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 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-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 = 29 (out of 136383: 0.021264) Ambiguous edge configurations... mri_pretess done \n mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix \n dev dev slice 60: 100 vertices, 122 faces slice 70: 2739 vertices, 2861 faces slice 80: 7515 vertices, 7678 faces slice 90: 13946 vertices, 14206 faces slice 100: 21755 vertices, 22036 faces slice 110: 30098 vertices, 30425 faces slice 120: 39312 vertices, 39654 faces slice 130: 50041 vertices, 50504 faces slice 140: 60629 vertices, 61088 faces slice 150: 69312 vertices, 69603 faces slice 160: 75353 vertices, 75660 faces slice 170: 80911 vertices, 81215 faces slice 180: 87218 vertices, 87516 faces slice 190: 91383 vertices, 91593 faces slice 200: 94162 vertices, 94336 faces slice 210: 95222 vertices, 95316 faces slice 220: 95222 vertices, 95316 faces slice 230: 95222 vertices, 95316 faces slice 240: 95222 vertices, 95316 faces slice 250: 95222 vertices, 95316 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; \n rm -f ../mri/filled-pretess255.mgz \n \n mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix \n counting number of connected components... 95222 voxel in cpt #1: X=-94 [v=95222,e=285948,f=190632] located at (-21.893555, -0.080160, 1.603075) For the whole surface: X=-94 [v=95222,e=285948,f=190632] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Tue Feb 11 18:49:02 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz \n Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 3 found - 3 modified | TOTAL: 7 pass 2 (yz-): 0 found - 3 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 3 found - 3 modified | TOTAL: 11 pass 2 (xz-): 0 found - 3 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 3 pass 2 (+++): 0 found - 2 modified | TOTAL: 3 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 288771: 0.004848) Ambiguous edge configurations... mri_pretess done \n mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix \n dev dev slice 60: 2649 vertices, 2825 faces slice 70: 10252 vertices, 10560 faces slice 80: 18273 vertices, 18568 faces slice 90: 28519 vertices, 28961 faces slice 100: 40575 vertices, 41018 faces slice 110: 52215 vertices, 52692 faces slice 120: 64940 vertices, 65405 faces slice 130: 78658 vertices, 79161 faces slice 140: 92207 vertices, 92709 faces slice 150: 105265 vertices, 105763 faces slice 160: 116633 vertices, 117091 faces slice 170: 126514 vertices, 126849 faces slice 180: 134217 vertices, 134539 faces slice 190: 141694 vertices, 141995 faces slice 200: 147390 vertices, 147639 faces slice 210: 151711 vertices, 151872 faces slice 220: 152448 vertices, 152502 faces slice 230: 152448 vertices, 152502 faces slice 240: 152448 vertices, 152502 faces slice 250: 152448 vertices, 152502 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; \n rm -f ../mri/filled-pretess127.mgz \n \n mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix \n counting number of connected components... 152448 voxel in cpt #1: X=-54 [v=152448,e=457506,f=305004] located at (29.876240, -0.020427, -0.245513) For the whole surface: X=-54 [v=152448,e=457506,f=305004] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Feb 11 18:49:03 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Tue Feb 11 18:49:04 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Feb 11 18:49:06 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix \n Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 40.9 mm, total surface area = 49036 mm^2 step 000: RMS=0.172 (target=0.015) step 005: RMS=0.134 (target=0.015) step 010: RMS=0.107 (target=0.015) step 015: RMS=0.097 (target=0.015) step 020: RMS=0.090 (target=0.015) step 025: RMS=0.085 (target=0.015) step 030: RMS=0.082 (target=0.015) step 035: RMS=0.080 (target=0.015) step 040: RMS=0.080 (target=0.015) step 045: RMS=0.079 (target=0.015) step 050: RMS=0.078 (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 0.1 minutes inflation complete. Not saving sulc mris_inflate utimesec 4.637651 mris_inflate stimesec 0.146424 mris_inflate ru_maxrss 377061376 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23201 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 76 #-------------------------------------------- #@# Inflation1 rh Tue Feb 11 18:49:11 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix \n Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 82677 mm^2 step 000: RMS=0.149 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.1 minutes inflation complete. Not saving sulc mris_inflate utimesec 8.124061 mris_inflate stimesec 0.238621 mris_inflate ru_maxrss 698417152 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 42812 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 92 #-------------------------------------------- #@# QSphere lh Tue Feb 11 18:49:19 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix \n doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: dev scaling brain by 0.370... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.16 +- 1.01 (0.00-->16.58) (max @ vno 46218 --> 47302) face area 0.04 +- 0.12 (-0.42-->4.41) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.318, avgs=0 005/300: dt: 0.9000, rms radial error=177.061, avgs=0 010/300: dt: 0.9000, rms radial error=176.512, avgs=0 015/300: dt: 0.9000, rms radial error=175.792, avgs=0 020/300: dt: 0.9000, rms radial error=174.976, avgs=0 025/300: dt: 0.9000, rms radial error=174.103, avgs=0 030/300: dt: 0.9000, rms radial error=173.199, avgs=0 035/300: dt: 0.9000, rms radial error=172.279, avgs=0 040/300: dt: 0.9000, rms radial error=171.352, avgs=0 045/300: dt: 0.9000, rms radial error=170.422, avgs=0 050/300: dt: 0.9000, rms radial error=169.493, avgs=0 055/300: dt: 0.9000, rms radial error=168.567, avgs=0 060/300: dt: 0.9000, rms radial error=167.645, avgs=0 065/300: dt: 0.9000, rms radial error=166.726, avgs=0 070/300: dt: 0.9000, rms radial error=165.813, avgs=0 075/300: dt: 0.9000, rms radial error=164.904, avgs=0 080/300: dt: 0.9000, rms radial error=163.999, avgs=0 085/300: dt: 0.9000, rms radial error=163.100, avgs=0 090/300: dt: 0.9000, rms radial error=162.205, avgs=0 095/300: dt: 0.9000, rms radial error=161.316, avgs=0 100/300: dt: 0.9000, rms radial error=160.431, avgs=0 105/300: dt: 0.9000, rms radial error=159.551, avgs=0 110/300: dt: 0.9000, rms radial error=158.677, avgs=0 115/300: dt: 0.9000, rms radial error=157.807, avgs=0 120/300: dt: 0.9000, rms radial error=156.942, avgs=0 125/300: dt: 0.9000, rms radial error=156.081, avgs=0 130/300: dt: 0.9000, rms radial error=155.226, avgs=0 135/300: dt: 0.9000, rms radial error=154.376, avgs=0 140/300: dt: 0.9000, rms radial error=153.530, avgs=0 145/300: dt: 0.9000, rms radial error=152.688, avgs=0 150/300: dt: 0.9000, rms radial error=151.852, avgs=0 155/300: dt: 0.9000, rms radial error=151.020, avgs=0 160/300: dt: 0.9000, rms radial error=150.193, avgs=0 165/300: dt: 0.9000, rms radial error=149.370, avgs=0 170/300: dt: 0.9000, rms radial error=148.552, avgs=0 175/300: dt: 0.9000, rms radial error=147.739, avgs=0 180/300: dt: 0.9000, rms radial error=146.930, avgs=0 185/300: dt: 0.9000, rms radial error=146.126, avgs=0 190/300: dt: 0.9000, rms radial error=145.326, avgs=0 195/300: dt: 0.9000, rms radial error=144.530, avgs=0 200/300: dt: 0.9000, rms radial error=143.739, avgs=0 205/300: dt: 0.9000, rms radial error=142.953, avgs=0 210/300: dt: 0.9000, rms radial error=142.171, avgs=0 215/300: dt: 0.9000, rms radial error=141.393, avgs=0 220/300: dt: 0.9000, rms radial error=140.620, avgs=0 225/300: dt: 0.9000, rms radial error=139.851, avgs=0 230/300: dt: 0.9000, rms radial error=139.087, avgs=0 235/300: dt: 0.9000, rms radial error=138.326, avgs=0 240/300: dt: 0.9000, rms radial error=137.571, avgs=0 245/300: dt: 0.9000, rms radial error=136.819, avgs=0 250/300: dt: 0.9000, rms radial error=136.072, avgs=0 255/300: dt: 0.9000, rms radial error=135.328, avgs=0 260/300: dt: 0.9000, rms radial error=134.589, avgs=0 265/300: dt: 0.9000, rms radial error=133.855, avgs=0 270/300: dt: 0.9000, rms radial error=133.124, avgs=0 275/300: dt: 0.9000, rms radial error=132.398, avgs=0 280/300: dt: 0.9000, rms radial error=131.675, avgs=0 285/300: dt: 0.9000, rms radial error=130.957, avgs=0 290/300: dt: 0.9000, rms radial error=130.243, avgs=0 295/300: dt: 0.9000, rms radial error=129.533, avgs=0 300/300: dt: 0.9000, rms radial error=128.826, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11331.60 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00113 epoch 2 (K=40.0), pass 1, starting sse = 2119.97 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/13 = 0.00188 epoch 3 (K=160.0), pass 1, starting sse = 346.78 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/14 = 0.00564 epoch 4 (K=640.0), pass 1, starting sse = 80.93 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.24/20 = 0.01196 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0097 hours FSRUNTIME@ mris_sphere 0.0097 hours 1 threads #VMPC# mris_sphere VmPeak 0 mris_sphere done #-------------------------------------------- #@# QSphere rh Tue Feb 11 18:49:55 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix \n doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: dev scaling brain by 0.299... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.55 (0.00-->7.23) (max @ vno 104881 --> 106152) face area 0.02 +- 0.03 (-0.30-->1.02) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.951, avgs=0 005/300: dt: 0.9000, rms radial error=176.692, avgs=0 010/300: dt: 0.9000, rms radial error=176.134, avgs=0 015/300: dt: 0.9000, rms radial error=175.402, avgs=0 020/300: dt: 0.9000, rms radial error=174.568, avgs=0 025/300: dt: 0.9000, rms radial error=173.680, avgs=0 030/300: dt: 0.9000, rms radial error=172.762, avgs=0 035/300: dt: 0.9000, rms radial error=171.827, avgs=0 040/300: dt: 0.9000, rms radial error=170.884, avgs=0 045/300: dt: 0.9000, rms radial error=169.939, avgs=0 050/300: dt: 0.9000, rms radial error=168.993, avgs=0 055/300: dt: 0.9000, rms radial error=168.050, avgs=0 060/300: dt: 0.9000, rms radial error=167.111, avgs=0 065/300: dt: 0.9000, rms radial error=166.175, avgs=0 070/300: dt: 0.9000, rms radial error=165.245, avgs=0 075/300: dt: 0.9000, rms radial error=164.319, avgs=0 080/300: dt: 0.9000, rms radial error=163.398, avgs=0 085/300: dt: 0.9000, rms radial error=162.482, avgs=0 090/300: dt: 0.9000, rms radial error=161.571, avgs=0 095/300: dt: 0.9000, rms radial error=160.665, avgs=0 100/300: dt: 0.9000, rms radial error=159.763, avgs=0 105/300: dt: 0.9000, rms radial error=158.867, avgs=0 110/300: dt: 0.9000, rms radial error=157.976, avgs=0 115/300: dt: 0.9000, rms radial error=157.089, avgs=0 120/300: dt: 0.9000, rms radial error=156.207, avgs=0 125/300: dt: 0.9000, rms radial error=155.330, avgs=0 130/300: dt: 0.9000, rms radial error=154.458, avgs=0 135/300: dt: 0.9000, rms radial error=153.590, avgs=0 140/300: dt: 0.9000, rms radial error=152.728, avgs=0 145/300: dt: 0.9000, rms radial error=151.870, avgs=0 150/300: dt: 0.9000, rms radial error=151.017, avgs=0 155/300: dt: 0.9000, rms radial error=150.168, avgs=0 160/300: dt: 0.9000, rms radial error=149.324, avgs=0 165/300: dt: 0.9000, rms radial error=148.485, avgs=0 170/300: dt: 0.9000, rms radial error=147.651, avgs=0 175/300: dt: 0.9000, rms radial error=146.821, avgs=0 180/300: dt: 0.9000, rms radial error=145.996, avgs=0 185/300: dt: 0.9000, rms radial error=145.175, avgs=0 190/300: dt: 0.9000, rms radial error=144.359, avgs=0 195/300: dt: 0.9000, rms radial error=143.547, avgs=0 200/300: dt: 0.9000, rms radial error=142.739, avgs=0 205/300: dt: 0.9000, rms radial error=141.936, avgs=0 210/300: dt: 0.9000, rms radial error=141.138, avgs=0 215/300: dt: 0.9000, rms radial error=140.343, avgs=0 220/300: dt: 0.9000, rms radial error=139.554, avgs=0 225/300: dt: 0.9000, rms radial error=138.768, avgs=0 230/300: dt: 0.9000, rms radial error=137.988, avgs=0 235/300: dt: 0.9000, rms radial error=137.211, avgs=0 240/300: dt: 0.9000, rms radial error=136.439, avgs=0 245/300: dt: 0.9000, rms radial error=135.671, avgs=0 250/300: dt: 0.9000, rms radial error=134.907, avgs=0 255/300: dt: 0.9000, rms radial error=134.147, avgs=0 260/300: dt: 0.9000, rms radial error=133.392, avgs=0 265/300: dt: 0.9000, rms radial error=132.641, avgs=0 270/300: dt: 0.9000, rms radial error=131.894, avgs=0 275/300: dt: 0.9000, rms radial error=131.152, avgs=0 280/300: dt: 0.9000, rms radial error=130.413, avgs=0 285/300: dt: 0.9000, rms radial error=129.679, avgs=0 290/300: dt: 0.9000, rms radial error=128.949, avgs=0 295/300: dt: 0.9000, rms radial error=128.222, avgs=0 300/300: dt: 0.9000, rms radial error=127.500, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17990.03 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00026 epoch 2 (K=40.0), pass 1, starting sse = 3024.80 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00019 epoch 3 (K=160.0), pass 1, starting sse = 329.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/13 = 0.00344 epoch 4 (K=640.0), pass 1, starting sse = 38.81 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/24 = 0.00761 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0168 hours FSRUNTIME@ mris_sphere 0.0168 hours 1 threads #VMPC# mris_sphere VmPeak 0 mris_sphere done #@# Fix Topology lh Tue Feb 11 18:50:55 CST 2025 \n mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 sub-01 lh \n Warning - built without openmp support Setting OMP_NUM_THREADS=1 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 Warning - built without openmp support Setting OMP_NUM_THREADS=1 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' dev dev before topology correction, eno=-94 (nv=95222, nf=190632, ne=285948, g=48) 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 11 iterations marking ambiguous vertices... 43687 ambiguous faces found in tessellation segmenting defects... 42 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 10 -merging segment 35 into 31 40 defects to be corrected 0 vertices coincident reading input surface /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.6435 (-4.8217) -vertex loglikelihood: -7.7068 (-3.8534) -normal dot loglikelihood: -3.6391 (-3.6391) -quad curv loglikelihood: -5.9185 (-2.9593) Total Loglikelihood : -26.9079 CORRECTING DEFECT 0 (vertices=1901, convex hull=546, v0=1449) 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 0 (v0=1449), euler #=-32 (71932,212819,140855) : difference with theory (-37) = -5 CORRECTING DEFECT 1 (vertices=29, convex hull=63, v0=7839) After retessellation of defect 1 (v0=7839), euler #=-31 (71941,212869,140897) : difference with theory (-36) = -5 CORRECTING DEFECT 2 (vertices=158, convex hull=135, v0=9794) After retessellation of defect 2 (v0=9794), euler #=-30 (72002,213120,141088) : difference with theory (-35) = -5 CORRECTING DEFECT 3 (vertices=259, convex hull=123, v0=10661) After retessellation of defect 3 (v0=10661), euler #=-29 (72049,213322,141244) : difference with theory (-34) = -5 CORRECTING DEFECT 4 (vertices=39, convex hull=39, v0=10670) After retessellation of defect 4 (v0=10670), euler #=-28 (72064,213384,141292) : difference with theory (-33) = -5 CORRECTING DEFECT 5 (vertices=1149, convex hull=424, v0=14162) 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 After retessellation of defect 5 (v0=14162), euler #=-27 (72074,213633,141532) : difference with theory (-32) = -5 CORRECTING DEFECT 6 (vertices=74, convex hull=75, v0=14310) After retessellation of defect 6 (v0=14310), euler #=-26 (72091,213716,141599) : difference with theory (-31) = -5 CORRECTING DEFECT 7 (vertices=19, convex hull=41, v0=16703) After retessellation of defect 7 (v0=16703), euler #=-25 (72098,213752,141629) : difference with theory (-30) = -5 CORRECTING DEFECT 8 (vertices=11, convex hull=20, v0=18308) After retessellation of defect 8 (v0=18308), euler #=-24 (72100,213762,141638) : difference with theory (-29) = -5 CORRECTING DEFECT 9 (vertices=5958, convex hull=842, v0=19515) 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 9 (v0=19515), euler #=-27 (73357,217991,144607) : difference with theory (-28) = -1 CORRECTING DEFECT 10 (vertices=9710, convex hull=1839, v0=21511) 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 87918 with 3 faces normal vector of length zero at vertex 87918 with 3 faces normal vector of length zero at vertex 87918 with 3 faces normal vector of length zero at vertex 87918 with 3 faces normal vector of length zero at vertex 87918 with 3 faces After retessellation of defect 10 (v0=21511), euler #=-27 (73404,219136,145705) : difference with theory (-27) = 0 CORRECTING DEFECT 11 (vertices=7, convex hull=26, v0=23206) After retessellation of defect 11 (v0=23206), euler #=-26 (73408,219155,145721) : difference with theory (-26) = 0 CORRECTING DEFECT 12 (vertices=42, convex hull=80, v0=26533) After retessellation of defect 12 (v0=26533), euler #=-25 (73435,219270,145810) : difference with theory (-25) = 0 CORRECTING DEFECT 13 (vertices=58, convex hull=102, v0=31693) After retessellation of defect 13 (v0=31693), euler #=-24 (73460,219391,145907) : difference with theory (-24) = 0 CORRECTING DEFECT 14 (vertices=6, convex hull=18, v0=34388) After retessellation of defect 14 (v0=34388), euler #=-23 (73461,219397,145913) : difference with theory (-23) = 0 CORRECTING DEFECT 15 (vertices=35, convex hull=66, v0=35614) After retessellation of defect 15 (v0=35614), euler #=-22 (73470,219451,145959) : difference with theory (-22) = 0 CORRECTING DEFECT 16 (vertices=6, convex hull=27, v0=36107) After retessellation of defect 16 (v0=36107), euler #=-21 (73473,219467,145973) : difference with theory (-21) = 0 CORRECTING DEFECT 17 (vertices=10, convex hull=22, v0=36252) After retessellation of defect 17 (v0=36252), euler #=-20 (73475,219477,145982) : difference with theory (-20) = 0 CORRECTING DEFECT 18 (vertices=5, convex hull=33, v0=37940) After retessellation of defect 18 (v0=37940), euler #=-19 (73477,219493,145997) : difference with theory (-19) = 0 CORRECTING DEFECT 19 (vertices=182, convex hull=78, v0=39098) After retessellation of defect 19 (v0=39098), euler #=-18 (73489,219566,146059) : difference with theory (-18) = 0 CORRECTING DEFECT 20 (vertices=11, convex hull=15, v0=40032) After retessellation of defect 20 (v0=40032), euler #=-17 (73490,219574,146067) : difference with theory (-17) = 0 CORRECTING DEFECT 21 (vertices=11, convex hull=33, v0=40985) After retessellation of defect 21 (v0=40985), euler #=-16 (73493,219591,146082) : difference with theory (-16) = 0 CORRECTING DEFECT 22 (vertices=21, convex hull=30, v0=43940) After retessellation of defect 22 (v0=43940), euler #=-15 (73497,219613,146101) : difference with theory (-15) = 0 CORRECTING DEFECT 23 (vertices=85, convex hull=45, v0=46122) After retessellation of defect 23 (v0=46122), euler #=-14 (73507,219660,146139) : difference with theory (-14) = 0 CORRECTING DEFECT 24 (vertices=18, convex hull=23, v0=46138) After retessellation of defect 24 (v0=46138), euler #=-13 (73512,219683,146158) : difference with theory (-13) = 0 CORRECTING DEFECT 25 (vertices=285, convex hull=125, v0=46787) After retessellation of defect 25 (v0=46787), euler #=-12 (73553,219869,146304) : difference with theory (-12) = 0 CORRECTING DEFECT 26 (vertices=6, convex hull=20, v0=47342) After retessellation of defect 26 (v0=47342), euler #=-11 (73556,219885,146318) : difference with theory (-11) = 0 CORRECTING DEFECT 27 (vertices=18, convex hull=22, v0=55820) After retessellation of defect 27 (v0=55820), euler #=-10 (73558,219900,146332) : difference with theory (-10) = 0 CORRECTING DEFECT 28 (vertices=968, convex hull=366, v0=55859) 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 After retessellation of defect 28 (v0=55859), euler #=-9 (73870,221025,147146) : difference with theory (-9) = 0 CORRECTING DEFECT 29 (vertices=11, convex hull=35, v0=61101) After retessellation of defect 29 (v0=61101), euler #=-8 (73878,221062,147176) : difference with theory (-8) = 0 CORRECTING DEFECT 30 (vertices=1705, convex hull=534, v0=64024) 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 After retessellation of defect 30 (v0=64024), euler #=-7 (73973,221661,147681) : difference with theory (-7) = 0 CORRECTING DEFECT 31 (vertices=234, convex hull=101, v0=65080) After retessellation of defect 31 (v0=65080), euler #=-6 (74025,221862,147831) : difference with theory (-6) = 0 CORRECTING DEFECT 32 (vertices=31, convex hull=90, v0=71253) After retessellation of defect 32 (v0=71253), euler #=-5 (74034,221925,147886) : difference with theory (-5) = 0 CORRECTING DEFECT 33 (vertices=14, convex hull=20, v0=71843) After retessellation of defect 33 (v0=71843), euler #=-4 (74037,221939,147898) : difference with theory (-4) = 0 CORRECTING DEFECT 34 (vertices=8, convex hull=15, v0=84514) After retessellation of defect 34 (v0=84514), euler #=-3 (74037,221943,147903) : difference with theory (-3) = 0 CORRECTING DEFECT 35 (vertices=28, convex hull=45, v0=84523) After retessellation of defect 35 (v0=84523), euler #=-2 (74045,221983,147936) : difference with theory (-2) = 0 CORRECTING DEFECT 36 (vertices=153, convex hull=63, v0=84726) After retessellation of defect 36 (v0=84726), euler #=-1 (74072,222090,148017) : difference with theory (-1) = 0 CORRECTING DEFECT 37 (vertices=35, convex hull=66, v0=87404) After retessellation of defect 37 (v0=87404), euler #=0 (74092,222174,148082) : difference with theory (0) = 0 CORRECTING DEFECT 38 (vertices=92, convex hull=114, v0=89236) After retessellation of defect 38 (v0=89236), euler #=1 (74145,222388,148244) : difference with theory (1) = 0 CORRECTING DEFECT 39 (vertices=88, convex hull=96, v0=91361) After retessellation of defect 39 (v0=91361), euler #=2 (74170,222504,148336) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.93 +- 0.57 (0.03-->35.02) (max @ vno 43792 --> 54913) face area nan +- nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.93 +- 0.57 (0.03-->35.02) (max @ vno 43792 --> 54913) face area nan +- nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 148 mutations (35.9%), 264 crossovers (64.1%), 3382 vertices were eliminated building final representation... 21052 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=74170, nf=148336, ne=222504, g=0) writing corrected surface to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig.premesh... defective orientation at vertex 47960(48384) with faces 93669 and 144584 defective orientation at vertex 47960(48385) with faces 93669 and 142811 defective orientation at vertex 47972(48401) with faces 93690 and 144586 defective orientation at vertex 47972(48402) with faces 93690 and 142686 defective orientation at vertex 48383(48384) with faces 94502 and 144584 defective orientation at vertex 48383(48389) with faces 94501 and 142680 defective orientation at vertex 48384(48383) with faces 144584 and 94502 defective orientation at vertex 48384(47960) with faces 144584 and 93669 defective orientation at vertex 48384(48385) with faces 93669 and 144587 defective orientation at vertex 48384(48390) with faces 94502 and 144587 defective orientation at vertex 48385(48384) with faces 93669 and 144587 defective orientation at vertex 48385(47960) with faces 93669 and 142811 defective orientation at vertex 48389(48383) with faces 94501 and 142680 defective orientation at vertex 48389(48395) with faces 94509 and 142678 defective orientation at vertex 48390(48384) with faces 94502 and 144587 defective orientation at vertex 48390(48396) with faces 94510 and 142812 defective orientation at vertex 48395(48389) with faces 94509 and 142678 defective orientation at vertex 48395(48401) with faces 94521 and 144586 defective orientation at vertex 48396(48390) with faces 94510 and 142812 defective orientation at vertex 48396(48402) with faces 94522 and 142813 defective orientation at vertex 48401(47972) with faces 144586 and 93690 defective orientation at vertex 48401(48395) with faces 144586 and 94521 defective orientation at vertex 48402(47972) with faces 93690 and 142686 defective orientation at vertex 48402(48396) with faces 94522 and 142813 0.032 % of the vertices (24 vertices) exhibit an orientation change removing intersecting faces 000: 3301 intersecting 001: 944 intersecting 002: 396 intersecting 003: 273 intersecting 004: 268 intersecting 005: 250 intersecting 006: 237 intersecting step 1 with no progress (num=237, old_num=237) 007: 237 intersecting step 2 with no progress (num=237, old_num=237) 008: 237 intersecting step 3 with no progress (num=237, old_num=237) 009: 237 intersecting step 4 with no progress (num=237, old_num=237) 010: 237 intersecting step 5 with no progress (num=237, old_num=237) 011: 237 intersecting step 6 with no progress (num=237, old_num=237) 012: 237 intersecting step 7 with no progress (num=237, old_num=237) 013: 237 intersecting step 8 with no progress (num=237, old_num=237) 014: 237 intersecting step 9 with no progress (num=237, old_num=237) 015: 237 intersecting step 10 with no progress (num=237, old_num=237) 016: 237 intersecting step 11 with no progress (num=237, old_num=237) 017: 237 intersecting step 12 with no progress (num=237, old_num=237) 018: 237 intersecting step 13 with no progress (num=237, old_num=237) 019: 237 intersecting step 14 with no progress (num=237, old_num=237) 020: 237 intersecting step 15 with no progress (num=237, old_num=237) 021: 237 intersecting step 16 with no progress (num=237, old_num=237) terminating search with 237 intersecting topology fixing took 10.3 minutes FSRUNTIME@ mris_fix_topology lh 0.1708 hours 1 threads #VMPC# mris_fix_topology VmPeak 0 #@# Fix Topology rh Tue Feb 11 19:01:10 CST 2025 \n mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 sub-01 rh \n Warning - built without openmp support Setting OMP_NUM_THREADS=1 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 Warning - built without openmp support Setting OMP_NUM_THREADS=1 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' dev dev before topology correction, eno=-54 (nv=152448, nf=305004, ne=457506, g=28) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 18858 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 21 defects to be corrected 0 vertices coincident reading input surface /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.5986 (-4.7993) -vertex loglikelihood: -6.6042 (-3.3021) -normal dot loglikelihood: -3.5258 (-3.5258) -quad curv loglikelihood: -5.7217 (-2.8609) Total Loglikelihood : -25.4504 CORRECTING DEFECT 0 (vertices=348, convex hull=164, v0=555) After retessellation of defect 0 (v0=555), euler #=-13 (142145,424418,282260) : difference with theory (-18) = -5 CORRECTING DEFECT 1 (vertices=1234, convex hull=503, v0=3852) 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 1 (v0=3852), euler #=-13 (142343,425283,282927) : difference with theory (-17) = -4 CORRECTING DEFECT 2 (vertices=304, convex hull=138, v0=6605) After retessellation of defect 2 (v0=6605), euler #=-12 (142367,425415,283036) : difference with theory (-16) = -4 CORRECTING DEFECT 3 (vertices=69, convex hull=82, v0=8513) After retessellation of defect 3 (v0=8513), euler #=-11 (142390,425521,283120) : difference with theory (-15) = -4 CORRECTING DEFECT 4 (vertices=5838, convex hull=1877, v0=24000) 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 4 (v0=24000), euler #=-14 (142577,427081,284490) : difference with theory (-14) = 0 CORRECTING DEFECT 5 (vertices=509, convex hull=231, v0=49398) After retessellation of defect 5 (v0=49398), euler #=-13 (142702,427573,284858) : difference with theory (-13) = 0 CORRECTING DEFECT 6 (vertices=20, convex hull=23, v0=58362) After retessellation of defect 6 (v0=58362), euler #=-12 (142706,427593,284875) : difference with theory (-12) = 0 CORRECTING DEFECT 7 (vertices=10, convex hull=21, v0=67403) After retessellation of defect 7 (v0=67403), euler #=-11 (142709,427608,284888) : difference with theory (-11) = 0 CORRECTING DEFECT 8 (vertices=163, convex hull=173, v0=72968) After retessellation of defect 8 (v0=72968), euler #=-10 (142792,427943,285141) : difference with theory (-10) = 0 CORRECTING DEFECT 9 (vertices=33, convex hull=42, v0=74696) After retessellation of defect 9 (v0=74696), euler #=-9 (142796,427971,285166) : difference with theory (-9) = 0 CORRECTING DEFECT 10 (vertices=37, convex hull=66, v0=77952) After retessellation of defect 10 (v0=77952), euler #=-8 (142808,428032,285216) : difference with theory (-8) = 0 CORRECTING DEFECT 11 (vertices=5, convex hull=29, v0=88571) After retessellation of defect 11 (v0=88571), euler #=-7 (142808,428040,285225) : difference with theory (-7) = 0 CORRECTING DEFECT 12 (vertices=7, convex hull=26, v0=93283) After retessellation of defect 12 (v0=93283), euler #=-6 (142810,428052,285236) : difference with theory (-6) = 0 CORRECTING DEFECT 13 (vertices=1263, convex hull=342, v0=93829) After retessellation of defect 13 (v0=93829), euler #=-5 (142890,428457,285562) : difference with theory (-5) = 0 CORRECTING DEFECT 14 (vertices=141, convex hull=58, v0=94794) After retessellation of defect 14 (v0=94794), euler #=-4 (142912,428547,285631) : difference with theory (-4) = 0 CORRECTING DEFECT 15 (vertices=30, convex hull=78, v0=99934) After retessellation of defect 15 (v0=99934), euler #=-3 (142921,428602,285678) : difference with theory (-3) = 0 CORRECTING DEFECT 16 (vertices=113, convex hull=41, v0=102381) After retessellation of defect 16 (v0=102381), euler #=-2 (142931,428646,285713) : difference with theory (-2) = 0 CORRECTING DEFECT 17 (vertices=138, convex hull=115, v0=120574) After retessellation of defect 17 (v0=120574), euler #=-1 (142990,428876,285885) : difference with theory (-1) = 0 CORRECTING DEFECT 18 (vertices=65, convex hull=81, v0=120598) After retessellation of defect 18 (v0=120598), euler #=0 (143019,428997,285978) : difference with theory (0) = 0 CORRECTING DEFECT 19 (vertices=32, convex hull=67, v0=145766) After retessellation of defect 19 (v0=145766), euler #=1 (143031,429061,286031) : difference with theory (1) = 0 CORRECTING DEFECT 20 (vertices=20, convex hull=63, v0=150139) After retessellation of defect 20 (v0=150139), euler #=2 (143040,429114,286076) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.38 (0.09-->33.75) (max @ vno 24170 --> 57247) face area nan +- nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.38 (0.09-->33.75) (max @ vno 24170 --> 57247) face area nan +- nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 73 mutations (32.7%), 150 crossovers (67.3%), 2111 vertices were eliminated building final representation... 9408 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=143040, nf=286076, ne=429114, g=0) writing corrected surface to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 1268 intersecting 001: 417 intersecting 002: 200 intersecting 003: 136 intersecting 004: 135 intersecting 005: 121 intersecting step 1 with no progress (num=121, old_num=121) 006: 121 intersecting step 2 with no progress (num=121, old_num=121) 007: 121 intersecting step 3 with no progress (num=121, old_num=121) 008: 121 intersecting step 4 with no progress (num=121, old_num=121) 009: 121 intersecting step 5 with no progress (num=121, old_num=121) 010: 121 intersecting step 6 with no progress (num=121, old_num=121) 011: 121 intersecting step 7 with no progress (num=121, old_num=121) 012: 121 intersecting step 8 with no progress (num=121, old_num=121) 013: 121 intersecting step 9 with no progress (num=121, old_num=121) 014: 121 intersecting step 10 with no progress (num=121, old_num=121) 015: 121 intersecting step 11 with no progress (num=121, old_num=121) 016: 121 intersecting step 12 with no progress (num=121, old_num=121) 017: 121 intersecting step 13 with no progress (num=121, old_num=121) 018: 121 intersecting step 14 with no progress (num=121, old_num=121) 019: 121 intersecting step 15 with no progress (num=121, old_num=121) 020: 121 intersecting step 16 with no progress (num=121, old_num=121) terminating search with 121 intersecting topology fixing took 3.9 minutes FSRUNTIME@ mris_fix_topology rh 0.0649 hours 1 threads #VMPC# mris_fix_topology VmPeak 0 \n mris_euler_number ../surf/lh.orig.premesh \n euler # = v-e+f = 2g-2: 74170 - 222504 + 148336 = 2 --> 0 holes F =2V-4: 148336 = 148340-4 (0) 2E=3F: 445008 = 445008 (0) total defect index = 0 \n mris_euler_number ../surf/rh.orig.premesh \n euler # = v-e+f = 2g-2: 143040 - 429114 + 286076 = 2 --> 0 holes F =2V-4: 286076 = 286080-4 (0) 2E=3F: 858228 = 858228 (0) total defect index = 0 Tue Feb 11 19:05:05 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts /Applications/freesurfer/8.0.0/bin/defect2seg --s sub-01 --cortex freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a defect2seg dev Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 19358 mri_label2label --label-cortex /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig.nofix /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/aseg.presurf.mgz 0 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 29 non-cortical segments detected only using segment with 8395 vertices erasing segment 0 (vno[0] = 2073) erasing segment 1 (vno[0] = 13946) erasing segment 2 (vno[0] = 23413) erasing segment 3 (vno[0] = 24370) erasing segment 4 (vno[0] = 25555) erasing segment 6 (vno[0] = 27631) erasing segment 7 (vno[0] = 28018) erasing segment 8 (vno[0] = 31967) erasing segment 9 (vno[0] = 33123) erasing segment 10 (vno[0] = 33404) erasing segment 11 (vno[0] = 38984) erasing segment 12 (vno[0] = 41587) erasing segment 13 (vno[0] = 41918) erasing segment 14 (vno[0] = 42782) erasing segment 15 (vno[0] = 42839) erasing segment 16 (vno[0] = 43914) erasing segment 17 (vno[0] = 45707) erasing segment 18 (vno[0] = 50707) erasing segment 19 (vno[0] = 53960) erasing segment 20 (vno[0] = 54268) erasing segment 21 (vno[0] = 61891) erasing segment 22 (vno[0] = 62158) erasing segment 23 (vno[0] = 63271) erasing segment 24 (vno[0] = 66017) erasing segment 25 (vno[0] = 67535) erasing segment 26 (vno[0] = 67753) erasing segment 27 (vno[0] = 69542) erasing segment 28 (vno[0] = 80695) mri_label2vol --defects /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig.nofix /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.defect_labels /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz 1000 0 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/surface.defects.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/lh.nofix.cortex.label supposed to be reproducible but seed not set Contraining to label /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/surface.defects.mgz mris_defects_pointset -s /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig.nofix -d /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.defect_labels -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.defects.pointset --label /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/lh.nofix.cortex.label Reading in surface /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig.nofix Reading in defect segmentation /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.defect_labels Reading in label /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 0 mris_defects_pointset done mri_label2label --label-cortex /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig.nofix /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/aseg.presurf.mgz 0 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 19 non-cortical segments detected only using segment with 7212 vertices erasing segment 0 (vno[0] = 43045) erasing segment 2 (vno[0] = 49698) erasing segment 3 (vno[0] = 53175) erasing segment 4 (vno[0] = 56315) erasing segment 5 (vno[0] = 58939) erasing segment 6 (vno[0] = 59468) erasing segment 7 (vno[0] = 59930) erasing segment 8 (vno[0] = 59937) erasing segment 9 (vno[0] = 64952) erasing segment 10 (vno[0] = 86137) erasing segment 11 (vno[0] = 101041) erasing segment 12 (vno[0] = 101103) erasing segment 13 (vno[0] = 102302) erasing segment 14 (vno[0] = 104820) erasing segment 15 (vno[0] = 108599) erasing segment 16 (vno[0] = 114436) erasing segment 17 (vno[0] = 115477) erasing segment 18 (vno[0] = 117348) mri_label2vol --defects /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig.nofix /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.defect_labels /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/surface.defects.mgz 2000 1 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/surface.defects.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/rh.nofix.cortex.label supposed to be reproducible but seed not set Contraining to label /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/surface.defects.mgz mris_defects_pointset -s /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig.nofix -d /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.defect_labels -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.defects.pointset --label /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/rh.nofix.cortex.label Reading in surface /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig.nofix Reading in defect segmentation /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.defect_labels Reading in label /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 0 mris_defects_pointset done Started at Tue Feb 11 19:05:05 CST 2025 Ended at Tue Feb 11 19:05:18 CST 2025 Defect2seg-Run-Time-Sec 13 Defect2seg-Run-Time-Min 0.26 Defect2seg-Run-Time-Hours 0.00 tkmeditfv sub-01 brain.finalsurfs.mgz -defect defect2seg Done \n mris_remesh --remesh --iters 3 --input /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig.premesh --output /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.orig \n iters = 3 standard remeshing without target adjusted l: 0.746063 remeshing to edge length 0.746063 with 3 iterations avg qual before : 0.875503 after: 0.969635 Removing intersections removing intersecting faces 000: 825 intersecting 001: 437 intersecting 002: 401 intersecting 003: 358 intersecting 004: 352 intersecting 005: 347 intersecting step 1 with no progress (num=347, old_num=347) 006: 347 intersecting step 2 with no progress (num=347, old_num=347) 007: 347 intersecting step 3 with no progress (num=347, old_num=347) 008: 347 intersecting step 4 with no progress (num=347, old_num=347) 009: 347 intersecting step 5 with no progress (num=347, old_num=347) 010: 347 intersecting step 6 with no progress (num=347, old_num=347) 011: 347 intersecting step 7 with no progress (num=347, old_num=347) 012: 347 intersecting step 8 with no progress (num=347, old_num=347) 013: 347 intersecting step 9 with no progress (num=347, old_num=347) 014: 347 intersecting step 10 with no progress (num=347, old_num=347) 015: 347 intersecting step 11 with no progress (num=347, old_num=347) 016: 347 intersecting step 12 with no progress (num=347, old_num=347) 017: 347 intersecting step 13 with no progress (num=347, old_num=347) 018: 347 intersecting step 14 with no progress (num=347, old_num=347) 019: 347 intersecting step 15 with no progress (num=347, old_num=347) 020: 347 intersecting step 16 with no progress (num=347, old_num=347) terminating search with 347 intersecting Remeshed surface quality stats nv0 = 74170 nv = 74544 1.00504 Area 149084 0.32866 0.04209 0.000104 0.7324 Corner 447252 60.00000 9.44614 0.018092 179.7353 Edge 223626 0.87979 0.09335 0.028760 1.7187 Hinge 223626 11.95045 13.44359 0.000000 179.6763 mris_remesh done \n mris_remesh --remesh --iters 3 --input /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig.premesh --output /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/rh.orig \n iters = 3 standard remeshing without target adjusted l: 0.720553 remeshing to edge length 0.720553 with 3 iterations avg qual before : 0.889687 after: 0.97142 Removing intersections removing intersecting faces 000: 402 intersecting 001: 306 intersecting 002: 286 intersecting 003: 284 intersecting 004: 282 intersecting step 1 with no progress (num=282, old_num=282) 005: 282 intersecting step 2 with no progress (num=282, old_num=282) 006: 282 intersecting step 3 with no progress (num=282, old_num=282) 007: 282 intersecting step 4 with no progress (num=282, old_num=282) 008: 282 intersecting step 5 with no progress (num=282, old_num=282) 009: 282 intersecting step 6 with no progress (num=282, old_num=282) 010: 282 intersecting step 7 with no progress (num=282, old_num=282) 011: 282 intersecting step 8 with no progress (num=282, old_num=282) 012: 282 intersecting step 9 with no progress (num=282, old_num=282) 013: 282 intersecting step 10 with no progress (num=282, old_num=282) 014: 282 intersecting step 11 with no progress (num=282, old_num=282) 015: 282 intersecting step 12 with no progress (num=282, old_num=282) 016: 282 intersecting step 13 with no progress (num=282, old_num=282) 017: 282 intersecting step 14 with no progress (num=282, old_num=282) 018: 282 intersecting step 15 with no progress (num=282, old_num=282) 019: 282 intersecting step 16 with no progress (num=282, old_num=282) terminating search with 282 intersecting Remeshed surface quality stats nv0 = 143040 nv = 149765 1.04701 Area 299526 0.31006 0.03485 0.000295 0.5109 Corner 898578 60.00000 8.81623 0.115635 178.7172 Edge 449289 0.85421 0.08367 0.051056 1.4574 Hinge 449289 9.71087 10.49087 0.000003 172.2772 mris_remesh done /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_remove_intersection ../surf/lh.orig ../surf/lh.orig \n intersection removal took 0.00 hours Found 389 intersections removing intersecting faces 000: 347 intersecting step 1 with no progress (num=347, old_num=347) 001: 347 intersecting step 2 with no progress (num=347, old_num=347) 002: 347 intersecting step 3 with no progress (num=347, old_num=347) 003: 347 intersecting step 4 with no progress (num=347, old_num=347) 004: 347 intersecting step 5 with no progress (num=347, old_num=347) 005: 347 intersecting step 6 with no progress (num=347, old_num=347) 006: 347 intersecting step 7 with no progress (num=347, old_num=347) 007: 347 intersecting step 8 with no progress (num=347, old_num=347) 008: 347 intersecting step 9 with no progress (num=347, old_num=347) 009: 347 intersecting step 10 with no progress (num=347, old_num=347) 010: 347 intersecting step 11 with no progress (num=347, old_num=347) 011: 347 intersecting step 12 with no progress (num=347, old_num=347) 012: 347 intersecting step 13 with no progress (num=347, old_num=347) 013: 347 intersecting step 14 with no progress (num=347, old_num=347) 014: 347 intersecting step 15 with no progress (num=347, old_num=347) 015: 347 intersecting step 16 with no progress (num=347, old_num=347) terminating search with 347 intersecting writing corrected surface to ../surf/lh.orig \n rm -f ../surf/lh.inflated \n /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/scripts \n mris_remove_intersection ../surf/rh.orig ../surf/rh.orig \n intersection removal took 0.00 hours Found 286 intersections removing intersecting faces 000: 282 intersecting step 1 with no progress (num=282, old_num=282) 001: 282 intersecting step 2 with no progress (num=282, old_num=282) 002: 282 intersecting step 3 with no progress (num=282, old_num=282) 003: 282 intersecting step 4 with no progress (num=282, old_num=282) 004: 282 intersecting step 5 with no progress (num=282, old_num=282) 005: 282 intersecting step 6 with no progress (num=282, old_num=282) 006: 282 intersecting step 7 with no progress (num=282, old_num=282) 007: 282 intersecting step 8 with no progress (num=282, old_num=282) 008: 282 intersecting step 9 with no progress (num=282, old_num=282) 009: 282 intersecting step 10 with no progress (num=282, old_num=282) 010: 282 intersecting step 11 with no progress (num=282, old_num=282) 011: 282 intersecting step 12 with no progress (num=282, old_num=282) 012: 282 intersecting step 13 with no progress (num=282, old_num=282) 013: 282 intersecting step 14 with no progress (num=282, old_num=282) 014: 282 intersecting step 15 with no progress (num=282, old_num=282) 015: 282 intersecting step 16 with no progress (num=282, old_num=282) terminating search with 282 intersecting writing corrected surface to ../surf/rh.orig \n rm -f ../surf/rh.inflated \n #-------------------------------------------- #@# AutoDetGWStats lh Tue Feb 11 19:06:05 CST 2025 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh dev cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 231717 voxels (1.38%) border gray 268831 voxels (1.60%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=16850, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (98.0): 97.4 +- 9.2 [70.0 --> 110.0] CCS GM (70.0) : 68.5 +- 13.9 [30.0 --> 110.0] white_mean = 97.364 +/- 9.24617, gray_mean = 68.4672 +/- 13.8669 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=101+-7.0, GM=57+-18.3 white_mode = 101, gray_mode = 57 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 43.1 (was 70.000000) setting MAX_BORDER_WHITE to 110.2 (was 105.000000) setting MIN_BORDER_WHITE to 57.0 (was 85.000000) setting MAX_CSF to 29.3 (was 40.000000) setting MAX_GRAY to 91.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 43.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 15.4 (was 40.000000) When placing the white surface white_border_hi = 110.246; white_border_low = 57; white_outside_low = 43.1331; white_inside_hi = 120; white_outside_hi = 110.246; When placing the pial surface pial_border_hi = 43.1331; pial_border_low = 15.3994; pial_outside_low = 10; pial_inside_hi = 91.7538; pial_outside_hi = 36.1997; #VMPC# mris_autodet_gwstats VmPeak 0 mris_autodet_gwstats done #-------------------------------------------- #@# AutoDetGWStats rh Tue Feb 11 19:06:07 CST 2025 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh dev cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 231717 voxels (1.38%) border gray 268831 voxels (1.60%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=16850, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (98.0): 97.4 +- 9.2 [70.0 --> 110.0] CCS GM (70.0) : 68.5 +- 13.9 [30.0 --> 110.0] white_mean = 97.364 +/- 9.24617, gray_mean = 68.4672 +/- 13.8669 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=103+-5.2, GM=69+-9.6 white_mode = 103, gray_mode = 69 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 55.1 (was 70.000000) setting MAX_BORDER_WHITE to 112.2 (was 105.000000) setting MIN_BORDER_WHITE to 69.0 (was 85.000000) setting MAX_CSF to 41.3 (was 40.000000) setting MAX_GRAY to 93.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 55.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 27.4 (was 40.000000) When placing the white surface white_border_hi = 112.246; white_border_low = 69; white_outside_low = 55.1331; white_inside_hi = 120; white_outside_hi = 112.246; When placing the pial surface pial_border_hi = 55.1331; pial_border_low = 27.3994; pial_outside_low = 10; pial_inside_hi = 93.7538; pial_outside_hi = 48.1997; #VMPC# mris_autodet_gwstats VmPeak 0 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Tue Feb 11 19:06:08 CST 2025 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --restore-255 --nsmooth 5 --rip-bg-no-annot --rip-bg --rip-bg-lof --restore-255 --outvol mrisps.wpa.mgz dev dev cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --restore-255 --nsmooth 5 --rip-bg-no-annot --rip-bg --rip-bg-lof --restore-255 --outvol mrisps.wpa.mgz Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations removing intersecting faces 000: 351 intersecting 001: 304 intersecting 002: 290 intersecting 003: 244 intersecting 004: 239 intersecting 005: 220 intersecting step 1 with no progress (num=226, old_num=220) 006: 226 intersecting step 2 with no progress (num=228, old_num=226) 007: 228 intersecting step 3 with no progress (num=234, old_num=228) 008: 234 intersecting 009: 223 intersecting step 1 with no progress (num=225, old_num=223) 010: 225 intersecting step 2 with no progress (num=225, old_num=225) 011: 225 intersecting step 3 with no progress (num=230, old_num=225) 012: 230 intersecting 013: 226 intersecting step 1 with no progress (num=227, old_num=226) 014: 227 intersecting step 2 with no progress (num=230, old_num=227) 015: 230 intersecting 016: 224 intersecting step 1 with no progress (num=227, old_num=224) 017: 227 intersecting step 2 with no progress (num=229, old_num=227) 018: 229 intersecting step 3 with no progress (num=229, old_num=229) 019: 229 intersecting step 4 with no progress (num=232, old_num=229) 020: 232 intersecting step 5 with no progress (num=248, old_num=232) 021: 248 intersecting 022: 246 intersecting 023: 245 intersecting 024: 239 intersecting step 1 with no progress (num=239, old_num=239) 025: 239 intersecting step 2 with no progress (num=239, old_num=239) 026: 239 intersecting step 3 with no progress (num=239, old_num=239) 027: 239 intersecting step 4 with no progress (num=239, old_num=239) 028: 239 intersecting step 5 with no progress (num=239, old_num=239) 029: 239 intersecting step 6 with no progress (num=239, old_num=239) 030: 239 intersecting step 7 with no progress (num=239, old_num=239) 031: 239 intersecting step 8 with no progress (num=239, old_num=239) 032: 239 intersecting step 9 with no progress (num=239, old_num=239) 033: 239 intersecting step 10 with no progress (num=239, old_num=239) 034: 239 intersecting step 11 with no progress (num=239, old_num=239) 035: 239 intersecting step 12 with no progress (num=239, old_num=239) 036: 239 intersecting step 13 with no progress (num=239, old_num=239) 037: 239 intersecting step 14 with no progress (num=239, old_num=239) 038: 239 intersecting step 15 with no progress (num=239, old_num=239) 039: 239 intersecting step 16 with no progress (num=239, old_num=239) terminating search with 220 intersecting Area 149084 0.27894 0.07589 0.000000 0.7578 Corner 447252 60.00000 11.32164 0.000112 179.9995 Edge 223626 0.80654 0.13522 0.000039 1.5835 Hinge 223626 7.50509 8.65374 0.000028 179.4040 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRItrack255() nhits = 1249 MRIclipBrightWM(): nthresh=16850, wmmin=5, clip=110 MRIfindBrightNonWM(): 2127 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Restoring 255->110 1249 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=4621, nmarked2=0, nripped=4621 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 66 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1 vertex 37272: xyz = (-36.8991,13.027,6.35333) oxyz = (-36.8991,13.027,6.35333) wxzy = (-36.8991,13.027,6.35333) pxyz = (0,0,0) CBVO Creating mask 74544 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=4687 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 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=4719, nmarked2=0, nripped=4719 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 0 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 = 110.2461700; border_low = 57.0000000; outside_low = 43.1331480; outside_hi = 110.2461700; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=74544 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=74544 Replacing 255s with 0s #SI# sigma=2 had to be increased for 3618 vertices, nripped=4719 mean border=74.6, 6672 (6672) missing vertices, mean dist 0.1 [1.3 (%40.4)->1.0 (%59.6))] %39 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0280 min Finding expansion regions mean absolute distance = 1.14 +- 1.53 2647 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 surface subiter 0 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=r5523, 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=6019906.5, rms=19.768 001: dt: 0.5000, sse=4372624.0, rms=16.359 (17.245%) 002: dt: 0.5000, sse=3177431.0, rms=13.999 (14.427%) 003: dt: 0.5000, sse=2620993.8, rms=12.516 (10.592%) 004: dt: 0.5000, sse=2273343.0, rms=11.612 (7.227%) 005: dt: 0.5000, sse=1987019.1, rms=11.009 (5.189%) 006: dt: 0.5000, sse=1882443.9, rms=10.596 (3.753%) 007: dt: 0.5000, sse=1805442.6, rms=10.291 (2.882%) 008: dt: 0.5000, sse=1760502.0, rms=10.067 (2.176%) 009: dt: 0.5000, sse=1719164.0, rms=9.871 (1.940%) 010: dt: 0.5000, sse=1585267.0, rms=9.731 (1.420%) rms = 9.5958/9.7313, sse=1636194.1/1585267.0, time step reduction 1 of 3 to 0.250 0 1 0 011: dt: 0.5000, sse=1636194.1, rms=9.596 (1.392%) 012: dt: 0.2500, sse=1465014.5, rms=9.007 (6.137%) 013: dt: 0.2500, sse=1361915.0, rms=8.832 (1.940%) 014: dt: 0.2500, sse=1321363.8, rms=8.753 (0.892%) 015: dt: 0.2500, sse=1242317.1, rms=8.685 (0.780%) rms = 8.6343/8.6851, sse=1287077.7/1242317.2, time step reduction 2 of 3 to 0.125 0 1 0 016: dt: 0.2500, sse=1287077.6, rms=8.634 (0.585%) 017: dt: 0.1250, sse=1276552.6, rms=8.520 (1.329%) rms = 8.4818/8.5196, sse=1369251.2/1276552.6, time step reduction 3 of 3 to 0.062 0 1 1 018: dt: 0.1250, sse=1369251.1, rms=8.482 (0.444%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface 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=4719 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 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=4939, nmarked2=0, nripped=4939 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 26 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 = 110.2461700; border_low = 57.0000000; outside_low = 43.1331480; outside_hi = 110.2461700; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=74544 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=74544 Replacing 255s with 0s #SI# sigma=1 had to be increased for 2032 vertices, nripped=4965 mean border=77.4, 6796 (5479) missing vertices, mean dist -0.3 [0.6 (%66.4)->0.3 (%33.6))] %40 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0194 min Finding expansion regions mean absolute distance = 0.49 +- 1.04 2054 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 surface subiter 0 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=r5523, 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=1863325.1, rms=10.338 019: dt: 0.5000, sse=1836292.2, rms=9.743 (5.761%) 020: dt: 0.5000, sse=1574955.8, rms=9.678 (0.661%) rms = 9.6288/9.6784, sse=1706163.4/1574955.7, time step reduction 1 of 3 to 0.250 0 1 1 021: dt: 0.5000, sse=1706163.4, rms=9.629 (0.512%) 022: dt: 0.2500, sse=1559268.2, rms=9.076 (5.745%) 023: dt: 0.2500, sse=1452028.5, rms=8.928 (1.630%) rms = 8.8529/8.9277, sse=1461571.8/1452028.5, time step reduction 2 of 3 to 0.125 0 1 0 024: dt: 0.2500, sse=1461571.9, rms=8.853 (0.837%) 025: dt: 0.1250, sse=1405728.5, rms=8.729 (1.395%) rms = 8.6827/8.7294, sse=1410215.1/1405728.6, time step reduction 3 of 3 to 0.062 0 1 1 026: dt: 0.1250, sse=1410215.1, rms=8.683 (0.536%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes done positioning surface 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=4965 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 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5055, nmarked2=0, nripped=5055 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 1 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 = 110.2461700; border_low = 57.0000000; outside_low = 43.1331480; outside_hi = 110.2461700; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=74544 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=74544 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 1307 vertices, nripped=5056 mean border=80.3, 6747 (5106) missing vertices, mean dist -0.3 [0.5 (%66.8)->0.3 (%33.2))] %51 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0109 min Finding expansion regions mean absolute distance = 0.43 +- 0.79 1716 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 surface subiter 0 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=r5523, 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=1769248.8, rms=10.149 027: dt: 0.5000, sse=1704992.2, rms=9.537 (6.033%) rms = 9.5535/9.5370, sse=1708213.2/1704992.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=1637629.0, rms=9.238 (3.137%) 029: dt: 0.2500, sse=1589119.0, rms=9.049 (2.042%) 030: dt: 0.2500, sse=1586967.2, rms=8.973 (0.841%) 031: dt: 0.2500, sse=1580882.8, rms=8.913 (0.669%) rms = 8.8714/8.9131, sse=1567134.7/1580882.7, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=1567134.8, rms=8.871 (0.467%) 033: dt: 0.1250, sse=1523363.8, rms=8.760 (1.254%) 034: dt: 0.1250, sse=1501908.9, rms=8.699 (0.701%) rms = 8.6586/8.6987, sse=1491851.2/1501908.9, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=1491851.2, rms=8.659 (0.461%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes done positioning surface 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=5056 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 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5133, nmarked2=0, nripped=5133 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 7 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 = 110.2461700; border_low = 57.0000000; outside_low = 43.1331480; outside_hi = 110.2461700; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=74544 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=74544 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 855 vertices, nripped=5140 mean border=82.1, 6877 (4929) missing vertices, mean dist -0.2 [0.4 (%62.2)->0.3 (%37.8))] %58 local maxima, %25 large gradients and % 1 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0075 min Finding expansion regions mean absolute distance = 0.34 +- 0.60 1953 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 surface subiter 0 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=r5523, 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=1610162.4, rms=9.196 rms = 9.0516/9.1964, sse=1632908.7/1610162.4, time step reduction 1 of 3 to 0.250 0 1 0 036: dt: 0.5000, sse=1632908.8, rms=9.052 (1.575%) 037: dt: 0.2500, sse=1541259.1, rms=8.727 (3.591%) 038: dt: 0.2500, sse=1521876.5, rms=8.648 (0.902%) rms = 8.6231/8.6479, sse=1493288.6/1521876.6, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=1493288.6, rms=8.623 (0.287%) 040: dt: 0.1250, sse=1489369.8, rms=8.465 (1.831%) rms = 8.4248/8.4652, sse=1456757.2/1489369.8, time step reduction 3 of 3 to 0.062 0 0 1 041: dt: 0.1250, sse=1456757.2, rms=8.425 (0.477%) maximum number of reductions reached, breaking from loop positioning took 0.1 minutes done positioning surface Removing intersections removing intersecting faces 000: 194 intersecting step 1 with no progress (num=256, old_num=194) 001: 256 intersecting 002: 216 intersecting step 1 with no progress (num=235, old_num=216) 003: 235 intersecting 004: 231 intersecting 005: 219 intersecting 006: 215 intersecting step 1 with no progress (num=217, old_num=215) 007: 217 intersecting step 2 with no progress (num=217, old_num=217) 008: 217 intersecting 009: 212 intersecting step 1 with no progress (num=221, old_num=212) 010: 221 intersecting 011: 214 intersecting step 1 with no progress (num=214, old_num=214) 012: 214 intersecting step 2 with no progress (num=214, old_num=214) 013: 214 intersecting 014: 213 intersecting step 1 with no progress (num=218, old_num=213) 015: 218 intersecting 016: 214 intersecting step 1 with no progress (num=221, old_num=214) 017: 221 intersecting step 2 with no progress (num=221, old_num=221) 018: 221 intersecting 019: 216 intersecting step 1 with no progress (num=228, old_num=216) 020: 228 intersecting 021: 217 intersecting step 1 with no progress (num=220, old_num=217) 022: 220 intersecting step 2 with no progress (num=220, old_num=220) 023: 220 intersecting 024: 219 intersecting step 1 with no progress (num=220, old_num=219) 025: 220 intersecting step 2 with no progress (num=224, old_num=220) 026: 224 intersecting step 3 with no progress (num=224, old_num=224) 027: 224 intersecting step 4 with no progress (num=224, old_num=224) 028: 224 intersecting step 5 with no progress (num=224, old_num=224) 029: 224 intersecting step 6 with no progress (num=224, old_num=224) 030: 224 intersecting step 7 with no progress (num=224, old_num=224) 031: 224 intersecting step 8 with no progress (num=224, old_num=224) 032: 224 intersecting step 9 with no progress (num=224, old_num=224) 033: 224 intersecting step 10 with no progress (num=224, old_num=224) 034: 224 intersecting step 11 with no progress (num=224, old_num=224) 035: 224 intersecting step 12 with no progress (num=224, old_num=224) 036: 224 intersecting step 13 with no progress (num=224, old_num=224) 037: 224 intersecting step 14 with no progress (num=224, old_num=224) 038: 224 intersecting step 15 with no progress (num=224, old_num=224) 039: 224 intersecting step 16 with no progress (num=224, old_num=224) terminating search with 194 intersecting #ET# mris_place_surface 1.05 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 0 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Tue Feb 11 19:07:26 CST 2025 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --restore-255 --nsmooth 5 --rip-bg-no-annot --rip-bg --rip-bg-lof --restore-255 --outvol mrisps.wpa.mgz dev dev cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --restore-255 --nsmooth 5 --rip-bg-no-annot --rip-bg --rip-bg-lof --restore-255 --outvol mrisps.wpa.mgz Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations removing intersecting faces 000: 244 intersecting 001: 207 intersecting 002: 186 intersecting 003: 173 intersecting step 1 with no progress (num=173, old_num=173) 004: 173 intersecting step 2 with no progress (num=173, old_num=173) 005: 173 intersecting step 3 with no progress (num=173, old_num=173) 006: 173 intersecting step 4 with no progress (num=173, old_num=173) 007: 173 intersecting step 5 with no progress (num=173, old_num=173) 008: 173 intersecting step 6 with no progress (num=173, old_num=173) 009: 173 intersecting step 7 with no progress (num=173, old_num=173) 010: 173 intersecting step 8 with no progress (num=173, old_num=173) 011: 173 intersecting step 9 with no progress (num=173, old_num=173) 012: 173 intersecting step 10 with no progress (num=173, old_num=173) 013: 173 intersecting step 11 with no progress (num=173, old_num=173) 014: 173 intersecting step 12 with no progress (num=173, old_num=173) 015: 173 intersecting step 13 with no progress (num=173, old_num=173) 016: 173 intersecting step 14 with no progress (num=173, old_num=173) 017: 173 intersecting step 15 with no progress (num=173, old_num=173) 018: 173 intersecting step 16 with no progress (num=173, old_num=173) terminating search with 173 intersecting Area 299526 0.27334 0.06460 0.003181 0.6077 Corner 898578 60.00000 9.60598 4.136776 167.6128 Edge 449289 0.79847 0.11600 0.056563 1.5849 Hinge 449289 6.45300 6.64941 0.000005 166.2641 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRItrack255() nhits = 1249 MRIclipBrightWM(): nthresh=16850, wmmin=5, clip=110 MRIfindBrightNonWM(): 2127 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Restoring 255->110 1249 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5165, nmarked2=0, nripped=5165 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 52 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1 vertex 74883: xyz = (24.6788,14.4301,24.4307) oxyz = (24.6788,14.4301,24.4307) wxzy = (24.6788,14.4301,24.4307) pxyz = (0,0,0) CBVO Creating mask 149765 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=5217 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5263, nmarked2=0, nripped=5263 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 0 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 = 112.2461700; border_low = 69.0000000; outside_low = 55.1331480; outside_hi = 112.2461700; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=149765 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=149765 Replacing 255s with 0s #SI# sigma=2 had to be increased for 750 vertices, nripped=5263 mean border=81.4, 935 (935) missing vertices, mean dist 0.1 [0.7 (%42.7)->0.8 (%57.3))] %55 local maxima, %40 large gradients and % 1 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0656 min Finding expansion regions mean absolute distance = 0.77 +- 0.98 4740 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 surface subiter 0 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=r5523, 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=6516112.0, rms=14.797 001: dt: 0.5000, sse=3692562.0, rms=10.972 (25.851%) 002: dt: 0.5000, sse=2207119.5, rms=8.263 (24.692%) 003: dt: 0.5000, sse=1476707.4, rms=6.486 (21.508%) 004: dt: 0.5000, sse=1191865.0, rms=5.498 (15.223%) 005: dt: 0.5000, sse=1061747.1, rms=4.937 (10.203%) 006: dt: 0.5000, sse=980277.2, rms=4.662 (5.584%) 007: dt: 0.5000, sse=953978.8, rms=4.476 (3.991%) 008: dt: 0.5000, sse=946361.3, rms=4.410 (1.475%) 009: dt: 0.5000, sse=926036.2, rms=4.332 (1.754%) rms = 4.2985/4.3323, sse=912125.3/926036.2, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=912125.3, rms=4.298 (0.782%) 011: dt: 0.2500, sse=666833.3, rms=3.298 (23.266%) 012: dt: 0.2500, sse=626062.9, rms=3.092 (6.243%) rms = 3.0395/3.0925, sse=636644.8/626063.0, time step reduction 2 of 3 to 0.125 0 1 0 013: dt: 0.2500, sse=636644.8, rms=3.039 (1.714%) 014: dt: 0.1250, sse=566702.0, rms=2.905 (4.430%) 015: dt: 0.1250, sse=545620.1, rms=2.853 (1.770%) rms = 2.8369/2.8534, sse=542791.2/545620.1, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=542791.2, rms=2.837 (0.579%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface 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=5263 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5340, nmarked2=0, nripped=5340 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 9 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 = 112.2461700; border_low = 69.0000000; outside_low = 55.1331480; outside_hi = 112.2461700; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=149765 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=149765 Replacing 255s with 0s #SI# sigma=1 had to be increased for 547 vertices, nripped=5349 mean border=83.6, 995 (438) missing vertices, mean dist -0.2 [0.4 (%66.4)->0.2 (%33.6))] %62 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0455 min Finding expansion regions mean absolute distance = 0.36 +- 0.71 3225 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 surface subiter 0 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=r5523, 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=1160290.4, rms=5.246 017: dt: 0.5000, sse=1007874.2, rms=4.115 (21.550%) 018: dt: 0.5000, sse=916258.3, rms=4.035 (1.950%) rms = 4.0297/4.0351, sse=926347.2/916258.3, time step reduction 1 of 3 to 0.250 0 1 1 019: dt: 0.5000, sse=926347.2, rms=4.030 (0.134%) 020: dt: 0.2500, sse=719649.8, rms=3.157 (21.668%) 021: dt: 0.2500, sse=649232.0, rms=2.987 (5.372%) rms = 2.9449/2.9870, sse=651126.0/649232.0, time step reduction 2 of 3 to 0.125 0 1 1 022: dt: 0.2500, sse=651126.0, rms=2.945 (1.409%) 023: dt: 0.1250, sse=622662.2, rms=2.838 (3.622%) rms = 2.7899/2.8382, sse=630949.0/622662.2, time step reduction 3 of 3 to 0.062 0 1 1 024: dt: 0.1250, sse=630949.0, rms=2.790 (1.704%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface 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=5349 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 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5432, nmarked2=0, nripped=5432 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 11 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 = 112.2461700; border_low = 69.0000000; outside_low = 55.1331480; outside_hi = 112.2461700; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=149765 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=149765 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 423 vertices, nripped=5443 mean border=86.1, 985 (332) missing vertices, mean dist -0.2 [0.4 (%71.8)->0.2 (%28.2))] %73 local maxima, %22 large gradients and % 1 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0254 min Finding expansion regions mean absolute distance = 0.31 +- 0.52 3773 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 surface subiter 0 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=r5523, 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=1032828.9, rms=4.677 025: dt: 0.5000, sse=852780.9, rms=3.881 (17.015%) rms = 3.8940/3.8812, sse=887164.5/852780.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=746475.1, rms=3.303 (14.892%) 027: dt: 0.2500, sse=666729.1, rms=3.038 (8.044%) rms = 2.9377/3.0375, sse=674501.1/666729.1, time step reduction 2 of 3 to 0.125 0 1 0 028: dt: 0.2500, sse=674501.1, rms=2.938 (3.287%) 029: dt: 0.1250, sse=624384.8, rms=2.831 (3.631%) 030: dt: 0.1250, sse=599221.8, rms=2.775 (1.973%) rms = 2.7480/2.7751, sse=559753.8/599221.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=559753.8, rms=2.748 (0.977%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface 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=5443 removing 2 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 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5514, nmarked2=0, nripped=5514 Ripping BG MRISripBasalGanglia(): 0 -2 2 0.5 MRISripBasalGanglia(): 0 -2 2 0.5 ripped 6 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 = 112.2461700; border_low = 69.0000000; outside_low = 55.1331480; outside_hi = 112.2461700; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=149765 Gdiag_no=-1 VMPeak = 0 vno start=0, stop=149765 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 329 vertices, nripped=5520 mean border=87.1, 1057 (291) missing vertices, mean dist -0.1 [0.3 (%60.9)->0.2 (%39.1))] %79 local maxima, %16 large gradients and % 1 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0167 min Finding expansion regions mean absolute distance = 0.25 +- 0.41 4107 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 surface subiter 0 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=r5523, 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=658425.2, rms=3.336 rms = 3.3582/3.3365, sse=707923.4/658425.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=586442.4, rms=2.980 (10.682%) rms = 2.7478/2.9801, sse=601917.7/586442.4, time step reduction 2 of 3 to 0.125 0 1 0 033: dt: 0.2500, sse=601917.7, rms=2.748 (7.796%) 034: dt: 0.1250, sse=584627.8, rms=2.693 (1.995%) rms = 2.6534/2.6930, sse=588950.8/584627.7, time step reduction 3 of 3 to 0.062 0 1 1 035: dt: 0.1250, sse=588950.8, rms=2.653 (1.470%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes done positioning surface Removing intersections removing intersecting faces 000: 173 intersecting step 1 with no progress (num=210, old_num=173) 001: 210 intersecting step 2 with no progress (num=210, old_num=210) 002: 210 intersecting 003: 200 intersecting 004: 191 intersecting 005: 184 intersecting 006: 178 intersecting step 1 with no progress (num=191, old_num=178) 007: 191 intersecting 008: 172 intersecting step 1 with no progress (num=172, old_num=172) 009: 172 intersecting step 2 with no progress (num=172, old_num=172) 010: 172 intersecting step 3 with no progress (num=172, old_num=172) 011: 172 intersecting step 4 with no progress (num=172, old_num=172) 012: 172 intersecting step 5 with no progress (num=172, old_num=172) 013: 172 intersecting step 6 with no progress (num=172, old_num=172) 014: 172 intersecting step 7 with no progress (num=172, old_num=172) 015: 172 intersecting step 8 with no progress (num=172, old_num=172) 016: 172 intersecting step 9 with no progress (num=172, old_num=172) 017: 172 intersecting step 10 with no progress (num=172, old_num=172) 018: 172 intersecting step 11 with no progress (num=172, old_num=172) 019: 172 intersecting step 12 with no progress (num=172, old_num=172) 020: 172 intersecting step 13 with no progress (num=172, old_num=172) 021: 172 intersecting step 14 with no progress (num=172, old_num=172) 022: 172 intersecting step 15 with no progress (num=172, old_num=172) 023: 172 intersecting step 16 with no progress (num=172, old_num=172) terminating search with 172 intersecting #ET# mris_place_surface 1.83 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 0 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Tue Feb 11 19:09:30 CST 2025 Tue Feb 11 19:09:31 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri /Applications/freesurfer/8.0.0/bin/label-cortex --s sub-01 --lh --fix-ga -rwxr-xr-x 1 root wheel 14140 Feb 5 03:54 /Applications/freesurfer/8.0.0/bin/label-cortex freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 19843 mri_label2label --label-cortex /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/aseg.presurf.mgz 0 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.cortex-no-ga.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 15 non-cortical segments detected only using segment with 6250 vertices erasing segment 0 (vno[0] = 19294) erasing segment 2 (vno[0] = 23328) erasing segment 3 (vno[0] = 23733) erasing segment 4 (vno[0] = 25047) erasing segment 5 (vno[0] = 27251) erasing segment 6 (vno[0] = 27793) erasing segment 7 (vno[0] = 31617) erasing segment 8 (vno[0] = 32716) erasing segment 9 (vno[0] = 37019) erasing segment 10 (vno[0] = 39385) erasing segment 11 (vno[0] = 39387) erasing segment 12 (vno[0] = 39741) erasing segment 13 (vno[0] = 39954) erasing segment 14 (vno[0] = 59960) mri_binarize --match 3201 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/entowm.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/gyrus-ambiens.lh.mgz dev cwd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri cmdline mri_binarize --match 3201 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/entowm.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/gyrus-ambiens.lh.mgz sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe input /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/entowm.mgz frame 0 nErode3d 0 nErode2d 0 output /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/gyrus-ambiens.lh.mgz Binarizing based on matching values nMatch 1 0 3201 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 262 values in range Counting number of voxels in first frame Found 262 voxels in final mask Writing output to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/gyrus-ambiens.lh.mgz Count: 262 262.000000 16777216 0.001562 mri_binarize done mri_vol2surf --regheader sub-01 --hemi lh --surf white.preaparc --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/gyrus-ambiens.lh.mgz --projdist-max -1 0 .1 --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz INFO: Delta=0.1 > Max=0, may be ok, maybe not srcvol = /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/gyrus-ambiens.lh.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white.preaparc hemi = lh ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 0 0.1 1 -1 -1 0 using old 2 -0.9 -1 0 using old 3 -0.8 -1 0 using old 4 -0.7 -1 0 using old 5 -0.6 -1 0 using old 6 -0.5 -1 0 using old 7 -0.4 -1 0 using old 8 -0.3 -1 0 using old 9 -0.2 -1 0 using old 10 -0.0999999 -1 0 using old Done mapping volume to surface Number of source voxels hit = 50662 Writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz Dim: 74544 1 1 mri_vol2surf done mris_convert --to-scanner -n /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz mris_convert --to-scanner -n /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz Reading in /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc Converting surface XYZ coordinates from tkr to scanner space. Outputting normals /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz mri_binarize --frame 0 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz --mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz --min +0.01 dev cwd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri cmdline mri_binarize --frame 0 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz --mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz --min +0.01 sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe input /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz frame 0 nErode3d 0 nErode2d 0 output /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz maskthresh 0.500000 Loading mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Writing output to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz Count: 0 0.000000 74544 0.000000 mri_binarize done mri_binarize --frame 2 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz --mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz --max -0.01 dev cwd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri cmdline mri_binarize --frame 2 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz --mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz --max -0.01 sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe input /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.white.preaparc.nxyz.mgz frame 2 nErode3d 0 nErode2d 0 output /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz Binarizing based on threshold min -infinity max -0.01 binval 1 binvalnot 0 mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz maskthresh 0.500000 Loading mask /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.mgz fstart = 2, fend = 2, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Writing output to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz Count: 0 0.000000 74544 0.000000 mri_binarize done fscalc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz and /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz Tue Feb 11 19:09:36 CST 2025 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/mri /Applications/freesurfer/8.0.0/bin/fscalc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz and /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nx.mask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh... ---------------------- mris_calc -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh and /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.nz.mask.mgz Packing Done packing Packing Done packing Unpacking Saving result to '/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 0 ---------------------- mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/tmp.AAfmW2/tmp.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz... mri_cor2label --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz --l /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.med.label --surf-path /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc --id 1 --thresh 0.5 Loading mri /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/label/tmpdir.label-cortex.19843/lh.gyrus-ambiens.lat.mask.mgz dev ------- Vox2RAS of input volume ----------- -1.00000 0.00000 0.00000 37272.00000; 0.00000 0.00000 1.00000 -0.50000; 0.00000 -1.00000 0.00000 0.50000; 0.00000 0.00000 0.00000 1.00000; Scanning the volume Loading surf /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparc Found 0 label voxels ERROR: found no voxels matching id 1 ERROR: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-01 exited with ERRORS at Tue Feb 11 19:09:36 CST 2025 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting