Mon Jan 9 11:06:46 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/recon-all -s Test -i Test1/t1.nii.gz -T2 Test1/t2.nii.gz -all -parallel subjid Test setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Actual FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 8223025 kbytes maxproc 256519 maxlocks unlimited maxsignal 256519 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 62Gi 8.9Gi 658Mi 93Mi 53Gi 53Gi Swap: 976Mi 108Mi 868Mi ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) 7.2.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.2.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/01/09-10:06:46-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: brainstimmaps Machine: sharky Platform: Linux PlatformVersion: 5.10.0-20-amd64 CompilerName: GCC CompilerVersion: 4.8.5 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test1/t1.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/001.mgz mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test1/t1.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/001.mgz reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test1/t1.nii.gz... INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00130218, -0.999999, 0.000694773) j_ras = (0.0980031, -0.000563811, -0.995186) k_ras = (0.995185, 0.001364, 0.0980023) writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Mon Jan 9 11:06:48 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test mri_convert --no_scale 1 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test1/t2.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz mri_convert --no_scale 1 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test1/t2.nii.gz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test1/t2.nii.gz... INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00118486, -0.999997, 0.00188591) j_ras = (0.0980046, -0.00176071, -0.995184) k_ras = (0.995185, 0.00136398, 0.0980023) writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Mon Jan 9 11:06:50 CET 2023 Found 1 runs /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/001.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz --conform mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz --conform reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00130218, -0.999999, 0.000694773) j_ras = (0.0980031, -0.000563811, -0.995186) k_ras = (0.995185, 0.001364, 0.0980023) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 2141 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz... mri_add_xform_to_header -c /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/talairach.xfm /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jan 9 11:06:59 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.2.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux Mon Jan 9 11:06:59 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.319120 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.319120/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.319120/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.319120/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.319120/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 5.82077e-11) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Mon Jan 9 11:09:20 CET 2023 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Jan 9 11:09:20 CET 2023 Ended at Mon Jan 9 11:10:23 CET 2023 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.2.0 --src: orig.mgz src image (geometry). --trg: /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.29835 -0.05142 0.13846 -2.79659; -0.04885 1.08246 0.60331 -2.39490; -0.11777 -0.64842 1.22302 -38.72926; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Mon Jan 9 11:10:25 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2877, pval=0.0254 >= threshold=0.0050) awk -f /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/extract_talairach_avi_QA.awk /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/talairach_avi.log tal_QC_AZS /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/talairach_avi.log TalAviQA: 0.96375 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Mon Jan 9 11:10:26 CET 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.2.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux Mon Jan 9 11:10:26 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.319394 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.319394/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.319394/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.319394/ones.mgz 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.319394/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.319394/ones.mgz sysname Linux hostname sharky machine x86_64 user brainstimmaps input ./tmp.mri_nu_correct.mni.319394/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.319394/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.319394/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.319394/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.319394/sum.junk --avgwf ./tmp.mri_nu_correct.mni.319394/input.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.319394/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.319394/sum.junk --avgwf ./tmp.mri_nu_correct.mni.319394/input.mean.dat sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.319394/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.319394/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.319394/ones.mgz --i ./tmp.mri_nu_correct.mni.319394/nu0.mgz --sum ./tmp.mri_nu_correct.mni.319394/sum.junk --avgwf ./tmp.mri_nu_correct.mni.319394/output.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.319394/ones.mgz --i ./tmp.mri_nu_correct.mni.319394/nu0.mgz --sum ./tmp.mri_nu_correct.mni.319394/sum.junk --avgwf ./tmp.mri_nu_correct.mni.319394/output.mean.dat sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.319394/ones.mgz Loading ./tmp.mri_nu_correct.mni.319394/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.319394/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.319394/nu0.mgz ./tmp.mri_nu_correct.mni.319394/nu0.mgz mul 1.19718070388619721578 Saving result to './tmp.mri_nu_correct.mni.319394/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.319394/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.319394/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.319394/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 5.82077e-11) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 5 seconds. mapping (27, 104) to ( 3, 110) Mon Jan 9 11:13:07 CET 2023 mri_nu_correct.mni done mri_add_xform_to_header -c /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Jan 9 11:13:07 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.29835 -0.05142 0.13846 -2.79659; -0.04885 1.08246 0.60331 -2.39490; -0.11777 -0.64842 1.22302 -38.72926; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 85 (85), valley at 58 (58) csf peak at 15, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 80 (80), valley at 41 (41) csf peak at 13, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 3 seconds. #-------------------------------------------- #@# Skull Stripping Mon Jan 9 11:14:11 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_em_register -skull nu.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=41.0 skull bounding box = (59, 23, 16) --> (202, 255, 237) finding center of left hemi white matter using (107, 100, 127) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (89,71,100) --> (124, 128,154) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 105 +- 8.2 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.705 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.683581 @ (-10.526, 10.526, -10.526) max log p = -4.646956 @ (5.263, 5.263, 5.263) max log p = -4.613106 @ (-2.632, -7.895, 2.632) max log p = -4.594662 @ (-1.316, 6.579, -1.316) max log p = -4.579548 @ (0.658, -8.553, 1.974) max log p = -4.579548 @ (0.000, 0.000, 0.000) max log p = -4.579548 @ (0.000, 0.000, 0.000) max log p = -4.579548 @ (0.000, 0.000, 0.000) Found translation: (-8.6, 5.9, -2.0): log p = -4.580 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.265, old_max_log_p =-4.580 (thresh=-4.6) 1.14016 0.13740 0.05966 -43.05135; -0.16136 1.12194 0.48712 -18.79495; 0.00000 -0.36573 0.93367 49.92541; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.250, old_max_log_p =-4.265 (thresh=-4.3) 1.05465 0.12710 0.05518 -30.43981; -0.16136 1.12194 0.48712 -18.79495; 0.00000 -0.39316 1.00369 45.33225; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.250, old_max_log_p =-4.250 (thresh=-4.2) 1.05465 0.12710 0.05518 -30.43981; -0.16136 1.12194 0.48712 -18.79495; 0.00000 -0.39316 1.00369 45.33225; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.196, old_max_log_p =-4.250 (thresh=-4.2) 1.12497 0.03639 -0.02837 -23.45767; -0.05244 1.07440 0.50190 -32.68821; 0.04334 -0.41126 0.95041 45.60533; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 15 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.194, old_max_log_p =-4.196 (thresh=-4.2) 1.12270 0.07106 -0.01092 -29.16448; -0.08942 1.07846 0.54337 -33.00732; 0.04419 -0.43782 0.91598 50.60607; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 14 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.173, old_max_log_p =-4.194 (thresh=-4.2) 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 14 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.173, old_max_log_p =-4.173 (thresh=-4.2) 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.173 (old=-4.705) transform before final EM align: 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.11601 0.09244 0.03648 -35.26467; -0.12669 1.08175 0.52678 -26.58919; 0.00599 -0.42371 0.92786 53.56373; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 807224 FSRUNTIME@ mri_em_register 0.0383 hours 4 threads registration took 2 minutes and 18 seconds. mri_watershed -T1 -brain_atlas /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=132 y=99 z=105 r=86 first estimation of the main basin volume: 2667298 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=116, y=91, z=64, Imax=255 CSF=22, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=8496177186 voxels, voxel volume =1.000 = 8496177186 mmm3 = 8496177.152 cm3 done. PostAnalyze...Basin Prior 1339 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=131,y=102, z=99, r=9057 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 44046 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 3006 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2502 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 18954 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 19044 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=20 , nb = 540 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 5, 53, 76 after analyzing : 3, 37, 53, 46 RIGHT_CER before analyzing : 4, 6, 53, 92 after analyzing : 4, 37, 53, 50 LEFT_CER before analyzing : 3, 5, 62, 90 after analyzing : 3, 43, 62, 54 RIGHT_BRAIN before analyzing : 3, 5, 53, 76 after analyzing : 3, 37, 53, 46 LEFT_BRAIN before analyzing : 3, 5, 54, 76 after analyzing : 3, 37, 54, 46 OTHER before analyzing : 20, 30, 65, 95 after analyzing : 20, 53, 65, 63 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.012 curvature mean = 66.514, std = 8.193 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.59, sigma = 12.74 after rotation: sse = 5.59, sigma = 12.74 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.50, its var is 22.70 before Erosion-Dilatation 9.22% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...35 iterations mri_strip_skull: done peeling brain Brain Size = 1392599 voxels, voxel volume = 1.000 mm3 = 1392599 mmm3 = 1392.599 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 15.920219 mri_watershed stimesec 0.253340 mri_watershed ru_maxrss 812216 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 188189 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2104 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 375 mri_watershed ru_nivcsw 40 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Jan 9 11:16:40 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (69, 41, 37) --> (194, 171, 175) finding center of left hemi white matter using (111, 84, 106) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (96,68,89) --> (126, 99,122) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 4.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.334 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.215806 @ (-10.526, 10.526, -10.526) max log p = -4.037384 @ (5.263, 5.263, 5.263) max log p = -4.037384 @ (0.000, 0.000, 0.000) max log p = -4.035995 @ (-1.316, -1.316, 1.316) max log p = -4.009858 @ (0.658, 1.974, -0.658) max log p = -4.009858 @ (0.000, 0.000, 0.000) max log p = -4.009858 @ (0.000, 0.000, 0.000) max log p = -4.009858 @ (0.000, 0.000, 0.000) Found translation: (-5.9, 16.4, -4.6): log p = -4.010 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.669, old_max_log_p =-4.010 (thresh=-4.0) 1.14016 0.12059 0.04995 -42.67701; -0.16136 0.98467 0.40787 -0.02242; 0.00000 -0.38268 0.92388 50.49792; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 14 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.612, old_max_log_p =-3.669 (thresh=-3.7) 1.14016 0.12059 0.04995 -42.67701; -0.18557 1.13237 0.46905 -17.91932; 0.00000 -0.38268 0.92388 50.49792; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 14 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.612, old_max_log_p =-3.612 (thresh=-3.6) 1.14016 0.12059 0.04995 -42.67701; -0.18557 1.13237 0.46905 -17.91932; 0.00000 -0.38268 0.92388 50.49792; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.547, old_max_log_p =-3.612 (thresh=-3.6) 1.12827 0.04717 0.01499 -28.25086; -0.10607 1.06880 0.51070 -26.32786; 0.01259 -0.47302 0.92465 57.87077; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.533, old_max_log_p =-3.547 (thresh=-3.5) 1.10623 0.06031 -0.01550 -23.58337; -0.10643 1.08371 0.48018 -24.69410; 0.04603 -0.43602 0.94085 48.08654; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.533, old_max_log_p =-3.533 (thresh=-3.5) 1.10623 0.06031 -0.01550 -23.58337; -0.10643 1.08371 0.48018 -24.69410; 0.04603 -0.43602 0.94085 48.08654; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.521, old_max_log_p =-3.533 (thresh=-3.5) 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 13 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.521, old_max_log_p =-3.521 (thresh=-3.5) 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.521 (old=-4.334) transform before final EM align: 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.0 tol 0.000000 final transform: 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 794664 FSRUNTIME@ mri_em_register 0.0369 hours 4 threads registration took 2 minutes and 13 seconds. #-------------------------------------- #@# CA Normalize Mon Jan 9 11:18:53 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (69, 41, 37) --> (194, 171, 175) finding center of left hemi white matter using (111, 84, 106) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (96,68,89) --> (126, 99,122) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 4.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.11217 0.03154 -0.04637 -18.33589; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21300; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 44, 31) --> (190, 154, 186) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 3803 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (73, 42, 32) --> (135, 144, 187) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 1 of 4230 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 123, 63) --> (174, 166, 114) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 25 of 90 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (90, 123, 62) --> (130, 161, 115) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 1 of 31 (3.2%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (116, 110, 94) --> (147, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 60 (0.0%) samples deleted using 8214 total control points for intensity normalization... bias field = 0.984 +- 0.055 78 of 8187 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 44, 31) --> (190, 154, 186) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 4071 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (73, 42, 32) --> (135, 144, 187) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 4464 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 123, 63) --> (174, 166, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 164 (9.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (90, 123, 62) --> (130, 161, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 100 (15.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (116, 110, 94) --> (147, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 48 of 119 (40.3%) samples deleted using 8918 total control points for intensity normalization... bias field = 1.021 +- 0.059 0 of 8747 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 44, 31) --> (190, 154, 186) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 4048 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (73, 42, 32) --> (135, 144, 187) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 4440 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 123, 63) --> (174, 166, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 162 (13.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (90, 123, 62) --> (130, 161, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 53 of 116 (45.7%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (116, 110, 94) --> (147, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 149 of 216 (69.0%) samples deleted using 8982 total control points for intensity normalization... bias field = 1.017 +- 0.055 2 of 8554 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 16 seconds. #-------------------------------------- #@# CA Reg Mon Jan 9 11:20:09 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.973061 #FOTS# QuadFit found better minimum quadopt=(dt=232.21,rms=0.920212) vs oldopt=(dt=369.92,rms=0.933193) #GCMRL# 0 dt 232.210101 rms 0.920 5.431% neg 0 invalid 762 tFOTS 7.1820 tGradient 3.2030 tsec 10.7840 #FOTS# QuadFit found better minimum quadopt=(dt=405.743,rms=0.897842) vs oldopt=(dt=369.92,rms=0.897895) #GCMRL# 1 dt 405.743274 rms 0.898 2.431% neg 0 invalid 762 tFOTS 7.3300 tGradient 3.0960 tsec 10.9520 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.894447) vs oldopt=(dt=92.48,rms=0.894501) #GCMRL# 2 dt 110.976000 rms 0.894 0.378% neg 0 invalid 762 tFOTS 7.3590 tGradient 2.7960 tsec 10.6790 #GCMRL# 3 dt 369.920000 rms 0.893 0.000% neg 0 invalid 762 tFOTS 7.3450 tGradient 2.1880 tsec 10.0720 #GCMRL# 4 dt 369.920000 rms 0.888 0.560% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1860 tsec 2.5770 #GCMRL# 5 dt 369.920000 rms 0.884 0.398% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2070 tsec 2.5980 #GCMRL# 6 dt 369.920000 rms 0.883 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1520 tsec 2.5440 #GCMRL# 7 dt 369.920000 rms 0.882 0.196% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2050 tsec 2.7160 #GCMRL# 8 dt 369.920000 rms 0.881 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2390 tsec 2.6440 #GCMRL# 9 dt 369.920000 rms 0.880 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1420 tsec 2.5340 #GCMRL# 10 dt 369.920000 rms 0.880 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1800 tsec 2.5950 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.879021) vs oldopt=(dt=92.48,rms=0.879022) #GCMRL# 11 dt 73.984000 rms 0.879 0.000% neg 0 invalid 762 tFOTS 5.2570 tGradient 2.1380 tsec 7.8110 #GCMRL# 12 dt 73.984000 rms 0.879 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2250 tsec 2.7390 #GCMRL# 13 dt 73.984000 rms 0.879 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2290 tsec 2.6210 #GCMRL# 14 dt 73.984000 rms 0.879 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1930 tsec 2.5860 #GCMRL# 15 dt 73.984000 rms 0.878 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2530 tsec 2.6590 #GCMRL# 16 dt 73.984000 rms 0.877 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2640 tsec 2.6560 #GCAMreg# pass 0 level1 5 level2 1 tsec 92.797 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.877305 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.874722) vs oldopt=(dt=92.48,rms=0.875015) #GCMRL# 18 dt 129.472000 rms 0.875 0.294% neg 0 invalid 762 tFOTS 5.2560 tGradient 2.1410 tsec 7.7940 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.874395) vs oldopt=(dt=92.48,rms=0.874428) #GCMRL# 19 dt 129.472000 rms 0.874 0.000% neg 0 invalid 762 tFOTS 5.3340 tGradient 2.1670 tsec 7.9240 #GCMRL# 20 dt 129.472000 rms 0.874 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1490 tsec 2.5440 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.887705 #FOTS# QuadFit found better minimum quadopt=(dt=65.2736,rms=0.881811) vs oldopt=(dt=103.68,rms=0.883454) #GCMRL# 22 dt 65.273632 rms 0.882 0.664% neg 0 invalid 762 tFOTS 5.3270 tGradient 1.9050 tsec 7.6300 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.865784) vs oldopt=(dt=414.72,rms=0.870859) #GCMRL# 23 dt 248.832000 rms 0.866 1.818% neg 0 invalid 762 tFOTS 5.2970 tGradient 1.9040 tsec 7.5990 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.864406) vs oldopt=(dt=25.92,rms=0.864428) #GCMRL# 24 dt 31.104000 rms 0.864 0.000% neg 0 invalid 762 tFOTS 7.2240 tGradient 1.7850 tsec 9.5680 #GCMRL# 25 dt 31.104000 rms 0.864 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8700 tsec 2.3880 #GCAMreg# pass 0 level1 4 level2 1 tsec 37.511 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.864497 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.86245) vs oldopt=(dt=25.92,rms=0.862702) #GCMRL# 27 dt 36.288000 rms 0.862 0.237% neg 0 invalid 762 tFOTS 7.3010 tGradient 1.8780 tsec 9.6960 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.862379) vs oldopt=(dt=6.48,rms=0.862397) #GCMRL# 28 dt 9.072000 rms 0.862 0.000% neg 0 invalid 762 tFOTS 6.9260 tGradient 1.8960 tsec 9.2370 #GCMRL# 29 dt 9.072000 rms 0.862 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9160 tsec 2.4210 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.885462 #FOTS# QuadFit found better minimum quadopt=(dt=13.2857,rms=0.881217) vs oldopt=(dt=8,rms=0.881623) #GCMRL# 31 dt 13.285714 rms 0.881 0.479% neg 0 invalid 762 tFOTS 5.9400 tGradient 1.7950 tsec 8.1330 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.87691) vs oldopt=(dt=32,rms=0.87713) #GCMRL# 32 dt 38.400000 rms 0.877 0.489% neg 0 invalid 762 tFOTS 7.0230 tGradient 1.7550 tsec 9.1790 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.873796) vs oldopt=(dt=32,rms=0.874021) #GCMRL# 33 dt 44.800000 rms 0.874 0.355% neg 0 invalid 762 tFOTS 7.0800 tGradient 1.8230 tsec 9.3100 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.873665) vs oldopt=(dt=8,rms=0.873671) #GCMRL# 34 dt 6.400000 rms 0.874 0.000% neg 0 invalid 762 tFOTS 6.6170 tGradient 1.7570 tsec 8.7880 #GCMRL# 35 dt 6.400000 rms 0.874 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7190 tsec 2.2170 #GCAMreg# pass 0 level1 3 level2 1 tsec 48.05 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.874052 #GCMRL# 37 dt 0.000000 rms 0.874 0.047% neg 0 invalid 762 tFOTS 5.7730 tGradient 1.6660 tsec 7.8440 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.905529 #FOTS# QuadFit found better minimum quadopt=(dt=0.216,rms=0.90508) vs oldopt=(dt=0.18,rms=0.905081) #GCMRL# 39 dt 0.216000 rms 0.905 0.049% neg 0 invalid 762 tFOTS 6.6890 tGradient 1.7280 tsec 8.8210 #FOTS# QuadFit found better minimum quadopt=(dt=0.063,rms=0.905074) vs oldopt=(dt=0.045,rms=0.905075) #GCMRL# 40 dt 0.063000 rms 0.905 0.000% neg 0 invalid 762 tFOTS 6.3320 tGradient 1.6890 tsec 8.4360 #GCAMreg# pass 0 level1 2 level2 1 tsec 27.579 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.905469 #FOTS# QuadFit found better minimum quadopt=(dt=0.00675,rms=0.905075) vs oldopt=(dt=0.01125,rms=0.905075) #GCMRL# 42 dt 0.006750 rms 0.905 0.043% neg 0 invalid 762 tFOTS 6.4400 tGradient 1.6760 tsec 8.5200 #FOTS# QuadFit found better minimum quadopt=(dt=0.000421875,rms=0.905076) vs oldopt=(dt=0.000703125,rms=0.905076) setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.965325 #FOTS# QuadFit found better minimum quadopt=(dt=0.505076,rms=0.957562) vs oldopt=(dt=0.32,rms=0.958943) #GCMRL# 44 dt 0.505076 rms 0.958 0.804% neg 0 invalid 762 tFOTS 6.6040 tGradient 1.5880 tsec 8.5910 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.953522) vs oldopt=(dt=0.32,rms=0.953867) #GCMRL# 45 dt 0.448000 rms 0.954 0.422% neg 0 invalid 762 tFOTS 5.7500 tGradient 1.6160 tsec 7.7660 #GCMRL# 46 dt 0.320000 rms 0.950 0.331% neg 0 invalid 762 tFOTS 5.7830 tGradient 1.6230 tsec 7.8070 #GCMRL# 47 dt 0.320000 rms 0.949 0.000% neg 0 invalid 762 tFOTS 6.7490 tGradient 1.6500 tsec 8.8250 #GCMRL# 48 dt 0.320000 rms 0.947 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6140 tsec 2.1530 #GCMRL# 49 dt 0.320000 rms 0.945 0.216% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6210 tsec 2.1520 #GCMRL# 50 dt 0.320000 rms 0.943 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6770 tsec 2.2050 #GCMRL# 51 dt 0.320000 rms 0.943 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6730 tsec 2.2240 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.940839) vs oldopt=(dt=0.32,rms=0.941091) #GCMRL# 52 dt 0.448000 rms 0.941 0.204% neg 0 invalid 762 tFOTS 6.2160 tGradient 1.6650 tsec 8.2790 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.94038) vs oldopt=(dt=0.08,rms=0.940467) #GCMRL# 53 dt 0.112000 rms 0.940 0.000% neg 0 invalid 762 tFOTS 6.7070 tGradient 1.6310 tsec 8.7580 #GCMRL# 54 dt 0.112000 rms 0.940 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5860 tsec 2.0470 #GCMRL# 55 dt 0.112000 rms 0.940 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6230 tsec 2.1460 #GCMRL# 56 dt 0.112000 rms 0.939 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5820 tsec 2.0440 #GCMRL# 57 dt 0.112000 rms 0.939 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5590 tsec 2.0890 #GCMRL# 58 dt 0.112000 rms 0.938 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5870 tsec 2.1180 #GCMRL# 59 dt 0.112000 rms 0.938 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8060 tsec 2.3380 #GCAMreg# pass 0 level1 1 level2 1 tsec 81.509 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.937514 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.936529) vs oldopt=(dt=0.32,rms=0.936575) #GCMRL# 61 dt 0.448000 rms 0.937 0.105% neg 0 invalid 762 tFOTS 6.6870 tGradient 1.6060 tsec 8.6960 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.936193) vs oldopt=(dt=0.32,rms=0.936215) #GCMRL# 62 dt 0.256000 rms 0.936 0.000% neg 0 invalid 762 tFOTS 6.6410 tGradient 1.5970 tsec 8.6690 #GCMRL# 63 dt 0.256000 rms 0.936 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6400 tsec 2.1630 #GCMRL# 64 dt 0.256000 rms 0.935 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6730 tsec 2.2040 #GCMRL# 65 dt 0.256000 rms 0.935 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6420 tsec 2.1980 #GCMRL# 66 dt 0.256000 rms 0.934 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6940 tsec 2.2300 #GCMRL# 67 dt 0.256000 rms 0.934 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6280 tsec 2.0920 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.912733 #FOTS# QuadFit found better minimum quadopt=(dt=0.336415,rms=0.902018) vs oldopt=(dt=0.32,rms=0.902083) #GCMRL# 69 dt 0.336415 rms 0.902 1.174% neg 0 invalid 762 tFOTS 4.9080 tGradient 1.2000 tsec 6.5140 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.901555) vs oldopt=(dt=0.02,rms=0.901615) #GCMRL# 70 dt 0.028000 rms 0.902 0.000% neg 0 invalid 762 tFOTS 5.0730 tGradient 1.2370 tsec 6.7390 #GCAMreg# pass 0 level1 0 level2 1 tsec 22.985 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.901926 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.901349) vs oldopt=(dt=0.02,rms=0.901359) #GCMRL# 72 dt 0.024000 rms 0.901 0.064% neg 0 invalid 762 tFOTS 5.0600 tGradient 1.2430 tsec 6.7070 #FOTS# QuadFit found better minimum quadopt=(dt=0.00175,rms=0.901349) vs oldopt=(dt=0.00125,rms=0.901349) GCAMregister done in 7.38137 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.23588 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (822 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (822 voxels, peak = 5), gca=6.4 gca peak = 0.17690 (16) mri peak = 0.19356 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (375 voxels, overlap=0.035) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (375 voxels, peak = 7), gca=7.0 gca peak = 0.28275 (96) mri peak = 0.13191 (94) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (782 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (782 voxels, peak = 95), gca=94.6 gca peak = 0.18948 (93) mri peak = 0.11240 (94) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (597 voxels, overlap=1.001) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (597 voxels, peak = 93), gca=92.5 gca peak = 0.20755 (55) mri peak = 0.10151 (74) Right_Hippocampus (53): linear fit = 1.24 x + 0.0 (718 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.24 x + 0.0 (718 voxels, peak = 68), gca=67.9 gca peak = 0.31831 (58) mri peak = 0.12195 (69) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (612 voxels, overlap=0.063) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (612 voxels, peak = 68), gca=67.6 gca peak = 0.11957 (102) mri peak = 0.06560 (109) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (53864 voxels, overlap=0.645) Right_Cerebral_White_Matter (41): linear fit = 1.08 x + 0.0 (53864 voxels, peak = 110), gca=109.7 gca peak = 0.11429 (102) mri peak = 0.06787 (106) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (55813 voxels, overlap=0.663) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (55813 voxels, peak = 109), gca=108.6 gca peak = 0.14521 (59) mri peak = 0.04901 (75) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (15129 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (15129 voxels, peak = 76), gca=76.4 gca peak = 0.14336 (58) mri peak = 0.04166 (75) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (16802 voxels, overlap=0.011) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (16802 voxels, peak = 71), gca=71.1 gca peak = 0.13305 (70) mri peak = 0.17512 (81) Right_Caudate (50): linear fit = 1.22 x + 0.0 (398 voxels, overlap=0.011) Right_Caudate (50): linear fit = 1.22 x + 0.0 (398 voxels, peak = 85), gca=85.1 gca peak = 0.15761 (71) mri peak = 0.11950 (88) Left_Caudate (11): linear fit = 1.23 x + 0.0 (879 voxels, overlap=0.021) Left_Caudate (11): linear fit = 1.23 x + 0.0 (879 voxels, peak = 87), gca=87.0 gca peak = 0.13537 (57) mri peak = 0.06499 (77) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (19309 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (19309 voxels, peak = 76), gca=75.5 gca peak = 0.13487 (56) mri peak = 0.06519 (77) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (23533 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (23533 voxels, peak = 75), gca=74.8 gca peak = 0.19040 (84) mri peak = 0.08638 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (7726 voxels, overlap=0.512) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (7726 voxels, peak = 93), gca=92.8 gca peak = 0.18871 (83) mri peak = 0.09992 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6223 voxels, overlap=0.937) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6223 voxels, peak = 88), gca=87.6 gca peak = 0.24248 (57) mri peak = 0.11015 (69) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (316 voxels, overlap=0.042) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (316 voxels, peak = 68), gca=67.5 gca peak = 0.35833 (56) mri peak = 0.10667 (65) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (375 voxels, overlap=0.163) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (375 voxels, peak = 64), gca=63.6 gca peak = 0.12897 (85) mri peak = 0.09218 (92) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4503 voxels, overlap=0.760) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4503 voxels, peak = 91), gca=90.5 gca peak = 0.13127 (83) mri peak = 0.09268 (89) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3498 voxels, overlap=0.682) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3498 voxels, peak = 88), gca=88.4 gca peak = 0.12974 (78) mri peak = 0.09969 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1947 voxels, overlap=0.026) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1947 voxels, peak = 90), gca=90.1 gca peak = 0.17796 (79) mri peak = 0.09490 (94) Right_Putamen (51): linear fit = 1.20 x + 0.0 (1863 voxels, overlap=0.060) Right_Putamen (51): linear fit = 1.20 x + 0.0 (1863 voxels, peak = 94), gca=94.4 gca peak = 0.10999 (80) mri peak = 0.11000 (87) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9578 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9578 voxels, peak = 88), gca=88.4 gca peak = 0.13215 (88) mri peak = 0.09125 (93) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (869 voxels, overlap=0.577) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (869 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.08513 (92) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1070 voxels, overlap=0.638) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1070 voxels, peak = 93), gca=93.0 gca peak = 0.20775 (25) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13297 (21) mri peak = 0.13890 (11) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (229 voxels, overlap=0.506) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (229 voxels, peak = 12), gca=12.1 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.21 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 0.42 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 2.75405 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.897575 #FOTS# QuadFit found better minimum quadopt=(dt=198.857,rms=0.868808) vs oldopt=(dt=92.48,rms=0.876485) #GCMRL# 74 dt 198.857143 rms 0.869 3.205% neg 0 invalid 762 tFOTS 5.1970 tGradient 3.0130 tsec 8.6030 #GCMRL# 75 dt 369.920000 rms 0.850 2.158% neg 0 invalid 762 tFOTS 5.2390 tGradient 2.9920 tsec 8.6280 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.847187) vs oldopt=(dt=92.48,rms=0.847455) #GCMRL# 76 dt 129.472000 rms 0.847 0.338% neg 0 invalid 762 tFOTS 5.2340 tGradient 2.9710 tsec 8.6030 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.839849) vs oldopt=(dt=1479.68,rms=0.840574) #GCMRL# 77 dt 1183.744000 rms 0.840 0.866% neg 0 invalid 762 tFOTS 5.3230 tGradient 3.0070 tsec 8.7300 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.834892) vs oldopt=(dt=369.92,rms=0.83569) #GCMRL# 78 dt 295.936000 rms 0.835 0.590% neg 0 invalid 762 tFOTS 5.2680 tGradient 2.9600 tsec 8.6280 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.834096) vs oldopt=(dt=92.48,rms=0.834112) #GCMRL# 79 dt 110.976000 rms 0.834 0.095% neg 0 invalid 762 tFOTS 5.3010 tGradient 3.0030 tsec 8.6970 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.832332) vs oldopt=(dt=369.92,rms=0.832596) #GCMRL# 80 dt 517.888000 rms 0.832 0.212% neg 0 invalid 762 tFOTS 5.3300 tGradient 3.1190 tsec 8.8470 #GCMRL# 81 dt 369.920000 rms 0.830 0.290% neg 0 invalid 762 tFOTS 5.2780 tGradient 3.0410 tsec 8.7150 #GCMRL# 82 dt 92.480000 rms 0.830 0.000% neg 0 invalid 762 tFOTS 5.2130 tGradient 3.0350 tsec 8.6620 #GCMRL# 83 dt 92.480000 rms 0.829 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0340 tsec 3.4260 #GCMRL# 84 dt 92.480000 rms 0.829 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0230 tsec 3.5430 #GCMRL# 85 dt 92.480000 rms 0.828 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0340 tsec 3.5570 #GCMRL# 86 dt 92.480000 rms 0.827 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0260 tsec 3.4240 #GCMRL# 87 dt 92.480000 rms 0.826 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0390 tsec 3.4350 #GCMRL# 88 dt 92.480000 rms 0.824 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0070 tsec 3.5070 #GCMRL# 89 dt 92.480000 rms 0.823 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9770 tsec 3.4130 #GCMRL# 90 dt 92.480000 rms 0.822 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9690 tsec 3.4070 #GCMRL# 91 dt 92.480000 rms 0.821 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9850 tsec 3.4880 #GCMRL# 92 dt 92.480000 rms 0.820 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 3.4440 #GCMRL# 93 dt 92.480000 rms 0.819 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9880 tsec 3.3800 #GCMRL# 94 dt 92.480000 rms 0.818 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9350 tsec 3.3760 #GCMRL# 95 dt 92.480000 rms 0.817 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9750 tsec 3.4760 #GCMRL# 96 dt 92.480000 rms 0.816 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9500 tsec 3.3930 #GCMRL# 97 dt 92.480000 rms 0.815 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0080 tsec 3.4030 #GCMRL# 98 dt 92.480000 rms 0.814 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0160 tsec 3.5170 #GCMRL# 99 dt 92.480000 rms 0.813 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 3.5130 #GCMRL# 100 dt 92.480000 rms 0.812 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0340 tsec 3.4730 #GCMRL# 101 dt 92.480000 rms 0.811 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0310 tsec 3.4730 #GCMRL# 102 dt 92.480000 rms 0.810 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9230 tsec 3.4270 #GCMRL# 103 dt 92.480000 rms 0.809 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9450 tsec 3.3820 #GCMRL# 104 dt 92.480000 rms 0.808 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 3.5070 #GCMRL# 105 dt 92.480000 rms 0.807 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0340 tsec 3.5110 #GCMRL# 106 dt 92.480000 rms 0.806 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9670 tsec 3.4110 #GCMRL# 107 dt 92.480000 rms 0.806 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0140 tsec 3.4560 #GCMRL# 108 dt 92.480000 rms 0.805 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0280 tsec 3.4670 #GCMRL# 109 dt 92.480000 rms 0.804 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9970 tsec 3.5040 #GCMRL# 110 dt 92.480000 rms 0.803 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0320 tsec 3.5370 #GCMRL# 111 dt 92.480000 rms 0.802 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0000 tsec 3.4380 #GCMRL# 112 dt 92.480000 rms 0.802 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9680 tsec 3.3630 #GCMRL# 113 dt 92.480000 rms 0.801 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9410 tsec 3.4510 #GCMRL# 114 dt 92.480000 rms 0.801 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9900 tsec 3.4350 #GCMRL# 115 dt 92.480000 rms 0.801 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0230 tsec 3.4180 #GCMRL# 116 dt 92.480000 rms 0.800 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0270 tsec 3.4200 #GCMRL# 117 dt 92.480000 rms 0.799 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0050 tsec 3.3980 #GCMRL# 118 dt 92.480000 rms 0.799 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0260 tsec 3.4200 #GCMRL# 119 dt 92.480000 rms 0.798 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0270 tsec 3.5330 #GCMRL# 120 dt 92.480000 rms 0.798 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0410 tsec 3.4780 #GCMRL# 121 dt 92.480000 rms 0.798 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0400 tsec 3.5460 #GCMRL# 122 dt 92.480000 rms 0.797 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0490 tsec 3.4410 #GCMRL# 123 dt 92.480000 rms 0.797 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0190 tsec 3.4680 #GCMRL# 124 dt 92.480000 rms 0.796 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0070 tsec 3.5130 #GCMRL# 125 dt 92.480000 rms 0.796 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0820 tsec 3.5860 #GCMRL# 126 dt 92.480000 rms 0.795 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1250 tsec 3.5630 #GCMRL# 127 dt 92.480000 rms 0.795 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1330 tsec 3.5280 #GCMRL# 128 dt 92.480000 rms 0.795 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0130 tsec 3.5310 #GCMRL# 129 dt 92.480000 rms 0.794 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1190 tsec 3.5190 #GCMRL# 130 dt 92.480000 rms 0.794 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0500 tsec 3.5530 #GCMRL# 131 dt 92.480000 rms 0.794 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9850 tsec 3.3820 #GCMRL# 132 dt 92.480000 rms 0.793 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9870 tsec 3.4910 #GCMRL# 133 dt 92.480000 rms 0.793 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9870 tsec 3.4950 #GCMRL# 134 dt 92.480000 rms 0.793 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9960 tsec 3.5050 #GCMRL# 135 dt 92.480000 rms 0.792 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9970 tsec 3.5020 #GCMRL# 136 dt 92.480000 rms 0.792 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0200 tsec 3.4150 #GCMRL# 137 dt 92.480000 rms 0.792 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1070 tsec 3.6150 #GCMRL# 138 dt 92.480000 rms 0.791 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1200 tsec 3.6110 #GCMRL# 139 dt 92.480000 rms 0.791 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0250 tsec 3.5260 #GCMRL# 140 dt 92.480000 rms 0.791 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9950 tsec 3.4760 #GCMRL# 141 dt 92.480000 rms 0.791 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0020 tsec 3.4870 #GCMRL# 142 dt 92.480000 rms 0.790 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0230 tsec 3.5080 #GCMRL# 143 dt 92.480000 rms 0.790 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0340 tsec 3.4330 #GCMRL# 144 dt 92.480000 rms 0.790 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0130 tsec 3.4090 #GCMRL# 145 dt 92.480000 rms 0.790 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0220 tsec 3.5130 #GCMRL# 146 dt 92.480000 rms 0.789 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0250 tsec 3.5260 #GCMRL# 147 dt 92.480000 rms 0.789 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0060 tsec 3.5070 #GCMRL# 148 dt 92.480000 rms 0.789 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0280 tsec 3.5310 #GCMRL# 149 dt 92.480000 rms 0.789 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9800 tsec 3.4660 #GCMRL# 150 dt 92.480000 rms 0.789 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9920 tsec 3.4970 #GCMRL# 151 dt 92.480000 rms 0.788 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 3.5200 #GCMRL# 152 dt 92.480000 rms 0.788 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 3.3970 #GCMRL# 153 dt 92.480000 rms 0.788 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0080 tsec 3.5160 #FOTS# QuadFit found better minimum quadopt=(dt=-0.0961538,rms=0.788135) vs oldopt=(dt=0.36125,rms=0.788135) #GCAMreg# pass 0 level1 5 level2 1 tsec 343.019 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.788702 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.78789) vs oldopt=(dt=92.48,rms=0.787945) #GCMRL# 155 dt 73.984000 rms 0.788 0.103% neg 0 invalid 762 tFOTS 4.9170 tGradient 3.0070 tsec 8.3180 #GCMRL# 156 dt 23.120000 rms 0.788 0.000% neg 0 invalid 762 tFOTS 5.4900 tGradient 2.9990 tsec 9.2010 #GCMRL# 157 dt 23.120000 rms 0.788 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0330 tsec 3.4270 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.790113 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.779506) vs oldopt=(dt=414.72,rms=0.781896) #GCMRL# 159 dt 248.832000 rms 0.780 1.343% neg 0 invalid 762 tFOTS 4.8870 tGradient 2.3330 tsec 7.6140 #FOTS# QuadFit found better minimum quadopt=(dt=68.5128,rms=0.774609) vs oldopt=(dt=25.92,rms=0.77615) #GCMRL# 160 dt 68.512821 rms 0.775 0.628% neg 0 invalid 762 tFOTS 5.1510 tGradient 2.3300 tsec 7.8840 #FOTS# QuadFit found better minimum quadopt=(dt=117.096,rms=0.770793) vs oldopt=(dt=103.68,rms=0.770808) #GCMRL# 161 dt 117.096296 rms 0.771 0.493% neg 0 invalid 762 tFOTS 5.2930 tGradient 2.2980 tsec 7.9950 #FOTS# QuadFit found better minimum quadopt=(dt=66.2857,rms=0.768359) vs oldopt=(dt=25.92,rms=0.768953) #GCMRL# 162 dt 66.285714 rms 0.768 0.316% neg 0 invalid 762 tFOTS 5.1720 tGradient 2.3150 tsec 7.8770 #FOTS# QuadFit found better minimum quadopt=(dt=98.7884,rms=0.765757) vs oldopt=(dt=103.68,rms=0.76578) #GCMRL# 163 dt 98.788382 rms 0.766 0.339% neg 0 invalid 762 tFOTS 5.1580 tGradient 2.3490 tsec 7.8950 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.764231) vs oldopt=(dt=25.92,rms=0.764515) #GCMRL# 164 dt 36.288000 rms 0.764 0.199% neg 0 invalid 762 tFOTS 5.1490 tGradient 2.3360 tsec 7.8800 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.758294) vs oldopt=(dt=414.72,rms=0.758609) #GCMRL# 165 dt 580.608000 rms 0.758 0.777% neg 0 invalid 762 tFOTS 6.3670 tGradient 2.3340 tsec 9.2110 #FOTS# QuadFit found better minimum quadopt=(dt=54.7009,rms=0.753736) vs oldopt=(dt=25.92,rms=0.754599) #GCMRL# 166 dt 54.700855 rms 0.754 0.601% neg 0 invalid 762 tFOTS 4.9500 tGradient 2.2830 tsec 7.6280 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.752963) vs oldopt=(dt=25.92,rms=0.753077) #GCMRL# 167 dt 36.288000 rms 0.753 0.103% neg 0 invalid 762 tFOTS 6.7500 tGradient 2.2540 tsec 9.5130 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.74792) vs oldopt=(dt=414.72,rms=0.749111) #GCMRL# 168 dt 580.608000 rms 0.748 0.670% neg 0 invalid 762 tFOTS 6.2200 tGradient 2.2890 tsec 8.9880 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.747212) vs oldopt=(dt=25.92,rms=0.747348) #GCMRL# 169 dt 36.288000 rms 0.747 0.095% neg 0 invalid 762 tFOTS 4.5660 tGradient 2.3320 tsec 7.2870 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.74611) vs oldopt=(dt=414.72,rms=0.746356) #GCMRL# 170 dt 248.832000 rms 0.746 0.148% neg 0 invalid 762 tFOTS 6.6410 tGradient 2.3270 tsec 9.4710 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.745543) vs oldopt=(dt=25.92,rms=0.745652) #GCMRL# 171 dt 36.288000 rms 0.746 0.076% neg 0 invalid 762 tFOTS 7.0830 tGradient 2.3370 tsec 9.9210 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.744298) vs oldopt=(dt=414.72,rms=0.744458) #GCMRL# 172 dt 331.776000 rms 0.744 0.167% neg 0 invalid 762 tFOTS 6.6360 tGradient 2.3270 tsec 9.4650 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.743452) vs oldopt=(dt=25.92,rms=0.743512) #GCMRL# 173 dt 36.288000 rms 0.743 0.114% neg 0 invalid 762 tFOTS 6.3970 tGradient 2.3040 tsec 9.1920 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.743155) vs oldopt=(dt=103.68,rms=0.743179) #GCMRL# 174 dt 82.944000 rms 0.743 0.000% neg 0 invalid 762 tFOTS 4.5530 tGradient 2.2990 tsec 7.2730 #GCMRL# 175 dt 82.944000 rms 0.743 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3860 tsec 2.7790 #GCMRL# 176 dt 82.944000 rms 0.742 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3570 tsec 2.7540 #GCMRL# 177 dt 82.944000 rms 0.742 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3040 tsec 2.9050 #GCMRL# 178 dt 82.944000 rms 0.741 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3510 tsec 2.7380 #GCMRL# 179 dt 10.368000 rms 0.741 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3910 tsec 3.5150 #GCMRL# 180 dt 5.184000 rms 0.741 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3030 tsec 3.0980 #GCMRL# 181 dt 1.620000 rms 0.741 0.000% neg 0 invalid 762 tFOTS 4.0430 tGradient 2.3320 tsec 6.7960 #GCMRL# 182 dt 0.202500 rms 0.741 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3350 tsec 3.4560 #GCMRL# 183 dt 0.050625 rms 0.741 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3280 tsec 3.2670 #GCAMreg# pass 0 level1 4 level2 1 tsec 177.706 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.741367 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.740433) vs oldopt=(dt=25.92,rms=0.740464) #GCMRL# 185 dt 36.288000 rms 0.740 0.126% neg 0 invalid 762 tFOTS 4.9870 tGradient 2.3300 tsec 7.7110 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.739818) vs oldopt=(dt=103.68,rms=0.739976) #GCMRL# 186 dt 82.944000 rms 0.740 0.083% neg 0 invalid 762 tFOTS 5.2790 tGradient 2.3420 tsec 8.0240 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.738191) vs oldopt=(dt=414.72,rms=0.738511) #GCMRL# 187 dt 331.776000 rms 0.738 0.220% neg 0 invalid 762 tFOTS 5.3980 tGradient 2.3990 tsec 8.1950 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.737378) vs oldopt=(dt=25.92,rms=0.737466) #GCMRL# 188 dt 36.288000 rms 0.737 0.110% neg 0 invalid 762 tFOTS 5.3130 tGradient 2.2700 tsec 7.9900 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.736898) vs oldopt=(dt=103.68,rms=0.73695) #GCMRL# 189 dt 145.152000 rms 0.737 0.065% neg 0 invalid 762 tFOTS 5.3150 tGradient 2.2900 tsec 8.0000 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.734033) vs oldopt=(dt=414.72,rms=0.734344) #GCMRL# 190 dt 331.776000 rms 0.734 0.389% neg 0 invalid 762 tFOTS 5.2310 tGradient 2.3320 tsec 7.9560 #FOTS# QuadFit found better minimum quadopt=(dt=21.8734,rms=0.733497) vs oldopt=(dt=25.92,rms=0.733516) #GCMRL# 191 dt 21.873418 rms 0.733 0.073% neg 0 invalid 762 tFOTS 5.3240 tGradient 2.3170 tsec 8.0390 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.73348) vs oldopt=(dt=1.62,rms=0.733481) #GCMRL# 192 dt 2.268000 rms 0.733 0.000% neg 0 invalid 762 tFOTS 5.2640 tGradient 2.3270 tsec 8.0100 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.741573 #FOTS# QuadFit found better minimum quadopt=(dt=78.4724,rms=0.724624) vs oldopt=(dt=32,rms=0.729226) #GCMRL# 194 dt 78.472362 rms 0.725 2.286% neg 0 invalid 762 tFOTS 5.0600 tGradient 1.9940 tsec 7.4530 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.71483) vs oldopt=(dt=32,rms=0.715215) #GCMRL# 195 dt 25.600000 rms 0.715 1.352% neg 0 invalid 762 tFOTS 4.9710 tGradient 2.0040 tsec 7.3730 #FOTS# QuadFit found better minimum quadopt=(dt=20.8619,rms=0.710579) vs oldopt=(dt=32,rms=0.711355) #GCMRL# 196 dt 20.861878 rms 0.711 0.595% neg 0 invalid 762 tFOTS 4.9870 tGradient 1.9810 tsec 7.3700 #GCMRL# 197 dt 32.000000 rms 0.708 0.433% neg 0 invalid 762 tFOTS 4.9670 tGradient 1.9970 tsec 7.3650 #FOTS# QuadFit found better minimum quadopt=(dt=25.1429,rms=0.704997) vs oldopt=(dt=8,rms=0.705568) #GCMRL# 198 dt 25.142857 rms 0.705 0.354% neg 0 invalid 762 tFOTS 5.0260 tGradient 1.9710 tsec 7.3950 #FOTS# QuadFit found better minimum quadopt=(dt=20.2222,rms=0.702497) vs oldopt=(dt=8,rms=0.703002) #GCMRL# 199 dt 20.222222 rms 0.702 0.355% neg 0 invalid 762 tFOTS 4.9640 tGradient 1.9960 tsec 7.3600 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.700721) vs oldopt=(dt=8,rms=0.701093) #GCMRL# 200 dt 11.200000 rms 0.701 0.253% neg 0 invalid 762 tFOTS 5.0430 tGradient 1.9750 tsec 7.4220 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.69685) vs oldopt=(dt=32,rms=0.697949) #GCMRL# 201 dt 44.800000 rms 0.697 0.552% neg 0 invalid 762 tFOTS 4.6960 tGradient 2.0030 tsec 7.1000 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.695971) vs oldopt=(dt=8,rms=0.696205) #GCMRL# 202 dt 11.200000 rms 0.696 0.126% neg 0 invalid 762 tFOTS 4.6810 tGradient 2.0130 tsec 7.1020 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.695202) vs oldopt=(dt=8,rms=0.695419) #GCMRL# 203 dt 11.200000 rms 0.695 0.110% neg 0 invalid 762 tFOTS 4.7110 tGradient 2.0550 tsec 7.1660 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.694548) vs oldopt=(dt=8,rms=0.694659) #GCMRL# 204 dt 9.600000 rms 0.695 0.094% neg 0 invalid 762 tFOTS 4.6690 tGradient 2.0130 tsec 7.0840 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.694533) vs oldopt=(dt=0.125,rms=0.694536) #GCMRL# 205 dt 0.175000 rms 0.695 0.000% neg 0 invalid 762 tFOTS 3.7820 tGradient 2.1070 tsec 6.3090 #GCMRL# 206 dt 0.175000 rms 0.695 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0520 tsec 2.4490 #GCMRL# 207 dt 0.021875 rms 0.695 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0510 tsec 3.1870 #GCMRL# 208 dt 0.010937 rms 0.695 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0420 tsec 2.8320 #FOTS# QuadFit found better minimum quadopt=(dt=0.009375,rms=0.694519) vs oldopt=(dt=0.0078125,rms=0.694519) #GCAMreg# pass 0 level1 3 level2 1 tsec 108.254 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.695032 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.693709) vs oldopt=(dt=8,rms=0.693856) #GCMRL# 210 dt 11.200000 rms 0.694 0.190% neg 0 invalid 762 tFOTS 5.2970 tGradient 2.0470 tsec 7.7500 #FOTS# QuadFit found better minimum quadopt=(dt=25.0435,rms=0.692956) vs oldopt=(dt=32,rms=0.693096) #GCMRL# 211 dt 25.043478 rms 0.693 0.109% neg 0 invalid 762 tFOTS 5.3400 tGradient 2.0230 tsec 7.7650 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.691331) vs oldopt=(dt=32,rms=0.691641) #GCMRL# 212 dt 44.800000 rms 0.691 0.235% neg 0 invalid 762 tFOTS 5.3410 tGradient 2.0090 tsec 7.7550 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.690523) vs oldopt=(dt=32,rms=0.690663) #GCMRL# 213 dt 44.800000 rms 0.691 0.117% neg 0 invalid 762 tFOTS 4.6980 tGradient 1.9780 tsec 7.0790 #FOTS# QuadFit found better minimum quadopt=(dt=93.0909,rms=0.687736) vs oldopt=(dt=32,rms=0.688266) #GCMRL# 214 dt 93.090909 rms 0.688 0.404% neg 0 invalid 762 tFOTS 5.3300 tGradient 2.1040 tsec 7.8380 #FOTS# QuadFit found better minimum quadopt=(dt=17.2174,rms=0.685405) vs oldopt=(dt=8,rms=0.685837) #GCMRL# 215 dt 17.217391 rms 0.685 0.339% neg 0 invalid 762 tFOTS 5.3010 tGradient 2.0620 tsec 7.7650 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.684547) vs oldopt=(dt=32,rms=0.68459) #GCMRL# 216 dt 25.600000 rms 0.685 0.125% neg 0 invalid 762 tFOTS 5.2940 tGradient 2.2400 tsec 7.9320 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.683624) vs oldopt=(dt=32,rms=0.683633) #GCMRL# 217 dt 25.600000 rms 0.684 0.135% neg 0 invalid 762 tFOTS 4.9970 tGradient 2.0000 tsec 7.3980 #FOTS# QuadFit found better minimum quadopt=(dt=24,rms=0.682825) vs oldopt=(dt=32,rms=0.683003) #GCMRL# 218 dt 24.000000 rms 0.683 0.117% neg 0 invalid 762 tFOTS 5.2880 tGradient 1.9790 tsec 7.6680 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.68189) vs oldopt=(dt=32,rms=0.68196) #GCMRL# 219 dt 25.600000 rms 0.682 0.137% neg 0 invalid 762 tFOTS 5.3180 tGradient 1.9770 tsec 7.6970 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.681321) vs oldopt=(dt=8,rms=0.681436) #GCMRL# 220 dt 11.200000 rms 0.681 0.083% neg 0 invalid 762 tFOTS 5.2850 tGradient 1.9710 tsec 7.6550 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.677104) vs oldopt=(dt=128,rms=0.678135) #GCMRL# 221 dt 179.200000 rms 0.677 0.619% neg 0 invalid 762 tFOTS 4.9870 tGradient 1.9760 tsec 7.3630 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.676113) vs oldopt=(dt=32,rms=0.676277) #GCMRL# 222 dt 19.200000 rms 0.676 0.146% neg 0 invalid 762 tFOTS 5.2990 tGradient 2.0440 tsec 7.7450 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.675539) vs oldopt=(dt=32,rms=0.675563) #GCMRL# 223 dt 25.600000 rms 0.676 0.085% neg 0 invalid 762 tFOTS 5.3050 tGradient 2.0850 tsec 7.7870 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.674798) vs oldopt=(dt=32,rms=0.674836) #GCMRL# 224 dt 25.600000 rms 0.675 0.110% neg 0 invalid 762 tFOTS 5.3150 tGradient 1.9570 tsec 7.6760 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.674412) vs oldopt=(dt=8,rms=0.674484) #GCMRL# 225 dt 11.200000 rms 0.674 0.057% neg 0 invalid 762 tFOTS 4.9920 tGradient 1.9780 tsec 7.3660 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.671199) vs oldopt=(dt=128,rms=0.671895) #GCMRL# 226 dt 179.200000 rms 0.671 0.476% neg 0 invalid 762 tFOTS 4.9850 tGradient 1.9880 tsec 7.3700 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.670666) vs oldopt=(dt=8,rms=0.670799) #GCMRL# 227 dt 11.200000 rms 0.671 0.079% neg 0 invalid 762 tFOTS 5.3160 tGradient 2.0420 tsec 7.7600 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.670375) vs oldopt=(dt=32,rms=0.670421) #GCMRL# 228 dt 19.200000 rms 0.670 0.000% neg 0 invalid 762 tFOTS 5.0080 tGradient 1.9950 tsec 7.4240 #GCMRL# 229 dt 19.200000 rms 0.670 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0010 tsec 2.3970 #GCMRL# 230 dt 19.200000 rms 0.670 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9770 tsec 2.3720 #GCMRL# 231 dt 19.200000 rms 0.669 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9460 tsec 2.3510 #GCMRL# 232 dt 19.200000 rms 0.668 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0420 tsec 2.4450 #GCMRL# 233 dt 19.200000 rms 0.667 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0400 tsec 2.4550 #GCMRL# 234 dt 19.200000 rms 0.666 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0280 tsec 2.4440 #GCMRL# 235 dt 19.200000 rms 0.664 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0040 tsec 2.4140 #GCMRL# 236 dt 19.200000 rms 0.663 0.212% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9500 tsec 2.3490 #GCMRL# 237 dt 19.200000 rms 0.661 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0170 tsec 2.4150 #GCMRL# 238 dt 19.200000 rms 0.660 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9900 tsec 2.3830 #GCMRL# 239 dt 19.200000 rms 0.659 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9630 tsec 2.3710 #GCMRL# 240 dt 19.200000 rms 0.657 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9810 tsec 2.3720 #GCMRL# 241 dt 19.200000 rms 0.656 0.225% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9170 tsec 2.3060 #GCMRL# 242 dt 19.200000 rms 0.654 0.203% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9020 tsec 2.3900 #GCMRL# 243 dt 19.200000 rms 0.653 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9170 tsec 2.3110 #GCMRL# 244 dt 19.200000 rms 0.652 0.173% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9310 tsec 2.3200 #GCMRL# 245 dt 19.200000 rms 0.651 0.180% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8970 tsec 2.2910 #GCMRL# 246 dt 19.200000 rms 0.650 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9810 tsec 2.3860 #GCMRL# 247 dt 19.200000 rms 0.649 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9790 tsec 2.4740 #GCMRL# 248 dt 19.200000 rms 0.648 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9580 tsec 2.4690 #GCMRL# 249 dt 19.200000 rms 0.647 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0400 tsec 2.4390 #GCMRL# 250 dt 19.200000 rms 0.646 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9670 tsec 2.3660 #GCMRL# 251 dt 19.200000 rms 0.645 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9770 tsec 2.3770 #GCMRL# 252 dt 19.200000 rms 0.645 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0130 tsec 2.4130 #GCMRL# 253 dt 19.200000 rms 0.644 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9590 tsec 2.3540 #GCMRL# 254 dt 19.200000 rms 0.644 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9470 tsec 2.3470 #GCMRL# 255 dt 19.200000 rms 0.643 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9340 tsec 2.3290 #GCMRL# 256 dt 19.200000 rms 0.642 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9410 tsec 2.4440 #GCMRL# 257 dt 19.200000 rms 0.642 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9370 tsec 2.3310 #GCMRL# 258 dt 19.200000 rms 0.641 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9380 tsec 2.3400 #GCMRL# 259 dt 19.200000 rms 0.641 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9290 tsec 2.3190 #GCMRL# 260 dt 19.200000 rms 0.640 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9290 tsec 2.3260 #GCMRL# 261 dt 19.200000 rms 0.640 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9120 tsec 2.3030 #GCMRL# 262 dt 19.200000 rms 0.639 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9350 tsec 2.3280 #GCMRL# 263 dt 19.200000 rms 0.639 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9260 tsec 2.3200 #GCMRL# 264 dt 19.200000 rms 0.639 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9660 tsec 2.3620 #GCMRL# 265 dt 19.200000 rms 0.638 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9520 tsec 2.4540 #GCMRL# 266 dt 19.200000 rms 0.638 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9430 tsec 2.3410 #GCMRL# 267 dt 19.200000 rms 0.638 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9010 tsec 2.4050 #GCMRL# 268 dt 19.200000 rms 0.637 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8880 tsec 2.3970 #GCMRL# 269 dt 19.200000 rms 0.637 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9170 tsec 2.4290 #GCMRL# 270 dt 19.200000 rms 0.637 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8830 tsec 2.2740 #GCMRL# 271 dt 19.200000 rms 0.637 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8760 tsec 2.2700 #GCMRL# 272 dt 19.200000 rms 0.636 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9610 tsec 2.3540 #GCMRL# 273 dt 19.200000 rms 0.636 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9580 tsec 2.3540 #GCMRL# 274 dt 19.200000 rms 0.636 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9670 tsec 2.3630 #GCMRL# 275 dt 19.200000 rms 0.635 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9550 tsec 2.3470 #GCMRL# 276 dt 19.200000 rms 0.635 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9270 tsec 2.3170 #GCMRL# 277 dt 19.200000 rms 0.635 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9190 tsec 2.4230 #GCMRL# 278 dt 19.200000 rms 0.635 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9620 tsec 2.3610 #GCMRL# 279 dt 19.200000 rms 0.634 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9100 tsec 2.3050 #GCMRL# 280 dt 19.200000 rms 0.634 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9880 tsec 2.3820 #GCMRL# 281 dt 19.200000 rms 0.634 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9500 tsec 2.3490 #GCMRL# 282 dt 19.200000 rms 0.634 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9600 tsec 2.3510 #GCMRL# 283 dt 19.200000 rms 0.633 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9270 tsec 2.4340 #GCMRL# 284 dt 19.200000 rms 0.633 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9100 tsec 2.3050 #GCMRL# 285 dt 19.200000 rms 0.633 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9220 tsec 2.3170 #GCMRL# 286 dt 19.200000 rms 0.633 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9190 tsec 2.4190 #GCMRL# 287 dt 19.200000 rms 0.632 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9270 tsec 2.3240 #GCMRL# 288 dt 19.200000 rms 0.632 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9270 tsec 2.3270 #GCMRL# 289 dt 19.200000 rms 0.632 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9370 tsec 2.3310 #GCMRL# 290 dt 19.200000 rms 0.632 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9170 tsec 2.3110 #GCMRL# 291 dt 19.200000 rms 0.631 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9250 tsec 2.3620 #GCMRL# 292 dt 19.200000 rms 0.631 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9220 tsec 2.3230 #GCMRL# 293 dt 19.200000 rms 0.631 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9520 tsec 2.4130 #GCMRL# 294 dt 19.200000 rms 0.631 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9500 tsec 2.3510 #GCMRL# 295 dt 19.200000 rms 0.631 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9780 tsec 2.3760 #GCMRL# 296 dt 19.200000 rms 0.631 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9370 tsec 2.3580 #GCMRL# 297 dt 32.000000 rms 0.631 0.000% neg 0 invalid 762 tFOTS 5.0020 tGradient 1.9120 tsec 7.3360 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.654368 #GCMRL# 299 dt 0.000000 rms 0.654 0.095% neg 0 invalid 762 tFOTS 4.6140 tGradient 1.7220 tsec 6.7340 #GCMRL# 300 dt 0.150000 rms 0.654 0.000% neg 0 invalid 762 tFOTS 4.6350 tGradient 1.7180 tsec 7.0700 #GCAMreg# pass 0 level1 2 level2 1 tsec 23.926 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.654368 #GCMRL# 302 dt 0.000000 rms 0.654 0.095% neg 0 invalid 762 tFOTS 4.9400 tGradient 1.7200 tsec 7.0590 #GCMRL# 303 dt 0.150000 rms 0.654 0.000% neg 0 invalid 762 tFOTS 4.9240 tGradient 1.7050 tsec 7.3480 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.701111 #FOTS# QuadFit found better minimum quadopt=(dt=0.786184,rms=0.698582) vs oldopt=(dt=1.28,rms=0.698924) #GCMRL# 305 dt 0.786184 rms 0.699 0.361% neg 0 invalid 762 tFOTS 5.8200 tGradient 1.5390 tsec 7.8700 #GCMRL# 306 dt 0.320000 rms 0.698 0.000% neg 0 invalid 762 tFOTS 6.7700 tGradient 1.5900 tsec 8.8960 #GCAMreg# pass 0 level1 1 level2 1 tsec 26.754 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.698959 #FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.697351) vs oldopt=(dt=1.28,rms=0.697594) #GCMRL# 308 dt 0.768000 rms 0.697 0.230% neg 0 invalid 762 tFOTS 6.5710 tGradient 1.5800 tsec 8.6270 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.697109) vs oldopt=(dt=0.32,rms=0.697139) #GCMRL# 309 dt 0.448000 rms 0.697 0.000% neg 0 invalid 762 tFOTS 6.8240 tGradient 1.6000 tsec 8.9580 #GCMRL# 310 dt 0.448000 rms 0.697 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5740 tsec 1.9880 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.643583 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.619219) vs oldopt=(dt=0.32,rms=0.625791) #GCMRL# 312 dt 0.448000 rms 0.619 3.786% neg 0 invalid 762 tFOTS 4.6790 tGradient 1.1410 tsec 6.2230 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.608906) vs oldopt=(dt=0.32,rms=0.611821) #GCMRL# 313 dt 0.448000 rms 0.609 1.666% neg 0 invalid 762 tFOTS 4.6730 tGradient 1.1600 tsec 6.2310 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.602571) vs oldopt=(dt=0.32,rms=0.604388) #GCMRL# 314 dt 0.448000 rms 0.603 1.040% neg 0 invalid 762 tFOTS 4.7220 tGradient 1.1550 tsec 6.2800 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.59948) vs oldopt=(dt=0.32,rms=0.600374) #GCMRL# 315 dt 0.448000 rms 0.599 0.513% neg 0 invalid 762 tFOTS 4.6980 tGradient 1.1630 tsec 6.2610 #GCMRL# 316 dt 0.320000 rms 0.598 0.250% neg 0 invalid 762 tFOTS 4.6910 tGradient 1.1830 tsec 6.2720 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.596487) vs oldopt=(dt=0.32,rms=0.596921) #GCMRL# 317 dt 0.448000 rms 0.596 0.250% neg 0 invalid 762 tFOTS 4.7120 tGradient 1.1700 tsec 6.2920 #FOTS# QuadFit found better minimum quadopt=(dt=0.388889,rms=0.59575) vs oldopt=(dt=0.32,rms=0.595874) #GCMRL# 318 dt 0.388889 rms 0.596 0.123% neg 0 invalid 762 tFOTS 4.7190 tGradient 1.1700 tsec 6.2940 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.595117) vs oldopt=(dt=0.32,rms=0.595272) #GCMRL# 319 dt 0.448000 rms 0.595 0.106% neg 0 invalid 762 tFOTS 4.6730 tGradient 1.1790 tsec 6.2450 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.594604) vs oldopt=(dt=0.32,rms=0.594714) #GCMRL# 320 dt 0.448000 rms 0.595 0.086% neg 0 invalid 762 tFOTS 4.6490 tGradient 1.1670 tsec 6.2120 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.594247) vs oldopt=(dt=0.32,rms=0.594309) #GCMRL# 321 dt 0.448000 rms 0.594 0.060% neg 0 invalid 762 tFOTS 4.6130 tGradient 1.1660 tsec 6.1710 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.593919) vs oldopt=(dt=0.32,rms=0.593971) #GCMRL# 322 dt 0.448000 rms 0.594 0.055% neg 0 invalid 762 tFOTS 4.6180 tGradient 1.1470 tsec 6.1670 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.593688) vs oldopt=(dt=0.32,rms=0.59371) #GCMRL# 323 dt 0.448000 rms 0.594 0.000% neg 0 invalid 762 tFOTS 4.7430 tGradient 1.1870 tsec 6.3530 #GCMRL# 324 dt 0.448000 rms 0.593 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1550 tsec 1.5580 #GCMRL# 325 dt 0.448000 rms 0.593 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2030 tsec 1.6070 #GCMRL# 326 dt 0.224000 rms 0.593 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1580 tsec 1.9430 #GCMRL# 327 dt 0.224000 rms 0.593 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1900 tsec 1.6010 #GCMRL# 328 dt 0.224000 rms 0.592 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1540 tsec 1.5570 #GCMRL# 329 dt 0.224000 rms 0.592 -0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1630 tsec 2.0750 #FOTS# QuadFit found better minimum quadopt=(dt=0,rms=0.592279) vs oldopt=(dt=0,rms=0.592279) #GCAMreg# pass 0 level1 0 level2 1 tsec 99.004 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.592963 #GCMRL# 331 dt 0.320000 rms 0.583 1.646% neg 0 invalid 762 tFOTS 4.6980 tGradient 1.1530 tsec 6.2520 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.577233) vs oldopt=(dt=0.32,rms=0.578213) #GCMRL# 332 dt 0.384000 rms 0.577 1.024% neg 0 invalid 762 tFOTS 4.7150 tGradient 1.1530 tsec 6.2700 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.574666) vs oldopt=(dt=0.32,rms=0.575078) #GCMRL# 333 dt 0.384000 rms 0.575 0.445% neg 0 invalid 762 tFOTS 4.6350 tGradient 1.1540 tsec 6.1850 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.572923) vs oldopt=(dt=0.32,rms=0.5732) #GCMRL# 334 dt 0.384000 rms 0.573 0.303% neg 0 invalid 762 tFOTS 4.6120 tGradient 1.1660 tsec 6.1750 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.572056) vs oldopt=(dt=0.32,rms=0.572185) #GCMRL# 335 dt 0.384000 rms 0.572 0.151% neg 0 invalid 762 tFOTS 4.7070 tGradient 1.1570 tsec 6.2670 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.57136) vs oldopt=(dt=0.32,rms=0.571456) #GCMRL# 336 dt 0.384000 rms 0.571 0.122% neg 0 invalid 762 tFOTS 4.7010 tGradient 1.1580 tsec 6.2660 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.571118) vs oldopt=(dt=0.32,rms=0.571141) #GCMRL# 337 dt 0.384000 rms 0.571 0.000% neg 0 invalid 762 tFOTS 4.6200 tGradient 1.1450 tsec 6.1840 #GCMRL# 338 dt 0.384000 rms 0.571 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1470 tsec 1.5380 #GCMRL# 339 dt 0.384000 rms 0.570 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1580 tsec 1.5500 #GCMRL# 340 dt 0.384000 rms 0.570 -0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1600 tsec 2.0650 #FOTS# QuadFit found better minimum quadopt=(dt=1e-05,rms=0.570316) vs oldopt=(dt=1.25e-05,rms=0.570316) #GCMRL# 341 dt 0.000010 rms 0.570 0.000% neg 0 invalid 762 tFOTS 6.1480 tGradient 1.1450 tsec 7.6870 GCAMregister done in 21.5936 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.568393 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.567505) vs oldopt=(dt=23.12,rms=0.567531) #GCMRL# 343 dt 32.368000 rms 0.568 0.156% neg 0 invalid 762 tFOTS 8.0170 tGradient 2.8750 tsec 11.2870 #FOTS# QuadFit found better minimum quadopt=(dt=0.00108375,rms=0.56751) vs oldopt=(dt=0.000903125,rms=0.56751) #GCAMreg# pass 0 level1 5 level2 1 tsec 32.936 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.568225 #GCMRL# 345 dt 0.000000 rms 0.568 0.126% neg 0 invalid 762 tFOTS 7.4960 tGradient 2.8790 tsec 10.8610 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.568255 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.567301) vs oldopt=(dt=6.48,rms=0.567348) #GCMRL# 347 dt 9.072000 rms 0.567 0.168% neg 0 invalid 762 tFOTS 7.9340 tGradient 2.2390 tsec 10.6770 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.567231) vs oldopt=(dt=6.48,rms=0.567237) #GCMRL# 348 dt 9.072000 rms 0.567 0.000% neg 0 invalid 762 tFOTS 7.6380 tGradient 2.1990 tsec 10.3800 #GCAMreg# pass 0 level1 4 level2 1 tsec 32.309 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.567952 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.56704) vs oldopt=(dt=6.48,rms=0.567076) #GCMRL# 350 dt 9.072000 rms 0.567 0.161% neg 0 invalid 762 tFOTS 7.7940 tGradient 2.2300 tsec 10.5540 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.566963) vs oldopt=(dt=6.48,rms=0.566974) #GCMRL# 351 dt 9.072000 rms 0.567 0.000% neg 0 invalid 762 tFOTS 7.9020 tGradient 2.2080 tsec 10.5290 #GCMRL# 352 dt 9.072000 rms 0.567 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2430 tsec 2.7380 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.567734 #FOTS# QuadFit found better minimum quadopt=(dt=22.5882,rms=0.562946) vs oldopt=(dt=8,rms=0.564118) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 354 dt 22.588235 rms 0.563 0.819% neg 0 invalid 762 tFOTS 7.5600 tGradient 1.8930 tsec 10.9800 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.5628) vs oldopt=(dt=8,rms=0.562802) iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 355 dt 9.600000 rms 0.563 0.000% neg 0 invalid 762 tFOTS 7.7450 tGradient 1.7790 tsec 10.7630 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 35.87 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.563511 #FOTS# QuadFit found better minimum quadopt=(dt=25.1733,rms=0.558593) vs oldopt=(dt=8,rms=0.559935) iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 357 dt 25.173333 rms 0.559 0.843% neg 0 invalid 762 tFOTS 7.7350 tGradient 1.7750 tsec 13.1470 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 358 dt 32.000000 rms 0.555 0.753% neg 0 invalid 762 tFOTS 7.3940 tGradient 1.8510 tsec 10.4410 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.553266) vs oldopt=(dt=8,rms=0.553301) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 359 dt 9.600000 rms 0.553 0.000% neg 0 invalid 762 tFOTS 7.7790 tGradient 1.7610 tsec 10.8050 #GCMRL# 360 dt 9.600000 rms 0.553 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8000 tsec 2.3120 #GCMRL# 361 dt 9.600000 rms 0.552 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8080 tsec 2.3250 #GCMRL# 362 dt 9.600000 rms 0.551 0.205% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8040 tsec 2.3120 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 363 dt 9.600000 rms 0.549 0.271% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8190 tsec 3.7100 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 364 dt 9.600000 rms 0.548 0.275% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8030 tsec 4.0500 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 365 dt 9.600000 rms 0.547 0.259% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8300 tsec 3.3950 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 366 dt 9.600000 rms 0.545 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8000 tsec 3.7170 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 367 dt 9.600000 rms 0.544 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7960 tsec 4.0260 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 368 dt 9.600000 rms 0.543 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7970 tsec 4.4030 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 369 dt 9.600000 rms 0.543 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8020 tsec 6.5440 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 370 dt 9.600000 rms 0.542 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8020 tsec 3.3720 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 371 dt 9.600000 rms 0.541 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8130 tsec 4.0720 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 372 dt 9.600000 rms 0.540 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8130 tsec 5.1680 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 373 dt 9.600000 rms 0.540 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8180 tsec 4.7950 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 374 dt 9.600000 rms 0.539 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8450 tsec 3.7850 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.538774) vs oldopt=(dt=32,rms=0.538779) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 375 dt 38.400000 rms 0.539 0.000% neg 0 invalid 762 tFOTS 7.2340 tGradient 1.8650 tsec 10.3520 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.543874 #FOTS# QuadFit found better minimum quadopt=(dt=5.45455,rms=0.540932) vs oldopt=(dt=2.88,rms=0.541427) iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 377 dt 5.454545 rms 0.541 0.540% neg 0 invalid 762 tFOTS 8.1780 tGradient 1.6790 tsec 13.1990 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.540894) vs oldopt=(dt=0.72,rms=0.540903) iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 378 dt 1.008000 rms 0.541 0.000% neg 0 invalid 762 tFOTS 8.1590 tGradient 1.7150 tsec 12.1710 #GCMRL# 379 dt 1.008000 rms 0.541 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7100 tsec 2.2210 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 39.756 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.541628 #FOTS# QuadFit found better minimum quadopt=(dt=6.05128,rms=0.539565) vs oldopt=(dt=2.88,rms=0.53991) #GCMRL# 381 dt 6.051282 rms 0.540 0.381% neg 0 invalid 762 tFOTS 8.1430 tGradient 1.6950 tsec 10.3540 #FOTS# QuadFit found better minimum quadopt=(dt=13.824,rms=0.537702) vs oldopt=(dt=11.52,rms=0.537754) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 382 dt 13.824000 rms 0.538 0.345% neg 0 invalid 762 tFOTS 8.1550 tGradient 1.6860 tsec 11.4180 #FOTS# QuadFit found better minimum quadopt=(dt=22.087,rms=0.535029) vs oldopt=(dt=11.52,rms=0.535589) iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 383 dt 22.086957 rms 0.535 0.498% neg 0 invalid 762 tFOTS 8.1180 tGradient 1.7090 tsec 11.7390 #FOTS# QuadFit found better minimum quadopt=(dt=6.912,rms=0.532627) vs oldopt=(dt=11.52,rms=0.53334) #GCMRL# 384 dt 6.912000 rms 0.533 0.449% neg 0 invalid 762 tFOTS 8.1250 tGradient 1.7480 tsec 10.3880 #FOTS# QuadFit found better minimum quadopt=(dt=4.54545,rms=0.532104) vs oldopt=(dt=2.88,rms=0.532172) #GCMRL# 385 dt 4.545455 rms 0.532 0.000% neg 0 invalid 762 tFOTS 8.0990 tGradient 1.7320 tsec 10.3640 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 386 dt 4.545455 rms 0.532 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6880 tsec 3.6230 #GCMRL# 387 dt 4.545455 rms 0.531 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6680 tsec 2.1850 #GCMRL# 388 dt 4.545455 rms 0.529 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6870 tsec 2.2100 #GCMRL# 389 dt 4.545455 rms 0.528 0.257% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7260 tsec 2.2400 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 390 dt 4.545455 rms 0.527 0.275% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7190 tsec 2.9600 #GCMRL# 391 dt 4.545455 rms 0.525 0.289% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7600 tsec 2.2720 #GCMRL# 392 dt 4.545455 rms 0.524 0.279% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7300 tsec 2.2410 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 393 dt 4.545455 rms 0.522 0.249% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6800 tsec 3.6220 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 394 dt 4.545455 rms 0.521 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6970 tsec 3.6030 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 395 dt 4.545455 rms 0.520 0.193% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7470 tsec 3.0060 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 396 dt 4.545455 rms 0.519 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7650 tsec 2.9980 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 397 dt 4.545455 rms 0.519 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7640 tsec 4.7800 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 398 dt 4.545455 rms 0.518 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6910 tsec 4.6880 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 399 dt 4.545455 rms 0.517 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7020 tsec 6.1200 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 400 dt 4.545455 rms 0.517 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7580 tsec 6.9110 #GCMRL# 401 dt 11.520000 rms 0.517 0.000% neg 0 invalid 762 tFOTS 8.0180 tGradient 1.7130 tsec 10.1520 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.523557 #GCMRL# 403 dt 0.000000 rms 0.523 0.140% neg 0 invalid 762 tFOTS 7.7080 tGradient 1.5930 tsec 9.6960 #GCAMreg# pass 0 level1 1 level2 1 tsec 26.314 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.523557 #GCMRL# 405 dt 0.000000 rms 0.523 0.140% neg 0 invalid 762 tFOTS 6.3620 tGradient 1.5830 tsec 8.3430 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.51366 #FOTS# QuadFit found better minimum quadopt=(dt=1.49611,rms=0.481296) vs oldopt=(dt=1.28,rms=0.482049) iter 0, gcam->neg = 1386 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 407 dt 1.496112 rms 0.490 4.690% neg 0 invalid 762 tFOTS 5.9040 tGradient 1.1840 tsec 12.9330 #GCMRL# 408 dt 0.000013 rms 0.490 0.000% neg 0 invalid 762 tFOTS 7.5290 tGradient 1.1670 tsec 9.1180 #GCAMreg# pass 0 level1 0 level2 1 tsec 31.855 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.490433 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.488417) vs oldopt=(dt=0.08,rms=0.488638) #GCMRL# 410 dt 0.112000 rms 0.488 0.411% neg 0 invalid 762 tFOTS 5.9290 tGradient 1.1580 tsec 7.4820 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.487903) vs oldopt=(dt=0.08,rms=0.487972) #GCMRL# 411 dt 0.112000 rms 0.488 0.000% neg 0 invalid 762 tFOTS 5.9030 tGradient 1.1490 tsec 7.4700 #GCMRL# 412 dt 0.112000 rms 0.488 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1550 tsec 1.5490 label assignment complete, 0 changed (0.00%) GCAMregister done in 8.704 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.4838 #GCMRL# 414 dt 5.780000 rms 0.484 0.002% neg 0 invalid 762 tFOTS 7.6550 tGradient 2.2720 tsec 10.3100 #FOTS# QuadFit found better minimum quadopt=(dt=0.00338672,rms=0.483792) vs oldopt=(dt=0.00564453,rms=0.483792) #GCMRL# 415 dt 0.003387 rms 0.484 0.000% neg 0 invalid 762 tFOTS 8.0700 tGradient 2.2660 tsec 10.7460 #GCAMreg# pass 0 level1 5 level2 1 tsec 32.161 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.483792 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.483848 #GCAMreg# pass 0 level1 4 level2 1 tsec 17.502 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.483848 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.484061 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.483899) vs oldopt=(dt=2,rms=0.483924) #GCMRL# 420 dt 2.800000 rms 0.484 0.033% neg 0 invalid 762 tFOTS 7.6300 tGradient 1.3910 tsec 9.3960 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.483891) vs oldopt=(dt=0.5,rms=0.483892) #GCMRL# 421 dt 0.700000 rms 0.484 0.000% neg 0 invalid 762 tFOTS 7.6460 tGradient 1.3910 tsec 9.4330 #GCAMreg# pass 0 level1 3 level2 1 tsec 29.023 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.483891 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.483168) vs oldopt=(dt=8,rms=0.483286) #GCMRL# 423 dt 11.200000 rms 0.483 0.149% neg 0 invalid 762 tFOTS 7.6340 tGradient 1.3960 tsec 9.4090 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.482199) vs oldopt=(dt=32,rms=0.482207) #GCMRL# 424 dt 38.400000 rms 0.482 0.200% neg 0 invalid 762 tFOTS 5.4900 tGradient 1.3830 tsec 7.2510 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.480649) vs oldopt=(dt=32,rms=0.480832) #GCMRL# 425 dt 44.800000 rms 0.481 0.321% neg 0 invalid 762 tFOTS 7.6790 tGradient 1.3840 tsec 9.4400 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.480145) vs oldopt=(dt=8,rms=0.480204) #GCMRL# 426 dt 11.200000 rms 0.480 0.000% neg 0 invalid 762 tFOTS 7.7090 tGradient 1.3800 tsec 9.4830 #GCMRL# 427 dt 11.200000 rms 0.480 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3840 tsec 1.8780 #GCMRL# 428 dt 11.200000 rms 0.480 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3960 tsec 1.8890 #GCMRL# 429 dt 11.200000 rms 0.480 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4130 tsec 1.9070 #GCMRL# 430 dt 11.200000 rms 0.479 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3900 tsec 1.8800 #GCMRL# 431 dt 11.200000 rms 0.478 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3840 tsec 1.8790 #GCMRL# 432 dt 11.200000 rms 0.478 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4000 tsec 1.8930 #GCMRL# 433 dt 11.200000 rms 0.477 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4080 tsec 1.9220 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.478978 #FOTS# QuadFit found better minimum quadopt=(dt=2.75,rms=0.478507) vs oldopt=(dt=2.88,rms=0.478509) #GCMRL# 435 dt 2.750000 rms 0.479 0.098% neg 0 invalid 762 tFOTS 7.7000 tGradient 1.2810 tsec 9.3570 #GCAMreg# pass 0 level1 2 level2 1 tsec 26.522 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.478507 #FOTS# QuadFit found better minimum quadopt=(dt=11.8319,rms=0.476535) vs oldopt=(dt=11.52,rms=0.476536) #GCMRL# 437 dt 11.831933 rms 0.477 0.412% neg 0 invalid 762 tFOTS 7.6680 tGradient 1.2280 tsec 9.2690 #FOTS# QuadFit found better minimum quadopt=(dt=15.4315,rms=0.473586) vs oldopt=(dt=11.52,rms=0.473766) iter 0, gcam->neg = 11 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 438 dt 15.431472 rms 0.474 0.602% neg 0 invalid 762 tFOTS 7.6330 tGradient 1.2700 tsec 13.5170 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.472906) vs oldopt=(dt=2.88,rms=0.472959) #GCMRL# 439 dt 4.032000 rms 0.473 0.000% neg 0 invalid 762 tFOTS 7.5770 tGradient 1.2500 tsec 9.2340 #GCMRL# 440 dt 4.032000 rms 0.473 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2720 tsec 1.7670 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 441 dt 4.032000 rms 0.472 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2700 tsec 2.4650 #GCMRL# 442 dt 4.032000 rms 0.471 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2530 tsec 1.7470 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 443 dt 4.032000 rms 0.470 0.210% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2560 tsec 5.2930 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 444 dt 4.032000 rms 0.469 0.213% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2430 tsec 3.4140 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 445 dt 4.032000 rms 0.469 0.194% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2430 tsec 3.4390 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 446 dt 4.032000 rms 0.468 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2560 tsec 3.1940 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 447 dt 4.032000 rms 0.467 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2580 tsec 3.5350 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 448 dt 4.032000 rms 0.466 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2470 tsec 5.9760 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 449 dt 4.032000 rms 0.466 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2340 tsec 3.8470 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 450 dt 4.032000 rms 0.465 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2370 tsec 3.8290 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.465332) vs oldopt=(dt=2.88,rms=0.46534) iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 451 dt 4.032000 rms 0.465 0.000% neg 0 invalid 762 tFOTS 7.6640 tGradient 1.2460 tsec 10.8480 #GCMRL# 452 dt 4.032000 rms 0.465 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2540 tsec 1.7530 #GCMRL# 453 dt 4.032000 rms 0.465 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2480 tsec 1.7400 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.468914 #GCAMreg# pass 0 level1 1 level2 1 tsec 17.109 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.468914 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.462883 #FOTS# QuadFit found better minimum quadopt=(dt=1.10552,rms=0.449105) vs oldopt=(dt=1.28,rms=0.449427) iter 0, gcam->neg = 805 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 457 dt 1.105516 rms 0.455 1.649% neg 0 invalid 762 tFOTS 5.6110 tGradient 0.7190 tsec 13.5480 #FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.455249) vs oldopt=(dt=1.95313e-05,rms=0.455249) #GCMRL# 458 dt 0.000023 rms 0.455 0.000% neg 0 invalid 762 tFOTS 7.1520 tGradient 0.7200 tsec 8.2750 #GCAMreg# pass 0 level1 0 level2 1 tsec 31.029 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.455249 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.453271) vs oldopt=(dt=0.32,rms=0.453294) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 460 dt 0.256000 rms 0.453 0.435% neg 0 invalid 762 tFOTS 5.6210 tGradient 0.7050 tsec 7.8720 #FOTS# QuadFit found better minimum quadopt=(dt=0.511905,rms=0.450053) vs oldopt=(dt=0.32,rms=0.450666) iter 0, gcam->neg = 14 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 461 dt 0.511905 rms 0.450 0.698% neg 0 invalid 762 tFOTS 5.6230 tGradient 0.7210 tsec 8.1820 #FOTS# QuadFit found better minimum quadopt=(dt=0.62,rms=0.446491) vs oldopt=(dt=0.32,rms=0.447535) iter 0, gcam->neg = 116 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 462 dt 0.620000 rms 0.447 0.649% neg 0 invalid 762 tFOTS 5.6090 tGradient 0.7020 tsec 11.7440 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 463 dt 0.320000 rms 0.446 0.256% neg 0 invalid 762 tFOTS 5.5150 tGradient 0.7160 tsec 7.3580 #FOTS# QuadFit found better minimum quadopt=(dt=0.521277,rms=0.444001) vs oldopt=(dt=0.32,rms=0.444467) iter 0, gcam->neg = 41 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 464 dt 0.521277 rms 0.444 0.348% neg 0 invalid 762 tFOTS 5.6410 tGradient 0.7240 tsec 11.0900 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.444313) vs oldopt=(dt=0.08,rms=0.444335) #GCMRL# 465 dt 0.112000 rms 0.444 0.000% neg 0 invalid 762 tFOTS 5.5090 tGradient 0.7120 tsec 6.6180 #GCMRL# 466 dt 0.112000 rms 0.444 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7040 tsec 1.0820 #GCMRL# 467 dt 0.112000 rms 0.444 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7100 tsec 1.0830 #GCMRL# 468 dt 0.112000 rms 0.444 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7090 tsec 1.0820 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 469 dt 0.112000 rms 0.443 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7070 tsec 2.2640 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 470 dt 0.112000 rms 0.442 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7030 tsec 1.9060 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 471 dt 0.112000 rms 0.442 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7110 tsec 1.9320 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 472 dt 0.112000 rms 0.442 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.6970 tsec 2.2390 #FOTS# QuadFit found better minimum quadopt=(dt=0.004,rms=0.441676) vs oldopt=(dt=0.005,rms=0.441676) #GCMRL# 473 dt 0.004000 rms 0.442 0.000% neg 0 invalid 762 tFOTS 5.4980 tGradient 0.7050 tsec 6.5990 GCAMregister done in 6.80737 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 3949 tmin = 3.33073 Calls to gcamLabelEnergy 3287 tmin = 0.780433 Calls to gcamJacobianEnergy 3949 tmin = 2.04542 Calls to gcamSmoothnessEnergy 3949 tmin = 8.17697 Calls to gcamLogLikelihoodTerm 475 tmin = 1.20035 Calls to gcamLabelTerm 414 tmin = 3.5489 Calls to gcamJacobianTerm 475 tmin = 2.31997 Calls to gcamSmoothnessTerm 475 tmin = 1.1469 Calls to gcamComputeGradient 475 tmin = 15.6732 Calls to gcamComputeMetricProperties 5540 tmin = 4.25668 mri_ca_register took 0 hours, 47 minutes and 25 seconds. #VMPC# mri_ca_register VmPeak 2305152 FSRUNTIME@ mri_ca_register 0.7902 hours 4 threads #-------------------------------------- #@# SubCort Seg Mon Jan 9 12:07:34 CET 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname sharky machine x86_64 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.82 Atlas used for the 3D morph was /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.14999 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.29 x + 0.0 (1385 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1385 voxels, peak = 6), gca=8.0 gca peak = 0.20380 (13) mri peak = 0.14964 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.47 x + 0.0 (810 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.47 x + 0.0 (810 voxels, peak = 6), gca=6.0 gca peak = 0.26283 (96) mri peak = 0.11820 (100) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (423 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (423 voxels, peak = 97), gca=97.4 gca peak = 0.15814 (97) mri peak = 0.12253 (97) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (501 voxels, overlap=0.833) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (501 voxels, peak = 99), gca=99.4 gca peak = 0.27624 (56) mri peak = 0.11045 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (584 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (584 voxels, peak = 69), gca=68.6 gca peak = 0.28723 (59) mri peak = 0.13407 (69) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (540 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (540 voxels, peak = 70), gca=69.9 gca peak = 0.07623 (103) mri peak = 0.07867 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (34922 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (34922 voxels, peak = 109), gca=108.7 gca peak = 0.07837 (105) mri peak = 0.07601 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (34085 voxels, overlap=0.620) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (34085 voxels, peak = 110), gca=109.7 gca peak = 0.10165 (58) mri peak = 0.04929 (75) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (22723 voxels, overlap=0.055) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (22723 voxels, peak = 73), gca=72.8 gca peak = 0.11113 (58) mri peak = 0.04865 (71) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (22186 voxels, overlap=0.350) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (22186 voxels, peak = 71), gca=71.1 gca peak = 0.27796 (67) mri peak = 0.10595 (84) Right_Caudate (50): linear fit = 1.25 x + 0.0 (537 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.25 x + 0.0 (537 voxels, peak = 83), gca=83.4 gca peak = 0.14473 (69) mri peak = 0.15469 (88) Left_Caudate (11): linear fit = 1.13 x + 0.0 (626 voxels, overlap=0.018) Left_Caudate (11): linear fit = 1.13 x + 0.0 (626 voxels, peak = 78), gca=78.3 gca peak = 0.14301 (56) mri peak = 0.07191 (77) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (22864 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (22864 voxels, peak = 76), gca=75.9 gca peak = 0.14610 (55) mri peak = 0.07495 (77) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (22972 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (22972 voxels, peak = 73), gca=73.4 gca peak = 0.16309 (85) mri peak = 0.10769 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (5362 voxels, overlap=0.427) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (5362 voxels, peak = 93), gca=93.1 gca peak = 0.15172 (84) mri peak = 0.12295 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5859 voxels, overlap=0.354) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5859 voxels, peak = 92), gca=92.0 gca peak = 0.30461 (58) mri peak = 0.15974 (69) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (313 voxels, overlap=0.048) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (313 voxels, peak = 69), gca=69.3 gca peak = 0.32293 (57) mri peak = 0.11202 (73) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (309 voxels, overlap=0.043) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (309 voxels, peak = 70), gca=70.4 gca peak = 0.11083 (90) mri peak = 0.09037 (92) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (4397 voxels, overlap=0.804) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (4397 voxels, peak = 93), gca=93.1 gca peak = 0.11393 (83) mri peak = 0.08423 (89) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (4199 voxels, overlap=0.670) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (4199 voxels, peak = 90), gca=90.1 gca peak = 0.08575 (81) mri peak = 0.12928 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1050 voxels, overlap=0.125) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1050 voxels, peak = 94), gca=93.6 gca peak = 0.08618 (78) mri peak = 0.10660 (92) Right_Putamen (51): linear fit = 1.16 x + 0.0 (993 voxels, overlap=0.179) Right_Putamen (51): linear fit = 1.16 x + 0.0 (993 voxels, peak = 91), gca=90.9 gca peak = 0.08005 (78) mri peak = 0.09865 (87) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12109 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12109 voxels, peak = 83), gca=83.1 gca peak = 0.12854 (88) mri peak = 0.10531 (91) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1260 voxels, overlap=0.671) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1260 voxels, peak = 93), gca=92.8 gca peak = 0.15703 (87) mri peak = 0.08775 (92) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1280 voxels, overlap=0.816) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1280 voxels, peak = 93), gca=92.7 gca peak = 0.17522 (25) mri peak = 0.06842 ( 4) gca peak = 0.17113 (14) mri peak = 0.15518 (13) Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (236 voxels, overlap=0.476) Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (236 voxels, peak = 10), gca=10.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.22 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.53 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31708 ( 7) mri peak = 0.14999 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.71 x + 0.0 (1385 voxels, overlap=0.497) Left_Lateral_Ventricle (4): linear fit = 0.71 x + 0.0 (1385 voxels, peak = 5), gca=5.0 gca peak = 0.33113 ( 6) mri peak = 0.14964 ( 9) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (810 voxels, overlap=0.809) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (810 voxels, peak = 7), gca=6.5 gca peak = 0.21938 (97) mri peak = 0.11820 (100) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (423 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (423 voxels, peak = 96), gca=95.5 gca peak = 0.16529 (99) mri peak = 0.12253 (97) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (501 voxels, overlap=0.976) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (501 voxels, peak = 99), gca=99.5 gca peak = 0.24482 (68) mri peak = 0.11045 (70) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (584 voxels, overlap=0.966) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (584 voxels, peak = 68), gca=68.0 gca peak = 0.32843 (67) mri peak = 0.13407 (69) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (540 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (540 voxels, peak = 68), gca=68.0 gca peak = 0.07413 (109) mri peak = 0.07867 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34922 voxels, overlap=0.829) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34922 voxels, peak = 109), gca=109.0 gca peak = 0.07449 (109) mri peak = 0.07601 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34085 voxels, overlap=0.809) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34085 voxels, peak = 109), gca=109.0 gca peak = 0.08198 (73) mri peak = 0.04929 (75) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (22723 voxels, overlap=0.961) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (22723 voxels, peak = 73), gca=73.0 gca peak = 0.09254 (71) mri peak = 0.04865 (71) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22186 voxels, overlap=0.974) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22186 voxels, peak = 71), gca=71.0 gca peak = 0.20518 (82) mri peak = 0.10595 (84) Right_Caudate (50): linear fit = 1.01 x + 0.0 (537 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.01 x + 0.0 (537 voxels, peak = 83), gca=83.2 gca peak = 0.15916 (88) mri peak = 0.15469 (88) Left_Caudate (11): linear fit = 0.99 x + 0.0 (626 voxels, overlap=0.832) Left_Caudate (11): linear fit = 0.99 x + 0.0 (626 voxels, peak = 87), gca=86.7 gca peak = 0.09990 (76) mri peak = 0.07191 (77) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (22864 voxels, overlap=0.957) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (22864 voxels, peak = 75), gca=74.9 gca peak = 0.11962 (74) mri peak = 0.07495 (77) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22972 voxels, overlap=0.906) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22972 voxels, peak = 73), gca=72.9 gca peak = 0.14900 (93) mri peak = 0.10769 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5362 voxels, overlap=0.953) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5362 voxels, peak = 93), gca=92.5 gca peak = 0.13878 (92) mri peak = 0.12295 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5859 voxels, overlap=0.909) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5859 voxels, peak = 92), gca=91.5 gca peak = 0.28856 (69) mri peak = 0.15974 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (313 voxels, overlap=0.942) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (313 voxels, peak = 69), gca=69.0 gca peak = 0.30235 (71) mri peak = 0.11202 (73) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (309 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (309 voxels, peak = 69), gca=69.2 gca peak = 0.10724 (93) mri peak = 0.09037 (92) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4397 voxels, overlap=0.939) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4397 voxels, peak = 93), gca=92.5 gca peak = 0.10473 (90) mri peak = 0.08423 (89) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4199 voxels, overlap=0.954) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4199 voxels, peak = 90), gca=89.6 gca peak = 0.08806 (87) mri peak = 0.12928 (92) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1050 voxels, overlap=0.736) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1050 voxels, peak = 87), gca=86.6 gca peak = 0.07835 (93) mri peak = 0.10660 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (993 voxels, overlap=0.903) Right_Putamen (51): linear fit = 1.00 x + 0.0 (993 voxels, peak = 93), gca=92.5 gca peak = 0.07384 (86) mri peak = 0.09865 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12109 voxels, overlap=0.739) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12109 voxels, peak = 86), gca=85.6 gca peak = 0.12598 (89) mri peak = 0.10531 (91) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1260 voxels, overlap=0.796) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1260 voxels, peak = 88), gca=87.7 gca peak = 0.14510 (91) mri peak = 0.08775 (92) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1280 voxels, overlap=0.853) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1280 voxels, peak = 90), gca=89.6 gca peak = 0.25694 (13) mri peak = 0.06842 ( 4) gca peak = 0.21036 (12) mri peak = 0.15518 (13) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (236 voxels, overlap=0.858) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (236 voxels, peak = 12), gca=12.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.15108 (33) gca peak Third_Ventricle = 0.25694 (13) gca peak CSF = 0.30158 (19) gca peak Left_Accumbens_area = 0.58924 (71) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.22810 (28) gca peak Right_Accumbens_area = 0.28338 (82) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.91795 (17) gca peak WM_hypointensities = 0.11613 (80) gca peak non_WM_hypointensities = 0.11377 (43) gca peak Optic_Chiasm = 0.51672 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 68789 voxels changed in iteration 0 of unlikely voxel relabeling 272 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 54 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 69140 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 578 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 72161 changed. image ll: -2.171, PF=0.500 pass 2: 16371 changed. image ll: -2.169, PF=0.500 pass 3: 4617 changed. 47995 voxels changed in iteration 0 of unlikely voxel relabeling 274 voxels changed in iteration 1 of unlikely voxel relabeling 28 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5843 voxels changed in iteration 0 of unlikely voxel relabeling 66 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5830 voxels changed in iteration 0 of unlikely voxel relabeling 50 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4559 voxels changed in iteration 0 of unlikely voxel relabeling 33 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 6483 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 4922 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 361 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1699.176414 mri_ca_label stimesec 0.715853 mri_ca_label ru_maxrss 2128500 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 570758 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 632 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 486 mri_ca_label ru_nivcsw 5534 auto-labeling took 27 minutes and 32 seconds. #-------------------------------------- #@# CC Seg Mon Jan 9 12:35:06 CET 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/cc_up.lta Test will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/cc_up.lta reading aseg from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/aseg.auto_noCCseg.mgz reading norm from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/norm.mgz MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 57485 voxels in left wm, 93161 in right wm, xrange [123, 139] searching rotation angles z=[-11 3], y=[-6 8] searching scale 1 Z rot -10.9 searching scale 1 Z rot -10.7 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.2 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 global minimum found at slice 133.0, rotations (0.56, -4.92) final transformation (x=133.0, yr=0.563, zr=-4.922): 0.99626 0.08580 0.00979 -12.59451; -0.08580 0.99631 -0.00084 56.80095; -0.00983 0.00000 0.99995 30.31233; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 131] in xformed coordinates best xformed slice 127 min_x_fornix = 122 min_x_fornix = 121 min_x_fornix = 121 min_x_fornix = 121 min_x_fornix = 121 cc center is found at 127 83 99 eigenvectors: 0.00223 0.01087 0.99994; -0.29135 -0.95655 0.01104; 0.95661 -0.29136 0.00104; MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab writing aseg with callosum to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #VMPC# mri_cc VmPeak 459224 mri_cc done #-------------------------------------- #@# Merge ASeg Mon Jan 9 12:35:44 CET 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Jan 9 12:35:44 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... NOT doing gentle normalization with control points/label processing with aseg MRIcopyHeader(): source has ctab removing outliers in the aseg WM... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 367 control points removed MRIcopyHeader(): source has ctab Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 80 (80), valley at 22 (22) csf peak at 10, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 79 (79), valley at 19 (19) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 25 seconds. #-------------------------------------------- #@# Mask BFS Mon Jan 9 12:38:11 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1291345 voxels in mask (pct= 7.70) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jan 9 12:38:11 CET 2023 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (102.0): 103.3 +- 6.8 [79.0 --> 125.0] CCS GM (77.0) : 74.4 +- 13.4 [30.0 --> 95.0] white_mean 103.309 white_sigma 6.81111 gray_mean 74.4249 gray_sigma 13.3689 setting bottom of white matter range wm_low to 87.8 setting top of gray matter range gray_hi to 101.2 wm_low 87.7939 wm_hi 125 gray_low 30 gray_hi 101.163 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 87.7939 wm_hi 125 gray_low 30 gray_hi 101.163 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 101.163, wm_low = 87.7939 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=101.163, wmlow=87.7939 163023 voxels processed (0.97%) 69508 voxels white (0.41%) 93515 voxels non-white (0.56%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=82.7939, gray_hi=101.163, wsize=13 350704 voxels tested (2.09%) 63182 voxels changed (0.38%) 79727 multi-scale searches (0.48%) Recovering bright white MRIrecoverBrightWhite() wm_low 87.7939 wm_hi 125 slack 6.81111 pct_thresh 0.33 intensity_thresh 131.811 nvox_thresh 8.58 3870 voxels tested (0.02%) 2265 voxels changed (0.01%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=82.7939, hithr=101.163 smoothing input volume with sigma = 0.250 148462 voxels tested (0.88%) 20523 voxels changed (0.12%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 15089 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 4025 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3329 filled MRIfindBrightNonWM(): 23269 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.37 minutes reading wm segmentation from wm.seg.mgz... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 0 voxels added to wm to prevent paths from MTL structures to cortex 5293 additional wm voxels added 0 additional wm voxels added SEG EDIT: 47098 voxels turned on, 11700 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 63 found - 63 modified | TOTAL: 63 pass 2 (xy+): 0 found - 63 modified | TOTAL: 63 pass 1 (xy-): 64 found - 64 modified | TOTAL: 127 pass 2 (xy-): 0 found - 64 modified | TOTAL: 127 pass 1 (yz+): 53 found - 53 modified | TOTAL: 180 pass 2 (yz+): 0 found - 53 modified | TOTAL: 180 pass 1 (yz-): 56 found - 56 modified | TOTAL: 236 pass 2 (yz-): 0 found - 56 modified | TOTAL: 236 pass 1 (xz+): 40 found - 40 modified | TOTAL: 276 pass 2 (xz+): 0 found - 40 modified | TOTAL: 276 pass 1 (xz-): 40 found - 40 modified | TOTAL: 316 pass 2 (xz-): 0 found - 40 modified | TOTAL: 316 Iteration Number : 1 pass 1 (+++): 115 found - 115 modified | TOTAL: 115 pass 2 (+++): 0 found - 115 modified | TOTAL: 115 pass 1 (+++): 145 found - 145 modified | TOTAL: 260 pass 2 (+++): 0 found - 145 modified | TOTAL: 260 pass 1 (+++): 98 found - 98 modified | TOTAL: 358 pass 2 (+++): 0 found - 98 modified | TOTAL: 358 pass 1 (+++): 91 found - 91 modified | TOTAL: 449 pass 2 (+++): 0 found - 91 modified | TOTAL: 449 Iteration Number : 1 pass 1 (++): 152 found - 152 modified | TOTAL: 152 pass 2 (++): 0 found - 152 modified | TOTAL: 152 pass 1 (+-): 91 found - 91 modified | TOTAL: 243 pass 2 (+-): 0 found - 91 modified | TOTAL: 243 pass 1 (--): 157 found - 157 modified | TOTAL: 400 pass 2 (--): 0 found - 157 modified | TOTAL: 400 pass 1 (-+): 88 found - 88 modified | TOTAL: 488 pass 2 (-+): 0 found - 88 modified | TOTAL: 488 Iteration Number : 2 pass 1 (xy+): 25 found - 25 modified | TOTAL: 25 pass 2 (xy+): 0 found - 25 modified | TOTAL: 25 pass 1 (xy-): 17 found - 17 modified | TOTAL: 42 pass 2 (xy-): 0 found - 17 modified | TOTAL: 42 pass 1 (yz+): 21 found - 21 modified | TOTAL: 63 pass 2 (yz+): 0 found - 21 modified | TOTAL: 63 pass 1 (yz-): 14 found - 14 modified | TOTAL: 77 pass 2 (yz-): 0 found - 14 modified | TOTAL: 77 pass 1 (xz+): 19 found - 19 modified | TOTAL: 96 pass 2 (xz+): 0 found - 19 modified | TOTAL: 96 pass 1 (xz-): 13 found - 13 modified | TOTAL: 109 pass 2 (xz-): 0 found - 13 modified | TOTAL: 109 Iteration Number : 2 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 6 found - 6 modified | TOTAL: 16 pass 2 (+++): 0 found - 6 modified | TOTAL: 16 pass 1 (+++): 4 found - 4 modified | TOTAL: 20 pass 2 (+++): 0 found - 4 modified | TOTAL: 20 pass 1 (+++): 4 found - 4 modified | TOTAL: 24 pass 2 (+++): 0 found - 4 modified | TOTAL: 24 Iteration Number : 2 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 14 found - 14 modified | TOTAL: 27 pass 2 (+-): 0 found - 14 modified | TOTAL: 27 pass 1 (--): 11 found - 11 modified | TOTAL: 38 pass 2 (--): 0 found - 11 modified | TOTAL: 38 pass 1 (-+): 9 found - 9 modified | TOTAL: 47 pass 2 (-+): 0 found - 9 modified | TOTAL: 47 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 5 found - 5 modified | TOTAL: 5 pass 2 (xy-): 0 found - 5 modified | TOTAL: 5 pass 1 (yz+): 1 found - 1 modified | TOTAL: 6 pass 2 (yz+): 0 found - 1 modified | TOTAL: 6 pass 1 (yz-): 5 found - 5 modified | TOTAL: 11 pass 2 (yz-): 0 found - 5 modified | TOTAL: 11 pass 1 (xz+): 2 found - 2 modified | TOTAL: 13 pass 2 (xz+): 0 found - 2 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 4 found - 4 modified | TOTAL: 4 pass 2 (--): 0 found - 4 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1451 (out of 481238: 0.301514) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Jan 9 12:40:03 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.11217 0.03154 -0.04637 -18.33588; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21301; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.11217 0.03154 -0.04637 -18.33588; -0.07102 1.09358 0.46400 -28.72086; 0.06245 -0.41768 0.94931 43.21301; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Looking for area (min, max) = (350, 1400) area[0] = 1795 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) need search nearby using seed (124, 120, 151), TAL = (4.0, 23.0, 8.0) talairach voxel to voxel transform 0.89598 -0.00769 0.04752 14.15422; 0.07011 0.76997 -0.37292 39.51464; -0.02809 0.33928 0.88620 -29.06593; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 120, 151) --> (4.0, 23.0, 8.0) done. filling took 1.0 minutes talairach cc position changed to (4.00, 23.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 23.00, 8.00) SRC: (115.38, 83.03, 142.49) search lh wm seed point around talairach space (-14.00, 23.00, 8.00), SRC: (147.64, 85.56, 141.47) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Mon Jan 9 12:41:00 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 9 found - 9 modified | TOTAL: 14 pass 2 (xy-): 0 found - 9 modified | TOTAL: 14 pass 1 (yz+): 10 found - 10 modified | TOTAL: 24 pass 2 (yz+): 0 found - 10 modified | TOTAL: 24 pass 1 (yz-): 5 found - 5 modified | TOTAL: 29 pass 2 (yz-): 0 found - 5 modified | TOTAL: 29 pass 1 (xz+): 3 found - 3 modified | TOTAL: 32 pass 2 (xz+): 0 found - 3 modified | TOTAL: 32 pass 1 (xz-): 1 found - 1 modified | TOTAL: 33 pass 2 (xz-): 0 found - 1 modified | TOTAL: 33 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 1 found - 1 modified | TOTAL: 6 pass 2 (+-): 0 found - 1 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 53 (out of 231176: 0.022926) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.2.0 7.2.0 slice 30: 23 vertices, 32 faces slice 40: 5295 vertices, 5583 faces slice 50: 15245 vertices, 15644 faces slice 60: 25697 vertices, 26118 faces slice 70: 36554 vertices, 37037 faces slice 80: 47216 vertices, 47677 faces slice 90: 58129 vertices, 58667 faces slice 100: 69147 vertices, 69655 faces slice 110: 79303 vertices, 79809 faces slice 120: 87834 vertices, 88330 faces slice 130: 96620 vertices, 97111 faces slice 140: 104146 vertices, 104608 faces slice 150: 111159 vertices, 111580 faces slice 160: 116501 vertices, 116875 faces slice 170: 120856 vertices, 121193 faces slice 180: 123144 vertices, 123408 faces slice 190: 123264 vertices, 123486 faces slice 200: 123264 vertices, 123486 faces slice 210: 123264 vertices, 123486 faces slice 220: 123264 vertices, 123486 faces slice 230: 123264 vertices, 123486 faces slice 240: 123264 vertices, 123486 faces slice 250: 123264 vertices, 123486 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 123256 voxel in cpt #1: X=-224 [v=123256,e=370440,f=246960] located at (-27.949211, -33.008633, 30.394667) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-4.000000, 2.000000, 34.000000) For the whole surface: X=-222 [v=123264,e=370458,f=246972] 2 components have been found keeping component #1 with 123256 vertices done #-------------------------------------------- #@# Tessellate rh Mon Jan 9 12:41:03 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 14 found - 14 modified | TOTAL: 20 pass 2 (xy-): 0 found - 14 modified | TOTAL: 20 pass 1 (yz+): 9 found - 9 modified | TOTAL: 29 pass 2 (yz+): 0 found - 9 modified | TOTAL: 29 pass 1 (yz-): 13 found - 13 modified | TOTAL: 42 pass 2 (yz-): 0 found - 13 modified | TOTAL: 42 pass 1 (xz+): 7 found - 7 modified | TOTAL: 49 pass 2 (xz+): 0 found - 7 modified | TOTAL: 49 pass 1 (xz-): 2 found - 2 modified | TOTAL: 51 pass 2 (xz-): 0 found - 2 modified | TOTAL: 51 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 1 found - 1 modified | TOTAL: 5 pass 2 (+++): 0 found - 1 modified | TOTAL: 5 pass 1 (+++): 2 found - 2 modified | TOTAL: 7 pass 2 (+++): 0 found - 2 modified | TOTAL: 7 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 4 found - 4 modified | TOTAL: 9 pass 2 (+-): 0 found - 4 modified | TOTAL: 9 pass 1 (--): 2 found - 2 modified | TOTAL: 11 pass 2 (--): 0 found - 2 modified | TOTAL: 11 pass 1 (-+): 0 found - 0 modified | TOTAL: 11 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 70 (out of 228304: 0.030661) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.2.0 7.2.0 slice 40: 3731 vertices, 3933 faces slice 50: 11617 vertices, 12029 faces slice 60: 24236 vertices, 24787 faces slice 70: 37038 vertices, 37572 faces slice 80: 48900 vertices, 49449 faces slice 90: 59407 vertices, 59960 faces slice 100: 70281 vertices, 70848 faces slice 110: 79982 vertices, 80530 faces slice 120: 89032 vertices, 89571 faces slice 130: 98132 vertices, 98661 faces slice 140: 106144 vertices, 106623 faces slice 150: 113156 vertices, 113625 faces slice 160: 118546 vertices, 118950 faces slice 170: 122305 vertices, 122662 faces slice 180: 124344 vertices, 124619 faces slice 190: 124470 vertices, 124716 faces slice 200: 124470 vertices, 124716 faces slice 210: 124470 vertices, 124716 faces slice 220: 124470 vertices, 124716 faces slice 230: 124470 vertices, 124716 faces slice 240: 124470 vertices, 124716 faces slice 250: 124470 vertices, 124716 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 124470 voxel in cpt #1: X=-246 [v=124470,e=374148,f=249432] located at (20.403656, -32.920368, 35.060471) For the whole surface: X=-246 [v=124470,e=374148,f=249432] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Jan 9 12:41:06 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Mon Jan 9 12:41:06 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 322849 of (322849 322852) to complete... Waiting for PID 322852 of (322849 322852) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (322849 322852) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Mon Jan 9 12:41:08 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Mon Jan 9 12:41:08 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 322903 of (322903 322906) to complete... Waiting for PID 322906 of (322903 322906) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.8 mm, total surface area = 63374 mm^2 step 000: RMS=0.175 (target=0.015) step 005: RMS=0.135 (target=0.015) step 010: RMS=0.108 (target=0.015) step 015: RMS=0.099 (target=0.015) step 020: RMS=0.093 (target=0.015) step 025: RMS=0.088 (target=0.015) step 030: RMS=0.083 (target=0.015) step 035: RMS=0.081 (target=0.015) step 040: RMS=0.078 (target=0.015) step 045: RMS=0.078 (target=0.015) step 050: RMS=0.077 (target=0.015) step 055: RMS=0.078 (target=0.015) step 060: RMS=0.079 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 28.910067 mris_inflate stimesec 0.743950 mris_inflate ru_maxrss 200664 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 410189 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8680 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 860 mris_inflate ru_nivcsw 118 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.1 mm, total surface area = 63475 mm^2 step 000: RMS=0.176 (target=0.015) step 005: RMS=0.135 (target=0.015) step 010: RMS=0.112 (target=0.015) step 015: RMS=0.104 (target=0.015) step 020: RMS=0.097 (target=0.015) step 025: RMS=0.093 (target=0.015) step 030: RMS=0.090 (target=0.015) step 035: RMS=0.087 (target=0.015) step 040: RMS=0.085 (target=0.015) step 045: RMS=0.084 (target=0.015) step 050: RMS=0.083 (target=0.015) step 055: RMS=0.085 (target=0.015) step 060: RMS=0.086 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 28.591559 mris_inflate stimesec 0.814733 mris_inflate ru_maxrss 202556 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 427088 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8768 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 816 mris_inflate ru_nivcsw 36 PIDs (322903 322906) completed and logs appended. #-------------------------------------------- #@# QSphere lh Mon Jan 9 12:41:20 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Mon Jan 9 12:41:20 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 322956 of (322956 322959) to complete... Waiting for PID 322959 of (322956 322959) to complete... mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 scaling brain by 0.346... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.65 (0.00-->6.46) (max @ vno 91904 --> 91905) face area 0.03 +- 0.04 (-0.25-->0.66) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.643, avgs=0 005/300: dt: 0.9000, rms radial error=175.387, avgs=0 010/300: dt: 0.9000, rms radial error=174.837, avgs=0 015/300: dt: 0.9000, rms radial error=174.116, avgs=0 020/300: dt: 0.9000, rms radial error=173.294, avgs=0 025/300: dt: 0.9000, rms radial error=172.415, avgs=0 030/300: dt: 0.9000, rms radial error=171.502, avgs=0 035/300: dt: 0.9000, rms radial error=170.572, avgs=0 040/300: dt: 0.9000, rms radial error=169.633, avgs=0 045/300: dt: 0.9000, rms radial error=168.693, avgs=0 050/300: dt: 0.9000, rms radial error=167.754, avgs=0 055/300: dt: 0.9000, rms radial error=166.815, avgs=0 060/300: dt: 0.9000, rms radial error=165.880, avgs=0 065/300: dt: 0.9000, rms radial error=164.948, avgs=0 070/300: dt: 0.9000, rms radial error=164.018, avgs=0 075/300: dt: 0.9000, rms radial error=163.093, avgs=0 080/300: dt: 0.9000, rms radial error=162.173, avgs=0 085/300: dt: 0.9000, rms radial error=161.257, avgs=0 090/300: dt: 0.9000, rms radial error=160.345, avgs=0 095/300: dt: 0.9000, rms radial error=159.437, avgs=0 100/300: dt: 0.9000, rms radial error=158.534, avgs=0 105/300: dt: 0.9000, rms radial error=157.635, avgs=0 110/300: dt: 0.9000, rms radial error=156.749, avgs=0 115/300: dt: 0.9000, rms radial error=155.867, avgs=0 120/300: dt: 0.9000, rms radial error=154.990, avgs=0 125/300: dt: 0.9000, rms radial error=154.118, avgs=0 130/300: dt: 0.9000, rms radial error=153.250, avgs=0 135/300: dt: 0.9000, rms radial error=152.388, avgs=0 140/300: dt: 0.9000, rms radial error=151.531, avgs=0 145/300: dt: 0.9000, rms radial error=150.678, avgs=0 150/300: dt: 0.9000, rms radial error=149.829, avgs=0 155/300: dt: 0.9000, rms radial error=148.985, avgs=0 160/300: dt: 0.9000, rms radial error=148.146, avgs=0 165/300: dt: 0.9000, rms radial error=147.312, avgs=0 170/300: dt: 0.9000, rms radial error=146.482, avgs=0 175/300: dt: 0.9000, rms radial error=145.656, avgs=0 180/300: dt: 0.9000, rms radial error=144.835, avgs=0 185/300: dt: 0.9000, rms radial error=144.019, avgs=0 190/300: dt: 0.9000, rms radial error=143.208, avgs=0 195/300: dt: 0.9000, rms radial error=142.401, avgs=0 200/300: dt: 0.9000, rms radial error=141.598, avgs=0 205/300: dt: 0.9000, rms radial error=140.800, avgs=0 210/300: dt: 0.9000, rms radial error=140.006, avgs=0 215/300: dt: 0.9000, rms radial error=139.217, avgs=0 220/300: dt: 0.9000, rms radial error=138.432, avgs=0 225/300: dt: 0.9000, rms radial error=137.651, avgs=0 230/300: dt: 0.9000, rms radial error=136.875, avgs=0 235/300: dt: 0.9000, rms radial error=136.103, avgs=0 240/300: dt: 0.9000, rms radial error=135.336, avgs=0 245/300: dt: 0.9000, rms radial error=134.573, avgs=0 250/300: dt: 0.9000, rms radial error=133.814, avgs=0 255/300: dt: 0.9000, rms radial error=133.059, avgs=0 260/300: dt: 0.9000, rms radial error=132.309, avgs=0 265/300: dt: 0.9000, rms radial error=131.562, avgs=0 270/300: dt: 0.9000, rms radial error=130.820, avgs=0 275/300: dt: 0.9000, rms radial error=130.081, avgs=0 280/300: dt: 0.9000, rms radial error=129.347, avgs=0 285/300: dt: 0.9000, rms radial error=128.617, avgs=0 290/300: dt: 0.9000, rms radial error=127.890, avgs=0 295/300: dt: 0.9000, rms radial error=127.168, avgs=0 300/300: dt: 0.9000, rms radial error=126.450, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14065.16 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00039 epoch 2 (K=40.0), pass 1, starting sse = 2282.13 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00047 epoch 3 (K=160.0), pass 1, starting sse = 269.31 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/14 = 0.00363 epoch 4 (K=640.0), pass 1, starting sse = 38.39 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/18 = 0.00486 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0166 hours FSRUNTIME@ mris_sphere 0.0166 hours 4 threads #VMPC# mris_sphere VmPeak 777136 mris_sphere done mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 scaling brain by 0.344... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.66 (0.00-->8.47) (max @ vno 100446 --> 100447) face area 0.03 +- 0.04 (-0.31-->0.77) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.706, avgs=0 005/300: dt: 0.9000, rms radial error=175.452, avgs=0 010/300: dt: 0.9000, rms radial error=174.906, avgs=0 015/300: dt: 0.9000, rms radial error=174.188, avgs=0 020/300: dt: 0.9000, rms radial error=173.370, avgs=0 025/300: dt: 0.9000, rms radial error=172.494, avgs=0 030/300: dt: 0.9000, rms radial error=171.586, avgs=0 035/300: dt: 0.9000, rms radial error=170.656, avgs=0 040/300: dt: 0.9000, rms radial error=169.717, avgs=0 045/300: dt: 0.9000, rms radial error=168.774, avgs=0 050/300: dt: 0.9000, rms radial error=167.832, avgs=0 055/300: dt: 0.9000, rms radial error=166.891, avgs=0 060/300: dt: 0.9000, rms radial error=165.954, avgs=0 065/300: dt: 0.9000, rms radial error=165.020, avgs=0 070/300: dt: 0.9000, rms radial error=164.090, avgs=0 075/300: dt: 0.9000, rms radial error=163.164, avgs=0 080/300: dt: 0.9000, rms radial error=162.243, avgs=0 085/300: dt: 0.9000, rms radial error=161.326, avgs=0 090/300: dt: 0.9000, rms radial error=160.420, avgs=0 095/300: dt: 0.9000, rms radial error=159.518, avgs=0 100/300: dt: 0.9000, rms radial error=158.621, avgs=0 105/300: dt: 0.9000, rms radial error=157.729, avgs=0 110/300: dt: 0.9000, rms radial error=156.841, avgs=0 115/300: dt: 0.9000, rms radial error=155.958, avgs=0 120/300: dt: 0.9000, rms radial error=155.079, avgs=0 125/300: dt: 0.9000, rms radial error=154.204, avgs=0 130/300: dt: 0.9000, rms radial error=153.334, avgs=0 135/300: dt: 0.9000, rms radial error=152.469, avgs=0 140/300: dt: 0.9000, rms radial error=151.607, avgs=0 145/300: dt: 0.9000, rms radial error=150.750, avgs=0 150/300: dt: 0.9000, rms radial error=149.900, avgs=0 155/300: dt: 0.9000, rms radial error=149.056, avgs=0 160/300: dt: 0.9000, rms radial error=148.217, avgs=0 165/300: dt: 0.9000, rms radial error=147.382, avgs=0 170/300: dt: 0.9000, rms radial error=146.552, avgs=0 175/300: dt: 0.9000, rms radial error=145.727, avgs=0 180/300: dt: 0.9000, rms radial error=144.905, avgs=0 185/300: dt: 0.9000, rms radial error=144.089, avgs=0 190/300: dt: 0.9000, rms radial error=143.277, avgs=0 195/300: dt: 0.9000, rms radial error=142.469, avgs=0 200/300: dt: 0.9000, rms radial error=141.667, avgs=0 205/300: dt: 0.9000, rms radial error=140.868, avgs=0 210/300: dt: 0.9000, rms radial error=140.074, avgs=0 215/300: dt: 0.9000, rms radial error=139.285, avgs=0 220/300: dt: 0.9000, rms radial error=138.499, avgs=0 225/300: dt: 0.9000, rms radial error=137.719, avgs=0 230/300: dt: 0.9000, rms radial error=136.942, avgs=0 235/300: dt: 0.9000, rms radial error=136.170, avgs=0 240/300: dt: 0.9000, rms radial error=135.402, avgs=0 245/300: dt: 0.9000, rms radial error=134.638, avgs=0 250/300: dt: 0.9000, rms radial error=133.878, avgs=0 255/300: dt: 0.9000, rms radial error=133.123, avgs=0 260/300: dt: 0.9000, rms radial error=132.372, avgs=0 265/300: dt: 0.9000, rms radial error=131.625, avgs=0 270/300: dt: 0.9000, rms radial error=130.882, avgs=0 275/300: dt: 0.9000, rms radial error=130.143, avgs=0 280/300: dt: 0.9000, rms radial error=129.408, avgs=0 285/300: dt: 0.9000, rms radial error=128.678, avgs=0 290/300: dt: 0.9000, rms radial error=127.952, avgs=0 295/300: dt: 0.9000, rms radial error=127.229, avgs=0 300/300: dt: 0.9000, rms radial error=126.511, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14240.30 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00036 epoch 2 (K=40.0), pass 1, starting sse = 2326.57 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00042 epoch 3 (K=160.0), pass 1, starting sse = 287.05 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/13 = 0.00383 epoch 4 (K=640.0), pass 1, starting sse = 44.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/16 = 0.00447 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0159 hours FSRUNTIME@ mris_sphere 0.0159 hours 4 threads #VMPC# mris_sphere VmPeak 778132 mris_sphere done PIDs (322956 322959) completed and logs appended. #@# Fix Topology lh Mon Jan 9 12:42:19 CET 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test lh #@# Fix Topology rh Mon Jan 9 12:42:19 CET 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test rh Waiting for PID 323002 of (323002 323005) to complete... Waiting for PID 323005 of (323002 323005) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.2.0 7.2.0 before topology correction, eno=-224 (nv=123256, nf=246960, ne=370440, g=113) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 24468 ambiguous faces found in tessellation segmenting defects... 102 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 22 -merging segment 30 into 29 -merging segment 45 into 39 -merging segment 67 into 57 -merging segment 65 into 59 -merging segment 73 into 60 96 defects to be corrected 0 vertices coincident reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.6270 (-4.3135) -vertex loglikelihood: -6.0766 (-3.0383) -normal dot loglikelihood: -3.5835 (-3.5835) -quad curv loglikelihood: -6.1487 (-3.0744) Total Loglikelihood : -24.4358 CORRECTING DEFECT 0 (vertices=28, convex hull=53, v0=0) After retessellation of defect 0 (v0=0), euler #=-96 (109387,324789,215306) : difference with theory (-93) = 3 CORRECTING DEFECT 1 (vertices=10, convex hull=19, v0=13) After retessellation of defect 1 (v0=13), euler #=-95 (109388,324798,215315) : difference with theory (-92) = 3 CORRECTING DEFECT 2 (vertices=181, convex hull=118, v0=23) After retessellation of defect 2 (v0=23), euler #=-94 (109433,324987,215460) : difference with theory (-91) = 3 CORRECTING DEFECT 3 (vertices=24, convex hull=35, v0=178) After retessellation of defect 3 (v0=178), euler #=-93 (109439,325016,215484) : difference with theory (-90) = 3 CORRECTING DEFECT 4 (vertices=49, convex hull=71, v0=267) After retessellation of defect 4 (v0=267), euler #=-92 (109452,325086,215542) : difference with theory (-89) = 3 CORRECTING DEFECT 5 (vertices=7, convex hull=17, v0=1113) After retessellation of defect 5 (v0=1113), euler #=-91 (109453,325093,215549) : difference with theory (-88) = 3 CORRECTING DEFECT 6 (vertices=88, convex hull=113, v0=1295) After retessellation of defect 6 (v0=1295), euler #=-90 (109494,325265,215681) : difference with theory (-87) = 3 CORRECTING DEFECT 7 (vertices=30, convex hull=30, v0=1301) After retessellation of defect 7 (v0=1301), euler #=-89 (109500,325291,215702) : difference with theory (-86) = 3 CORRECTING DEFECT 8 (vertices=7, convex hull=17, v0=1855) After retessellation of defect 8 (v0=1855), euler #=-88 (109500,325295,215707) : difference with theory (-85) = 3 CORRECTING DEFECT 9 (vertices=322, convex hull=137, v0=1950) After retessellation of defect 9 (v0=1950), euler #=-87 (109518,325412,215807) : difference with theory (-84) = 3 CORRECTING DEFECT 10 (vertices=203, convex hull=139, v0=2032) After retessellation of defect 10 (v0=2032), euler #=-86 (109584,325673,216003) : difference with theory (-83) = 3 CORRECTING DEFECT 11 (vertices=179, convex hull=130, v0=2205) After retessellation of defect 11 (v0=2205), euler #=-85 (109622,325847,216140) : difference with theory (-82) = 3 CORRECTING DEFECT 12 (vertices=15, convex hull=19, v0=2367) After retessellation of defect 12 (v0=2367), euler #=-84 (109622,325851,216145) : difference with theory (-81) = 3 CORRECTING DEFECT 13 (vertices=245, convex hull=103, v0=3404) After retessellation of defect 13 (v0=3404), euler #=-83 (109630,325920,216207) : difference with theory (-80) = 3 CORRECTING DEFECT 14 (vertices=800, convex hull=279, v0=3554) After retessellation of defect 14 (v0=3554), euler #=-82 (109653,326127,216392) : difference with theory (-79) = 3 CORRECTING DEFECT 15 (vertices=341, convex hull=65, v0=4778) After retessellation of defect 15 (v0=4778), euler #=-81 (109676,326221,216464) : difference with theory (-78) = 3 CORRECTING DEFECT 16 (vertices=135, convex hull=95, v0=8600) After retessellation of defect 16 (v0=8600), euler #=-80 (109712,326373,216581) : difference with theory (-77) = 3 CORRECTING DEFECT 17 (vertices=191, convex hull=77, v0=9050) After retessellation of defect 17 (v0=9050), euler #=-79 (109744,326500,216677) : difference with theory (-76) = 3 CORRECTING DEFECT 18 (vertices=60, convex hull=31, v0=9330) After retessellation of defect 18 (v0=9330), euler #=-78 (109750,326527,216699) : difference with theory (-75) = 3 CORRECTING DEFECT 19 (vertices=84, convex hull=30, v0=9814) After retessellation of defect 19 (v0=9814), euler #=-77 (109753,326543,216713) : difference with theory (-74) = 3 CORRECTING DEFECT 20 (vertices=47, convex hull=27, v0=10264) After retessellation of defect 20 (v0=10264), euler #=-76 (109756,326559,216727) : difference with theory (-73) = 3 CORRECTING DEFECT 21 (vertices=81, convex hull=104, v0=11186) After retessellation of defect 21 (v0=11186), euler #=-75 (109766,326640,216799) : difference with theory (-72) = 3 CORRECTING DEFECT 22 (vertices=22, convex hull=46, v0=12010) After retessellation of defect 22 (v0=12010), euler #=-73 (109770,326669,216826) : difference with theory (-71) = 2 CORRECTING DEFECT 23 (vertices=108, convex hull=51, v0=13338) After retessellation of defect 23 (v0=13338), euler #=-72 (109785,326736,216879) : difference with theory (-70) = 2 CORRECTING DEFECT 24 (vertices=25, convex hull=23, v0=13685) After retessellation of defect 24 (v0=13685), euler #=-71 (109786,326747,216890) : difference with theory (-69) = 2 CORRECTING DEFECT 25 (vertices=41, convex hull=71, v0=14387) After retessellation of defect 25 (v0=14387), euler #=-70 (109809,326846,216967) : difference with theory (-68) = 2 CORRECTING DEFECT 26 (vertices=214, convex hull=108, v0=15729) After retessellation of defect 26 (v0=15729), euler #=-69 (109827,326945,217049) : difference with theory (-67) = 2 CORRECTING DEFECT 27 (vertices=25, convex hull=61, v0=16344) After retessellation of defect 27 (v0=16344), euler #=-68 (109839,327006,217099) : difference with theory (-66) = 2 CORRECTING DEFECT 28 (vertices=351, convex hull=270, v0=16871) After retessellation of defect 28 (v0=16871), euler #=-66 (109935,327446,217445) : difference with theory (-65) = 1 CORRECTING DEFECT 29 (vertices=198, convex hull=82, v0=20320) After retessellation of defect 29 (v0=20320), euler #=-65 (109953,327541,217523) : difference with theory (-64) = 1 CORRECTING DEFECT 30 (vertices=33, convex hull=29, v0=23372) After retessellation of defect 30 (v0=23372), euler #=-64 (109956,327560,217540) : difference with theory (-63) = 1 CORRECTING DEFECT 31 (vertices=82, convex hull=57, v0=23795) After retessellation of defect 31 (v0=23795), euler #=-63 (109974,327637,217600) : difference with theory (-62) = 1 CORRECTING DEFECT 32 (vertices=22, convex hull=45, v0=25337) After retessellation of defect 32 (v0=25337), euler #=-62 (109986,327691,217643) : difference with theory (-61) = 1 CORRECTING DEFECT 33 (vertices=67, convex hull=53, v0=26540) After retessellation of defect 33 (v0=26540), euler #=-61 (109995,327738,217682) : difference with theory (-60) = 1 CORRECTING DEFECT 34 (vertices=28, convex hull=31, v0=26566) After retessellation of defect 34 (v0=26566), euler #=-60 (110000,327766,217706) : difference with theory (-59) = 1 CORRECTING DEFECT 35 (vertices=1368, convex hull=245, v0=26766) After retessellation of defect 35 (v0=26766), euler #=-59 (110149,328328,218120) : difference with theory (-58) = 1 CORRECTING DEFECT 36 (vertices=209, convex hull=61, v0=27445) After retessellation of defect 36 (v0=27445), euler #=-58 (110165,328400,218177) : difference with theory (-57) = 1 CORRECTING DEFECT 37 (vertices=190, convex hull=135, v0=27497) After retessellation of defect 37 (v0=27497), euler #=-56 (110228,328661,218377) : difference with theory (-56) = 0 CORRECTING DEFECT 38 (vertices=107, convex hull=87, v0=27609) After retessellation of defect 38 (v0=27609), euler #=-55 (110257,328784,218472) : difference with theory (-55) = 0 CORRECTING DEFECT 39 (vertices=43, convex hull=30, v0=29708) After retessellation of defect 39 (v0=29708), euler #=-54 (110263,328811,218494) : difference with theory (-54) = 0 CORRECTING DEFECT 40 (vertices=17, convex hull=25, v0=30030) After retessellation of defect 40 (v0=30030), euler #=-53 (110265,328825,218507) : difference with theory (-53) = 0 CORRECTING DEFECT 41 (vertices=101, convex hull=65, v0=30157) After retessellation of defect 41 (v0=30157), euler #=-52 (110281,328900,218567) : difference with theory (-52) = 0 CORRECTING DEFECT 42 (vertices=109, convex hull=60, v0=34121) After retessellation of defect 42 (v0=34121), euler #=-51 (110303,328985,218631) : difference with theory (-51) = 0 CORRECTING DEFECT 43 (vertices=56, convex hull=76, v0=35484) After retessellation of defect 43 (v0=35484), euler #=-50 (110331,329100,218719) : difference with theory (-50) = 0 CORRECTING DEFECT 44 (vertices=215, convex hull=76, v0=36022) After retessellation of defect 44 (v0=36022), euler #=-49 (110358,329211,218804) : difference with theory (-49) = 0 CORRECTING DEFECT 45 (vertices=22, convex hull=51, v0=38942) After retessellation of defect 45 (v0=38942), euler #=-48 (110372,329271,218851) : difference with theory (-48) = 0 CORRECTING DEFECT 46 (vertices=69, convex hull=50, v0=39690) After retessellation of defect 46 (v0=39690), euler #=-47 (110389,329344,218908) : difference with theory (-47) = 0 CORRECTING DEFECT 47 (vertices=74, convex hull=80, v0=39760) After retessellation of defect 47 (v0=39760), euler #=-46 (110416,329459,218997) : difference with theory (-46) = 0 CORRECTING DEFECT 48 (vertices=38, convex hull=47, v0=41586) After retessellation of defect 48 (v0=41586), euler #=-45 (110427,329507,219035) : difference with theory (-45) = 0 CORRECTING DEFECT 49 (vertices=15, convex hull=36, v0=42248) After retessellation of defect 49 (v0=42248), euler #=-44 (110429,329528,219055) : difference with theory (-44) = 0 CORRECTING DEFECT 50 (vertices=23, convex hull=32, v0=43161) After retessellation of defect 50 (v0=43161), euler #=-43 (110433,329551,219075) : difference with theory (-43) = 0 CORRECTING DEFECT 51 (vertices=10, convex hull=21, v0=45479) After retessellation of defect 51 (v0=45479), euler #=-42 (110434,329558,219082) : difference with theory (-42) = 0 CORRECTING DEFECT 52 (vertices=38, convex hull=45, v0=45996) After retessellation of defect 52 (v0=45996), euler #=-41 (110443,329598,219114) : difference with theory (-41) = 0 CORRECTING DEFECT 53 (vertices=15, convex hull=19, v0=46291) After retessellation of defect 53 (v0=46291), euler #=-40 (110445,329612,219127) : difference with theory (-40) = 0 CORRECTING DEFECT 54 (vertices=3641, convex hull=1051, v0=48001) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 54 (v0=48001), euler #=-41 (111591,333654,222022) : difference with theory (-39) = 2 CORRECTING DEFECT 55 (vertices=51, convex hull=80, v0=48079) After retessellation of defect 55 (v0=48079), euler #=-40 (111629,333800,222131) : difference with theory (-38) = 2 CORRECTING DEFECT 56 (vertices=388, convex hull=205, v0=50647) After retessellation of defect 56 (v0=50647), euler #=-38 (111673,334035,222324) : difference with theory (-37) = 1 CORRECTING DEFECT 57 (vertices=481, convex hull=108, v0=52808) v 120811 (69428) --> 120951 (72721), len = 95.743 INFLATED: (-59.5, -28.5, 49.5) --> (-54.5, -25.5, 45.5), len = 7.07 CANON: (-82.7, -24.5, 50.6) --> (-81.8, -19.5, 54.1), len = 6.17 CURRENT: (-59.5, -28.5, 49.5) --> (-54.5, -25.5, 45.5), len = 7.07 ORIG: (-59.2, -28.3, 49.9) --> (-54.3, -25.6, 45.6), len = 7.07 After retessellation of defect 57 (v0=52808), euler #=-36 (111695,334165,222434) : difference with theory (-36) = 0 CORRECTING DEFECT 58 (vertices=9, convex hull=24, v0=57448) After retessellation of defect 58 (v0=57448), euler #=-35 (111696,334174,222443) : difference with theory (-35) = 0 CORRECTING DEFECT 59 (vertices=20, convex hull=24, v0=57896) After retessellation of defect 59 (v0=57896), euler #=-34 (111699,334190,222457) : difference with theory (-34) = 0 CORRECTING DEFECT 60 (vertices=50, convex hull=51, v0=62316) After retessellation of defect 60 (v0=62316), euler #=-33 (111709,334237,222495) : difference with theory (-33) = 0 CORRECTING DEFECT 61 (vertices=38, convex hull=80, v0=63380) After retessellation of defect 61 (v0=63380), euler #=-32 (111727,334324,222565) : difference with theory (-32) = 0 CORRECTING DEFECT 62 (vertices=196, convex hull=40, v0=64246) After retessellation of defect 62 (v0=64246), euler #=-31 (111737,334367,222599) : difference with theory (-31) = 0 CORRECTING DEFECT 63 (vertices=63, convex hull=79, v0=66279) After retessellation of defect 63 (v0=66279), euler #=-30 (111751,334441,222660) : difference with theory (-30) = 0 CORRECTING DEFECT 64 (vertices=8, convex hull=8, v0=66290) After retessellation of defect 64 (v0=66290), euler #=-29 (111752,334445,222664) : difference with theory (-29) = 0 CORRECTING DEFECT 65 (vertices=17, convex hull=31, v0=70310) After retessellation of defect 65 (v0=70310), euler #=-28 (111755,334463,222680) : difference with theory (-28) = 0 CORRECTING DEFECT 66 (vertices=335, convex hull=85, v0=70639) After retessellation of defect 66 (v0=70639), euler #=-27 (111773,334552,222752) : difference with theory (-27) = 0 CORRECTING DEFECT 67 (vertices=45, convex hull=75, v0=72307) After retessellation of defect 67 (v0=72307), euler #=-26 (111789,334631,222816) : difference with theory (-26) = 0 CORRECTING DEFECT 68 (vertices=11, convex hull=27, v0=72791) After retessellation of defect 68 (v0=72791), euler #=-25 (111796,334658,222837) : difference with theory (-25) = 0 CORRECTING DEFECT 69 (vertices=65, convex hull=76, v0=73040) After retessellation of defect 69 (v0=73040), euler #=-24 (111813,334743,222906) : difference with theory (-24) = 0 CORRECTING DEFECT 70 (vertices=28, convex hull=64, v0=74348) After retessellation of defect 70 (v0=74348), euler #=-23 (111830,334817,222964) : difference with theory (-23) = 0 CORRECTING DEFECT 71 (vertices=21, convex hull=49, v0=79567) After retessellation of defect 71 (v0=79567), euler #=-22 (111839,334860,222999) : difference with theory (-22) = 0 CORRECTING DEFECT 72 (vertices=37, convex hull=70, v0=81742) After retessellation of defect 72 (v0=81742), euler #=-21 (111863,334961,223077) : difference with theory (-21) = 0 CORRECTING DEFECT 73 (vertices=74, convex hull=73, v0=83078) After retessellation of defect 73 (v0=83078), euler #=-20 (111898,335097,223179) : difference with theory (-20) = 0 CORRECTING DEFECT 74 (vertices=26, convex hull=69, v0=91263) After retessellation of defect 74 (v0=91263), euler #=-19 (111915,335174,223240) : difference with theory (-19) = 0 CORRECTING DEFECT 75 (vertices=36, convex hull=76, v0=91819) After retessellation of defect 75 (v0=91819), euler #=-18 (111939,335273,223316) : difference with theory (-18) = 0 CORRECTING DEFECT 76 (vertices=218, convex hull=166, v0=92025) After retessellation of defect 76 (v0=92025), euler #=-17 (112035,335640,223588) : difference with theory (-17) = 0 CORRECTING DEFECT 77 (vertices=24, convex hull=40, v0=94399) After retessellation of defect 77 (v0=94399), euler #=-16 (112048,335694,223630) : difference with theory (-16) = 0 CORRECTING DEFECT 78 (vertices=98, convex hull=47, v0=97181) After retessellation of defect 78 (v0=97181), euler #=-15 (112057,335741,223669) : difference with theory (-15) = 0 CORRECTING DEFECT 79 (vertices=33, convex hull=59, v0=97194) After retessellation of defect 79 (v0=97194), euler #=-14 (112070,335809,223725) : difference with theory (-14) = 0 CORRECTING DEFECT 80 (vertices=8, convex hull=13, v0=98443) After retessellation of defect 80 (v0=98443), euler #=-13 (112071,335815,223731) : difference with theory (-13) = 0 CORRECTING DEFECT 81 (vertices=12, convex hull=15, v0=99584) After retessellation of defect 81 (v0=99584), euler #=-12 (112072,335824,223740) : difference with theory (-12) = 0 CORRECTING DEFECT 82 (vertices=41, convex hull=75, v0=100321) After retessellation of defect 82 (v0=100321), euler #=-11 (112096,335928,223821) : difference with theory (-11) = 0 CORRECTING DEFECT 83 (vertices=24, convex hull=61, v0=101985) After retessellation of defect 83 (v0=101985), euler #=-10 (112107,335984,223867) : difference with theory (-10) = 0 CORRECTING DEFECT 84 (vertices=10, convex hull=14, v0=102296) After retessellation of defect 84 (v0=102296), euler #=-9 (112109,335994,223876) : difference with theory (-9) = 0 CORRECTING DEFECT 85 (vertices=58, convex hull=104, v0=103938) After retessellation of defect 85 (v0=103938), euler #=-8 (112122,336085,223955) : difference with theory (-8) = 0 CORRECTING DEFECT 86 (vertices=168, convex hull=39, v0=103951) After retessellation of defect 86 (v0=103951), euler #=-7 (112131,336126,223988) : difference with theory (-7) = 0 CORRECTING DEFECT 87 (vertices=6, convex hull=25, v0=105252) After retessellation of defect 87 (v0=105252), euler #=-6 (112133,336140,224001) : difference with theory (-6) = 0 CORRECTING DEFECT 88 (vertices=36, convex hull=32, v0=105485) After retessellation of defect 88 (v0=105485), euler #=-5 (112136,336163,224022) : difference with theory (-5) = 0 CORRECTING DEFECT 89 (vertices=26, convex hull=63, v0=109409) After retessellation of defect 89 (v0=109409), euler #=-4 (112145,336213,224064) : difference with theory (-4) = 0 CORRECTING DEFECT 90 (vertices=249, convex hull=158, v0=113733) After retessellation of defect 90 (v0=113733), euler #=-3 (112182,336402,224217) : difference with theory (-3) = 0 CORRECTING DEFECT 91 (vertices=36, convex hull=63, v0=117760) After retessellation of defect 91 (v0=117760), euler #=-2 (112197,336475,224276) : difference with theory (-2) = 0 CORRECTING DEFECT 92 (vertices=24, convex hull=57, v0=119758) After retessellation of defect 92 (v0=119758), euler #=-1 (112206,336523,224316) : difference with theory (-1) = 0 CORRECTING DEFECT 93 (vertices=28, convex hull=69, v0=120635) After retessellation of defect 93 (v0=120635), euler #=0 (112221,336596,224375) : difference with theory (0) = 0 CORRECTING DEFECT 94 (vertices=41, convex hull=80, v0=120866) After retessellation of defect 94 (v0=120866), euler #=1 (112247,336709,224463) : difference with theory (1) = 0 CORRECTING DEFECT 95 (vertices=32, convex hull=65, v0=122732) After retessellation of defect 95 (v0=122732), euler #=2 (112263,336783,224522) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.28 (0.03-->10.22) (max @ vno 3348 --> 3908) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.28 (0.03-->10.22) (max @ vno 3348 --> 3908) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 361 mutations (35.0%), 669 crossovers (65.0%), 777 vertices were eliminated building final representation... 10993 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=112263, nf=224522, ne=336783, g=0) writing corrected surface to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 1441 intersecting 001: 208 intersecting 002: 79 intersecting 003: 73 intersecting step 1 with no progress (num=88, old_num=73) 004: 88 intersecting step 2 with no progress (num=89, old_num=88) 005: 89 intersecting 006: 70 intersecting step 1 with no progress (num=70, old_num=70) 007: 70 intersecting step 2 with no progress (num=70, old_num=70) 008: 70 intersecting step 3 with no progress (num=70, old_num=70) 009: 70 intersecting step 4 with no progress (num=70, old_num=70) 010: 70 intersecting step 5 with no progress (num=70, old_num=70) 011: 70 intersecting step 6 with no progress (num=70, old_num=70) 012: 70 intersecting step 7 with no progress (num=70, old_num=70) 013: 70 intersecting step 8 with no progress (num=70, old_num=70) 014: 70 intersecting step 9 with no progress (num=70, old_num=70) 015: 70 intersecting step 10 with no progress (num=70, old_num=70) 016: 70 intersecting step 11 with no progress (num=70, old_num=70) 017: 70 intersecting step 12 with no progress (num=70, old_num=70) 018: 70 intersecting step 13 with no progress (num=70, old_num=70) 019: 70 intersecting step 14 with no progress (num=70, old_num=70) 020: 70 intersecting step 15 with no progress (num=70, old_num=70) 021: 70 intersecting step 16 with no progress (num=70, old_num=70) terminating search with 70 intersecting topology fixing took 6.4 minutes FSRUNTIME@ mris_fix_topology lh 0.1060 hours 4 threads #VMPC# mris_fix_topology VmPeak 958148 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Test rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.2.0 7.2.0 before topology correction, eno=-246 (nv=124470, nf=249432, ne=374148, g=124) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 31175 ambiguous faces found in tessellation segmenting defects... 83 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 4 -merging segment 7 into 6 -merging segment 16 into 13 -merging segment 67 into 69 -merging segment 78 into 77 78 defects to be corrected 0 vertices coincident reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7535 (-4.3767) -vertex loglikelihood: -6.0721 (-3.0361) -normal dot loglikelihood: -3.5467 (-3.5467) -quad curv loglikelihood: -6.0469 (-3.0235) Total Loglikelihood : -24.4193 CORRECTING DEFECT 0 (vertices=9, convex hull=28, v0=48) After retessellation of defect 0 (v0=48), euler #=-71 (107141,317893,210681) : difference with theory (-75) = -4 CORRECTING DEFECT 1 (vertices=18, convex hull=40, v0=95) After retessellation of defect 1 (v0=95), euler #=-70 (107150,317935,210715) : difference with theory (-74) = -4 CORRECTING DEFECT 2 (vertices=31, convex hull=43, v0=199) After retessellation of defect 2 (v0=199), euler #=-69 (107158,317977,210750) : difference with theory (-73) = -4 CORRECTING DEFECT 3 (vertices=147, convex hull=165, v0=201) After retessellation of defect 3 (v0=201), euler #=-68 (107180,318126,210878) : difference with theory (-72) = -4 CORRECTING DEFECT 4 (vertices=213, convex hull=152, v0=335) After retessellation of defect 4 (v0=335), euler #=-66 (107201,318259,210992) : difference with theory (-71) = -5 CORRECTING DEFECT 5 (vertices=62, convex hull=90, v0=384) After retessellation of defect 5 (v0=384), euler #=-64 (107225,318366,211077) : difference with theory (-70) = -6 CORRECTING DEFECT 6 (vertices=37, convex hull=75, v0=1803) After retessellation of defect 6 (v0=1803), euler #=-63 (107234,318424,211127) : difference with theory (-69) = -6 CORRECTING DEFECT 7 (vertices=80, convex hull=39, v0=2065) After retessellation of defect 7 (v0=2065), euler #=-62 (107240,318454,211152) : difference with theory (-68) = -6 CORRECTING DEFECT 8 (vertices=34, convex hull=36, v0=2563) After retessellation of defect 8 (v0=2563), euler #=-61 (107245,318483,211177) : difference with theory (-67) = -6 CORRECTING DEFECT 9 (vertices=50, convex hull=30, v0=2766) After retessellation of defect 9 (v0=2766), euler #=-60 (107248,318501,211193) : difference with theory (-66) = -6 CORRECTING DEFECT 10 (vertices=26, convex hull=58, v0=3182) After retessellation of defect 10 (v0=3182), euler #=-59 (107263,318567,211245) : difference with theory (-65) = -6 CORRECTING DEFECT 11 (vertices=430, convex hull=276, v0=3638) After retessellation of defect 11 (v0=3638), euler #=-57 (107279,318763,211427) : difference with theory (-64) = -7 CORRECTING DEFECT 12 (vertices=6, convex hull=21, v0=3904) After retessellation of defect 12 (v0=3904), euler #=-56 (107280,318771,211435) : difference with theory (-63) = -7 CORRECTING DEFECT 13 (vertices=1383, convex hull=757, v0=4708) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 13 (v0=4708), euler #=-56 (107705,320481,212720) : difference with theory (-62) = -6 CORRECTING DEFECT 14 (vertices=3260, convex hull=665, v0=8125) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces normal vector of length zero at vertex 111782 with 4 faces After retessellation of defect 14 (v0=8125), euler #=-55 (108260,322473,214158) : difference with theory (-61) = -6 CORRECTING DEFECT 15 (vertices=43, convex hull=35, v0=8591) After retessellation of defect 15 (v0=8591), euler #=-54 (108267,322507,214186) : difference with theory (-60) = -6 CORRECTING DEFECT 16 (vertices=14, convex hull=14, v0=9358) After retessellation of defect 16 (v0=9358), euler #=-53 (108267,322513,214193) : difference with theory (-59) = -6 CORRECTING DEFECT 17 (vertices=24, convex hull=41, v0=9437) After retessellation of defect 17 (v0=9437), euler #=-52 (108269,322533,214212) : difference with theory (-58) = -6 CORRECTING DEFECT 18 (vertices=379, convex hull=166, v0=10081) After retessellation of defect 18 (v0=10081), euler #=-51 (108329,322793,214413) : difference with theory (-57) = -6 CORRECTING DEFECT 19 (vertices=45, convex hull=99, v0=11509) After retessellation of defect 19 (v0=11509), euler #=-50 (108353,322908,214505) : difference with theory (-56) = -6 CORRECTING DEFECT 20 (vertices=226, convex hull=107, v0=12464) After retessellation of defect 20 (v0=12464), euler #=-49 (108390,323066,214627) : difference with theory (-55) = -6 CORRECTING DEFECT 21 (vertices=107, convex hull=48, v0=14977) After retessellation of defect 21 (v0=14977), euler #=-48 (108400,323116,214668) : difference with theory (-54) = -6 CORRECTING DEFECT 22 (vertices=4749, convex hull=862, v0=16341) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 22 (v0=16341), euler #=-51 (108799,324787,215937) : difference with theory (-53) = -2 CORRECTING DEFECT 23 (vertices=196, convex hull=144, v0=17306) After retessellation of defect 23 (v0=17306), euler #=-51 (108823,324937,216063) : difference with theory (-52) = -1 CORRECTING DEFECT 24 (vertices=23, convex hull=49, v0=17534) After retessellation of defect 24 (v0=17534), euler #=-50 (108832,324982,216100) : difference with theory (-51) = -1 CORRECTING DEFECT 25 (vertices=41, convex hull=72, v0=17858) After retessellation of defect 25 (v0=17858), euler #=-49 (108857,325087,216181) : difference with theory (-50) = -1 CORRECTING DEFECT 26 (vertices=21, convex hull=43, v0=19980) After retessellation of defect 26 (v0=19980), euler #=-48 (108867,325135,216220) : difference with theory (-49) = -1 CORRECTING DEFECT 27 (vertices=211, convex hull=108, v0=20074) After retessellation of defect 27 (v0=20074), euler #=-47 (108890,325256,216319) : difference with theory (-48) = -1 CORRECTING DEFECT 28 (vertices=73, convex hull=82, v0=20223) After retessellation of defect 28 (v0=20223), euler #=-46 (108914,325366,216406) : difference with theory (-47) = -1 CORRECTING DEFECT 29 (vertices=47, convex hull=66, v0=28501) After retessellation of defect 29 (v0=28501), euler #=-45 (108941,325474,216488) : difference with theory (-46) = -1 CORRECTING DEFECT 30 (vertices=48, convex hull=91, v0=31242) After retessellation of defect 30 (v0=31242), euler #=-44 (108968,325597,216585) : difference with theory (-45) = -1 CORRECTING DEFECT 31 (vertices=26, convex hull=68, v0=31955) After retessellation of defect 31 (v0=31955), euler #=-43 (108984,325672,216645) : difference with theory (-44) = -1 CORRECTING DEFECT 32 (vertices=15, convex hull=20, v0=37441) After retessellation of defect 32 (v0=37441), euler #=-42 (108986,325685,216657) : difference with theory (-43) = -1 CORRECTING DEFECT 33 (vertices=124, convex hull=73, v0=40050) After retessellation of defect 33 (v0=40050), euler #=-41 (109015,325799,216743) : difference with theory (-42) = -1 CORRECTING DEFECT 34 (vertices=88, convex hull=43, v0=42020) After retessellation of defect 34 (v0=42020), euler #=-40 (109031,325861,216790) : difference with theory (-41) = -1 CORRECTING DEFECT 35 (vertices=30, convex hull=51, v0=43203) After retessellation of defect 35 (v0=43203), euler #=-39 (109044,325918,216835) : difference with theory (-40) = -1 CORRECTING DEFECT 36 (vertices=30, convex hull=22, v0=46015) After retessellation of defect 36 (v0=46015), euler #=-38 (109048,325936,216850) : difference with theory (-39) = -1 CORRECTING DEFECT 37 (vertices=28, convex hull=74, v0=46904) After retessellation of defect 37 (v0=46904), euler #=-37 (109063,326009,216909) : difference with theory (-38) = -1 CORRECTING DEFECT 38 (vertices=20, convex hull=17, v0=48824) After retessellation of defect 38 (v0=48824), euler #=-36 (109066,326022,216920) : difference with theory (-37) = -1 CORRECTING DEFECT 39 (vertices=25, convex hull=37, v0=50013) After retessellation of defect 39 (v0=50013), euler #=-35 (109071,326050,216944) : difference with theory (-36) = -1 CORRECTING DEFECT 40 (vertices=32, convex hull=23, v0=50689) After retessellation of defect 40 (v0=50689), euler #=-34 (109077,326074,216963) : difference with theory (-35) = -1 CORRECTING DEFECT 41 (vertices=617, convex hull=291, v0=52324) After retessellation of defect 41 (v0=52324), euler #=-34 (109204,326606,217368) : difference with theory (-34) = 0 CORRECTING DEFECT 42 (vertices=1971, convex hull=414, v0=56047) A large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview Warning - incorrect dp selected!!!!(-114.214801 >= -114.212789 ) After retessellation of defect 42 (v0=56047), euler #=-33 (109226,326876,217617) : difference with theory (-33) = 0 CORRECTING DEFECT 43 (vertices=37, convex hull=29, v0=56408) After retessellation of defect 43 (v0=56408), euler #=-32 (109229,326894,217633) : difference with theory (-32) = 0 CORRECTING DEFECT 44 (vertices=46, convex hull=29, v0=56458) After retessellation of defect 44 (v0=56458), euler #=-31 (109237,326927,217659) : difference with theory (-31) = 0 CORRECTING DEFECT 45 (vertices=26, convex hull=29, v0=56976) After retessellation of defect 45 (v0=56976), euler #=-30 (109241,326948,217677) : difference with theory (-30) = 0 CORRECTING DEFECT 46 (vertices=187, convex hull=125, v0=64223) After retessellation of defect 46 (v0=64223), euler #=-29 (109297,327177,217851) : difference with theory (-29) = 0 CORRECTING DEFECT 47 (vertices=48, convex hull=67, v0=64550) After retessellation of defect 47 (v0=64550), euler #=-28 (109327,327292,217937) : difference with theory (-28) = 0 CORRECTING DEFECT 48 (vertices=45, convex hull=41, v0=67317) After retessellation of defect 48 (v0=67317), euler #=-27 (109333,327324,217964) : difference with theory (-27) = 0 CORRECTING DEFECT 49 (vertices=36, convex hull=53, v0=67750) After retessellation of defect 49 (v0=67750), euler #=-26 (109343,327375,218006) : difference with theory (-26) = 0 CORRECTING DEFECT 50 (vertices=34, convex hull=42, v0=67839) After retessellation of defect 50 (v0=67839), euler #=-26 (109359,327441,218056) : difference with theory (-25) = 1 CORRECTING DEFECT 51 (vertices=51, convex hull=38, v0=71899) After retessellation of defect 51 (v0=71899), euler #=-25 (109373,327497,218099) : difference with theory (-24) = 1 CORRECTING DEFECT 52 (vertices=75, convex hull=100, v0=75484) After retessellation of defect 52 (v0=75484), euler #=-24 (109413,327656,218219) : difference with theory (-23) = 1 CORRECTING DEFECT 53 (vertices=17, convex hull=58, v0=76350) After retessellation of defect 53 (v0=76350), euler #=-23 (109422,327700,218255) : difference with theory (-22) = 1 CORRECTING DEFECT 54 (vertices=50, convex hull=45, v0=76442) After retessellation of defect 54 (v0=76442), euler #=-22 (109435,327756,218299) : difference with theory (-21) = 1 CORRECTING DEFECT 55 (vertices=270, convex hull=69, v0=76700) After retessellation of defect 55 (v0=76700), euler #=-21 (109453,327839,218365) : difference with theory (-20) = 1 CORRECTING DEFECT 56 (vertices=30, convex hull=72, v0=81189) After retessellation of defect 56 (v0=81189), euler #=-20 (109465,327904,218419) : difference with theory (-19) = 1 CORRECTING DEFECT 57 (vertices=21, convex hull=30, v0=82149) After retessellation of defect 57 (v0=82149), euler #=-19 (109468,327919,218432) : difference with theory (-18) = 1 CORRECTING DEFECT 58 (vertices=18, convex hull=49, v0=82782) After retessellation of defect 58 (v0=82782), euler #=-18 (109478,327966,218470) : difference with theory (-17) = 1 CORRECTING DEFECT 59 (vertices=30, convex hull=34, v0=83311) After retessellation of defect 59 (v0=83311), euler #=-17 (109483,327992,218492) : difference with theory (-16) = 1 CORRECTING DEFECT 60 (vertices=132, convex hull=138, v0=92267) After retessellation of defect 60 (v0=92267), euler #=-16 (109531,328193,218646) : difference with theory (-15) = 1 CORRECTING DEFECT 61 (vertices=40, convex hull=51, v0=92355) After retessellation of defect 61 (v0=92355), euler #=-15 (109554,328283,218714) : difference with theory (-14) = 1 CORRECTING DEFECT 62 (vertices=18, convex hull=25, v0=97495) After retessellation of defect 62 (v0=97495), euler #=-14 (109559,328304,218731) : difference with theory (-13) = 1 CORRECTING DEFECT 63 (vertices=19, convex hull=44, v0=97634) After retessellation of defect 63 (v0=97634), euler #=-13 (109571,328355,218771) : difference with theory (-12) = 1 CORRECTING DEFECT 64 (vertices=101, convex hull=33, v0=97904) After retessellation of defect 64 (v0=97904), euler #=-12 (109579,328389,218798) : difference with theory (-11) = 1 CORRECTING DEFECT 65 (vertices=141, convex hull=171, v0=98776) After retessellation of defect 65 (v0=98776), euler #=-10 (109604,328542,218928) : difference with theory (-10) = 0 CORRECTING DEFECT 66 (vertices=79, convex hull=31, v0=100361) After retessellation of defect 66 (v0=100361), euler #=-9 (109612,328573,218952) : difference with theory (-9) = 0 CORRECTING DEFECT 67 (vertices=9, convex hull=22, v0=101123) After retessellation of defect 67 (v0=101123), euler #=-8 (109612,328579,218959) : difference with theory (-8) = 0 CORRECTING DEFECT 68 (vertices=40, convex hull=49, v0=101187) After retessellation of defect 68 (v0=101187), euler #=-7 (109621,328622,218994) : difference with theory (-7) = 0 CORRECTING DEFECT 69 (vertices=28, convex hull=36, v0=105321) After retessellation of defect 69 (v0=105321), euler #=-7 (109635,328680,219038) : difference with theory (-6) = 1 CORRECTING DEFECT 70 (vertices=249, convex hull=102, v0=108009) After retessellation of defect 70 (v0=108009), euler #=-6 (109668,328828,219154) : difference with theory (-5) = 1 CORRECTING DEFECT 71 (vertices=94, convex hull=54, v0=108653) After retessellation of defect 71 (v0=108653), euler #=-5 (109684,328897,219208) : difference with theory (-4) = 1 CORRECTING DEFECT 72 (vertices=50, convex hull=81, v0=108776) After retessellation of defect 72 (v0=108776), euler #=-4 (109716,329027,219307) : difference with theory (-3) = 1 CORRECTING DEFECT 73 (vertices=77, convex hull=110, v0=108953) After retessellation of defect 73 (v0=108953), euler #=-2 (109757,329200,219441) : difference with theory (-2) = 0 CORRECTING DEFECT 74 (vertices=29, convex hull=53, v0=111646) After retessellation of defect 74 (v0=111646), euler #=-1 (109772,329266,219493) : difference with theory (-1) = 0 CORRECTING DEFECT 75 (vertices=26, convex hull=29, v0=118540) After retessellation of defect 75 (v0=118540), euler #=0 (109777,329292,219515) : difference with theory (0) = 0 CORRECTING DEFECT 76 (vertices=103, convex hull=33, v0=122600) After retessellation of defect 76 (v0=122600), euler #=1 (109786,329333,219548) : difference with theory (1) = 0 CORRECTING DEFECT 77 (vertices=18, convex hull=50, v0=124007) After retessellation of defect 77 (v0=124007), euler #=2 (109794,329376,219584) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.35 (0.03-->21.11) (max @ vno 15149 --> 26597) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.35 (0.03-->21.11) (max @ vno 15149 --> 26597) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 287 mutations (34.6%), 543 crossovers (65.4%), 1157 vertices were eliminated building final representation... 14676 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109794, nf=219584, ne=329376, g=0) writing corrected surface to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig.premesh... defective orientation at vertex 15149(16198) with faces 30081 and 215875 defective orientation at vertex 15149(16199) with faces 30081 and 215878 defective orientation at vertex 16198(15149) with faces 30081 and 215875 defective orientation at vertex 16198(16199) with faces 30081 and 215876 defective orientation at vertex 16199(15149) with faces 30081 and 215878 defective orientation at vertex 16199(16198) with faces 30081 and 215876 0.005 % of the vertices (6 vertices) exhibit an orientation change removing intersecting faces 000: 1711 intersecting 001: 177 intersecting 002: 51 intersecting 003: 12 intersecting 004: 7 intersecting step 1 with no progress (num=7, old_num=7) 005: 7 intersecting step 2 with no progress (num=7, old_num=7) 006: 7 intersecting step 3 with no progress (num=7, old_num=7) 007: 7 intersecting step 4 with no progress (num=7, old_num=7) 008: 7 intersecting step 5 with no progress (num=7, old_num=7) 009: 7 intersecting step 6 with no progress (num=7, old_num=7) 010: 7 intersecting step 7 with no progress (num=7, old_num=7) 011: 7 intersecting step 8 with no progress (num=7, old_num=7) 012: 7 intersecting step 9 with no progress (num=7, old_num=7) 013: 7 intersecting step 10 with no progress (num=7, old_num=7) 014: 7 intersecting step 11 with no progress (num=7, old_num=7) 015: 7 intersecting step 12 with no progress (num=7, old_num=7) 016: 7 intersecting step 13 with no progress (num=7, old_num=7) 017: 7 intersecting step 14 with no progress (num=7, old_num=7) 018: 7 intersecting step 15 with no progress (num=7, old_num=7) 019: 7 intersecting step 16 with no progress (num=7, old_num=7) terminating search with 7 intersecting topology fixing took 6.5 minutes FSRUNTIME@ mris_fix_topology rh 0.1087 hours 4 threads #VMPC# mris_fix_topology VmPeak 959860 PIDs (323002 323005) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 112263 - 336783 + 224522 = 2 --> 0 holes F =2V-4: 224522 = 224526-4 (0) 2E=3F: 673566 = 673566 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 109794 - 329376 + 219584 = 2 --> 0 holes F =2V-4: 219584 = 219588-4 (0) 2E=3F: 658752 = 658752 (0) total defect index = 0 Mon Jan 9 12:48:51 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/defect2seg --s Test freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b defect2seg 7.2.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux pid 324142 mri_label2vol --defects /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig.nofix /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.defect_labels /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz 1000 0 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/surface.defects.mgz mris_defects_pointset -s /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig.nofix -d /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.defect_labels -o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.defects.pointset Reading in surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig.nofix Reading in defect segmentation /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.defect_labels #VMPC# mris_defects_pointset 535344 mris_defects_pointset done mri_label2vol --defects /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig.nofix /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.defect_labels /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/surface.defects.mgz 2000 1 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 MRIcopyHeader(): source has ctab Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/surface.defects.mgz mris_defects_pointset -s /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig.nofix -d /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.defect_labels -o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.defects.pointset Reading in surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig.nofix Reading in defect segmentation /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.defect_labels #VMPC# mris_defects_pointset 536340 mris_defects_pointset done Started at Mon Jan 9 12:48:51 CET 2023 Ended at Mon Jan 9 12:48:54 CET 2023 Defect2seg-Run-Time-Sec 3 Defect2seg-Run-Time-Min 0.06 Defect2seg-Run-Time-Hours 0.00 tkmeditfv Test brain.finalsurfs.mgz -defect defect2seg Done mris_remesh --remesh --iters 3 --input /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig.premesh --output /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.717484 remeshing to edge length 0.717484 with 3 iterations avg qual before : 0.883059 after: 0.971317 Removing intersections removing intersecting faces 000: 148 intersecting 001: 115 intersecting 002: 100 intersecting 003: 93 intersecting 004: 83 intersecting 005: 72 intersecting 006: 62 intersecting step 1 with no progress (num=62, old_num=62) 007: 62 intersecting step 2 with no progress (num=62, old_num=62) 008: 62 intersecting step 3 with no progress (num=62, old_num=62) 009: 62 intersecting step 4 with no progress (num=62, old_num=62) 010: 62 intersecting step 5 with no progress (num=62, old_num=62) 011: 62 intersecting step 6 with no progress (num=62, old_num=62) 012: 62 intersecting step 7 with no progress (num=62, old_num=62) 013: 62 intersecting step 8 with no progress (num=62, old_num=62) 014: 62 intersecting step 9 with no progress (num=62, old_num=62) 015: 62 intersecting step 10 with no progress (num=62, old_num=62) 016: 62 intersecting step 11 with no progress (num=62, old_num=62) 017: 62 intersecting step 12 with no progress (num=62, old_num=62) 018: 62 intersecting step 13 with no progress (num=62, old_num=62) 019: 62 intersecting step 14 with no progress (num=62, old_num=62) 020: 62 intersecting step 15 with no progress (num=62, old_num=62) 021: 62 intersecting step 16 with no progress (num=62, old_num=62) terminating search with 62 intersecting Remeshed surface quality stats nv0 = 112263 nv = 115656 1.03022 Area 231308 0.30728 0.03434 0.021150 0.4921 Corner 693924 60.00000 8.78124 5.652080 152.5449 Edge 346962 0.85038 0.08319 0.074343 1.4832 Hinge 346962 10.83366 11.84977 0.000016 179.3596 mris_remesh done mris_remesh --remesh --iters 3 --input /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig.premesh --output /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.718414 remeshing to edge length 0.718414 with 3 iterations avg qual before : 0.881857 after: 0.970453 Removing intersections removing intersecting faces 000: 321 intersecting 001: 152 intersecting 002: 106 intersecting 003: 98 intersecting step 1 with no progress (num=98, old_num=98) 004: 98 intersecting step 2 with no progress (num=98, old_num=98) 005: 98 intersecting step 3 with no progress (num=98, old_num=98) 006: 98 intersecting step 4 with no progress (num=98, old_num=98) 007: 98 intersecting step 5 with no progress (num=98, old_num=98) 008: 98 intersecting step 6 with no progress (num=98, old_num=98) 009: 98 intersecting step 7 with no progress (num=98, old_num=98) 010: 98 intersecting step 8 with no progress (num=98, old_num=98) 011: 98 intersecting step 9 with no progress (num=98, old_num=98) 012: 98 intersecting step 10 with no progress (num=98, old_num=98) 013: 98 intersecting step 11 with no progress (num=98, old_num=98) 014: 98 intersecting step 12 with no progress (num=98, old_num=98) 015: 98 intersecting step 13 with no progress (num=98, old_num=98) 016: 98 intersecting step 14 with no progress (num=98, old_num=98) 017: 98 intersecting step 15 with no progress (num=98, old_num=98) 018: 98 intersecting step 16 with no progress (num=98, old_num=98) terminating search with 98 intersecting Remeshed surface quality stats nv0 = 109794 nv = 112475 1.02442 Area 224946 0.30757 0.03658 0.000146 0.4700 Corner 674838 60.00000 9.12171 0.529625 178.8937 Edge 337419 0.85096 0.08593 0.013488 1.4612 Hinge 337419 10.86770 12.15421 0.000007 176.9184 mris_remesh done /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 62 intersecting step 1 with no progress (num=62, old_num=62) 001: 62 intersecting step 2 with no progress (num=62, old_num=62) 002: 62 intersecting step 3 with no progress (num=62, old_num=62) 003: 62 intersecting step 4 with no progress (num=62, old_num=62) 004: 62 intersecting step 5 with no progress (num=62, old_num=62) 005: 62 intersecting step 6 with no progress (num=62, old_num=62) 006: 62 intersecting step 7 with no progress (num=62, old_num=62) 007: 62 intersecting step 8 with no progress (num=62, old_num=62) 008: 62 intersecting step 9 with no progress (num=62, old_num=62) 009: 62 intersecting step 10 with no progress (num=62, old_num=62) 010: 62 intersecting step 11 with no progress (num=62, old_num=62) 011: 62 intersecting step 12 with no progress (num=62, old_num=62) 012: 62 intersecting step 13 with no progress (num=62, old_num=62) 013: 62 intersecting step 14 with no progress (num=62, old_num=62) 014: 62 intersecting step 15 with no progress (num=62, old_num=62) 015: 62 intersecting step 16 with no progress (num=62, old_num=62) terminating search with 62 intersecting writing corrected surface to ../surf/lh.orig rm -f ../surf/lh.inflated /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.01 hours removing intersecting faces 000: 98 intersecting step 1 with no progress (num=98, old_num=98) 001: 98 intersecting step 2 with no progress (num=98, old_num=98) 002: 98 intersecting step 3 with no progress (num=98, old_num=98) 003: 98 intersecting step 4 with no progress (num=98, old_num=98) 004: 98 intersecting step 5 with no progress (num=98, old_num=98) 005: 98 intersecting step 6 with no progress (num=98, old_num=98) 006: 98 intersecting step 7 with no progress (num=98, old_num=98) 007: 98 intersecting step 8 with no progress (num=98, old_num=98) 008: 98 intersecting step 9 with no progress (num=98, old_num=98) 009: 98 intersecting step 10 with no progress (num=98, old_num=98) 010: 98 intersecting step 11 with no progress (num=98, old_num=98) 011: 98 intersecting step 12 with no progress (num=98, old_num=98) 012: 98 intersecting step 13 with no progress (num=98, old_num=98) 013: 98 intersecting step 14 with no progress (num=98, old_num=98) 014: 98 intersecting step 15 with no progress (num=98, old_num=98) 015: 98 intersecting step 16 with no progress (num=98, old_num=98) terminating search with 98 intersecting writing corrected surface to ../surf/rh.orig rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Mon Jan 9 12:51:03 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 234700 voxels (1.40%) border gray 297479 voxels (1.77%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 81.7 +- 11.2 [30.0 --> 110.0] white_mean = 101.547 +/- 6.7521, gray_mean = 81.6967 +/- 11.2327 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=105+-5.2, GM=82+-7.0 white_mode = 105, gray_mode = 82 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 70.8 (was 70.000000) setting MAX_BORDER_WHITE to 111.8 (was 105.000000) setting MIN_BORDER_WHITE to 82.0 (was 85.000000) setting MAX_CSF to 59.5 (was 40.000000) setting MAX_GRAY to 98.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 70.8 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 48.3 (was 40.000000) When placing the white surface white_border_hi = 111.752; white_border_low = 82; white_outside_low = 70.7673; white_inside_hi = 120; white_outside_hi = 111.752; When placing the pial surface pial_border_hi = 70.7673; pial_border_low = 48.3018; pial_outside_low = 10; pial_inside_hi = 98.2479; pial_outside_hi = 65.1509; #VMPC# mris_autodet_gwstats VmPeak 562832 mris_autodet_gwstats done #-------------------------------------------- #@# AutoDetGWStats rh Mon Jan 9 12:51:05 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 234700 voxels (1.40%) border gray 297479 voxels (1.77%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 81.7 +- 11.2 [30.0 --> 110.0] white_mean = 101.547 +/- 6.7521, gray_mean = 81.6967 +/- 11.2327 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=105+-5.2, GM=83+-7.8 white_mode = 105, gray_mode = 83 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 71.8 (was 70.000000) setting MAX_BORDER_WHITE to 111.8 (was 105.000000) setting MIN_BORDER_WHITE to 83.0 (was 85.000000) setting MAX_CSF to 60.5 (was 40.000000) setting MAX_GRAY to 98.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 71.8 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 49.3 (was 40.000000) When placing the white surface white_border_hi = 111.752; white_border_low = 83; white_outside_low = 71.7673; white_inside_hi = 120; white_outside_hi = 111.752; When placing the pial surface pial_border_hi = 71.7673; pial_border_low = 49.3018; pial_outside_low = 10; pial_inside_hi = 98.2479; pial_outside_hi = 66.1509; #VMPC# mris_autodet_gwstats VmPeak 560952 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Mon Jan 9 12:51:08 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations removing intersecting faces 000: 55 intersecting 001: 49 intersecting 002: 36 intersecting step 1 with no progress (num=36, old_num=36) 003: 36 intersecting step 2 with no progress (num=36, old_num=36) 004: 36 intersecting step 3 with no progress (num=36, old_num=36) 005: 36 intersecting step 4 with no progress (num=36, old_num=36) 006: 36 intersecting step 5 with no progress (num=36, old_num=36) 007: 36 intersecting step 6 with no progress (num=36, old_num=36) 008: 36 intersecting step 7 with no progress (num=36, old_num=36) 009: 36 intersecting step 8 with no progress (num=36, old_num=36) 010: 36 intersecting step 9 with no progress (num=36, old_num=36) 011: 36 intersecting step 10 with no progress (num=36, old_num=36) 012: 36 intersecting step 11 with no progress (num=36, old_num=36) 013: 36 intersecting step 12 with no progress (num=36, old_num=36) 014: 36 intersecting step 13 with no progress (num=36, old_num=36) 015: 36 intersecting step 14 with no progress (num=36, old_num=36) 016: 36 intersecting step 15 with no progress (num=36, old_num=36) 017: 36 intersecting step 16 with no progress (num=36, old_num=36) terminating search with 36 intersecting Area 231308 0.26709 0.06714 0.000508 0.5676 Corner 693924 60.00000 9.85694 1.737635 170.8789 Edge 346962 0.78866 0.12184 0.008151 1.4321 Hinge 346962 6.82518 7.10687 0.000010 174.3819 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 MRIcopyHeader(): source has ctab removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6584, nmarked2=0, nripped=6584 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (0,0,0) CBVO Creating mask 115656 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6584 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6584, nmarked2=0, nripped=6584 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=2 had to be increased for 677 vertices, nripped=6584 mean border=90.4, 418 (418) missing vertices, mean dist 0.1 [0.9 (%43.4)->0.8 (%56.6))] %62 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0368 min Finding expansion regions mean absolute distance = 0.87 +- 1.13 3419 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=2528325.0, rms=10.486 001: dt: 0.5000, sse=1693316.8, rms=8.457 (19.344%) 002: dt: 0.5000, sse=1217312.6, rms=7.015 (17.053%) 003: dt: 0.5000, sse=936570.4, rms=6.037 (13.941%) 004: dt: 0.5000, sse=754438.1, rms=5.283 (12.489%) 005: dt: 0.5000, sse=624492.1, rms=4.647 (12.049%) 006: dt: 0.5000, sse=549059.0, rms=4.221 (9.151%) 007: dt: 0.5000, sse=499075.8, rms=3.941 (6.645%) 008: dt: 0.5000, sse=468261.2, rms=3.730 (5.360%) 009: dt: 0.5000, sse=456726.0, rms=3.596 (3.581%) 010: dt: 0.5000, sse=440985.1, rms=3.491 (2.934%) rms = 3.4497/3.4907, sse=444922.6/440985.1, time step reduction 1 of 3 to 0.250 0 1 1 011: dt: 0.5000, sse=444922.6, rms=3.450 (1.175%) 012: dt: 0.2500, sse=368516.5, rms=2.976 (13.717%) 013: dt: 0.2500, sse=345242.9, rms=2.869 (3.617%) rms = 2.8241/2.8688, sse=352332.0/345242.9, time step reduction 2 of 3 to 0.125 0 1 1 014: dt: 0.2500, sse=352332.0, rms=2.824 (1.558%) rms = 2.7922/2.8241, sse=360158.3/352332.0, time step reduction 3 of 3 to 0.062 0 1 1 015: dt: 0.1250, sse=360158.3, rms=2.792 (1.130%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6584 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7075, nmarked2=0, nripped=7075 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=1 had to be increased for 502 vertices, nripped=7075 mean border=92.1, 578 (181) missing vertices, mean dist -0.2 [0.5 (%65.3)->0.3 (%34.7))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0244 min Finding expansion regions mean absolute distance = 0.41 +- 0.70 3523 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=573027.4, rms=3.986 016: dt: 0.5000, sse=426386.6, rms=3.102 (22.173%) 017: dt: 0.5000, sse=394582.6, rms=2.810 (9.432%) rms = 2.7436/2.8096, sse=395322.5/394582.6, time step reduction 1 of 3 to 0.250 0 1 0 018: dt: 0.5000, sse=395322.5, rms=2.744 (2.350%) 019: dt: 0.2500, sse=361048.4, rms=2.452 (10.626%) 020: dt: 0.2500, sse=352249.1, rms=2.371 (3.286%) rms = 2.3524/2.3715, sse=352178.9/352249.1, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=352178.9, rms=2.352 (0.803%) rms = 2.3084/2.3524, sse=352116.0/352178.9, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=352116.0, rms=2.308 (1.872%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7075 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7132, nmarked2=0, nripped=7132 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 546 vertices, nripped=7132 mean border=92.9, 637 (144) missing vertices, mean dist -0.1 [0.3 (%58.7)->0.2 (%41.3))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0131 min Finding expansion regions mean absolute distance = 0.29 +- 0.46 3217 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=shark, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=400315.2, rms=2.756 023: dt: 0.5000, sse=379880.2, rms=2.438 (11.530%) 024: dt: 0.5000, sse=346875.2, rms=2.313 (5.147%) rms = 2.3770/2.3127, sse=367942.1/346875.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=325449.2, rms=2.149 (7.075%) rms = 2.0887/2.1491, sse=326212.0/325449.2, time step reduction 2 of 3 to 0.125 0 1 0 026: dt: 0.2500, sse=326212.0, rms=2.089 (2.808%) 027: dt: 0.1250, sse=320424.2, rms=2.037 (2.461%) rms = 2.0157/2.0373, sse=318933.4/320424.2, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=318933.4, rms=2.016 (1.064%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7132 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7184, nmarked2=0, nripped=7184 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 517 vertices, nripped=7184 mean border=93.2, 648 (123) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.2 (%47.7))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0084 min Finding expansion regions mean absolute distance = 0.26 +- 0.39 3157 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=shark, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=325650.7, rms=2.110 rms = 2.1141/2.1101, sse=320812.6/325650.7, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 029: dt: 0.2500, sse=299174.1, rms=1.955 (7.375%) 030: dt: 0.2500, sse=295661.8, rms=1.903 (2.654%) rms = 1.9392/1.9027, sse=300753.5/295661.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.8738/1.9027, sse=292140.1/295661.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=292140.2, rms=1.874 (1.517%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 36 intersecting step 1 with no progress (num=37, old_num=36) 001: 37 intersecting step 2 with no progress (num=39, old_num=37) 002: 39 intersecting 003: 29 intersecting step 1 with no progress (num=31, old_num=29) 004: 31 intersecting step 2 with no progress (num=31, old_num=31) 005: 31 intersecting step 3 with no progress (num=31, old_num=31) 006: 31 intersecting step 4 with no progress (num=31, old_num=31) 007: 31 intersecting step 5 with no progress (num=31, old_num=31) 008: 31 intersecting step 6 with no progress (num=31, old_num=31) 009: 31 intersecting step 7 with no progress (num=31, old_num=31) 010: 31 intersecting step 8 with no progress (num=31, old_num=31) 011: 31 intersecting step 9 with no progress (num=31, old_num=31) 012: 31 intersecting step 10 with no progress (num=31, old_num=31) 013: 31 intersecting step 11 with no progress (num=31, old_num=31) 014: 31 intersecting step 12 with no progress (num=31, old_num=31) 015: 31 intersecting step 13 with no progress (num=31, old_num=31) 016: 31 intersecting step 14 with no progress (num=31, old_num=31) 017: 31 intersecting step 15 with no progress (num=31, old_num=31) 018: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 29 intersecting Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 1.98 minutes #VMPC# mris_place_surfaces VmPeak 2084844 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Mon Jan 9 12:53:29 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface with 5 iterations removing intersecting faces 000: 172 intersecting 001: 144 intersecting 002: 141 intersecting step 1 with no progress (num=148, old_num=141) 003: 148 intersecting step 2 with no progress (num=149, old_num=148) 004: 149 intersecting 005: 134 intersecting step 1 with no progress (num=147, old_num=134) 006: 147 intersecting 007: 133 intersecting 008: 117 intersecting step 1 with no progress (num=158, old_num=117) 009: 158 intersecting 010: 147 intersecting step 1 with no progress (num=155, old_num=147) 011: 155 intersecting 012: 137 intersecting step 1 with no progress (num=150, old_num=137) 013: 150 intersecting step 2 with no progress (num=153, old_num=150) 014: 153 intersecting step 3 with no progress (num=159, old_num=153) 015: 159 intersecting 016: 149 intersecting 017: 146 intersecting step 1 with no progress (num=152, old_num=146) 018: 152 intersecting 019: 148 intersecting step 1 with no progress (num=154, old_num=148) 020: 154 intersecting step 2 with no progress (num=155, old_num=154) 021: 155 intersecting 022: 150 intersecting 023: 149 intersecting step 1 with no progress (num=151, old_num=149) 024: 151 intersecting step 2 with no progress (num=155, old_num=151) 025: 155 intersecting 026: 153 intersecting 027: 149 intersecting step 1 with no progress (num=152, old_num=149) 028: 152 intersecting 029: 149 intersecting 030: 146 intersecting step 1 with no progress (num=156, old_num=146) 031: 156 intersecting 032: 146 intersecting step 1 with no progress (num=167, old_num=146) 033: 167 intersecting 034: 147 intersecting step 1 with no progress (num=155, old_num=147) 035: 155 intersecting 036: 146 intersecting step 1 with no progress (num=154, old_num=146) 037: 154 intersecting step 2 with no progress (num=154, old_num=154) 038: 154 intersecting step 3 with no progress (num=156, old_num=154) 039: 156 intersecting 040: 152 intersecting step 1 with no progress (num=156, old_num=152) 041: 156 intersecting 042: 149 intersecting 043: 142 intersecting step 1 with no progress (num=157, old_num=142) 044: 157 intersecting step 2 with no progress (num=168, old_num=157) 045: 168 intersecting 046: 163 intersecting 047: 161 intersecting 048: 153 intersecting 049: 147 intersecting 050: 145 intersecting 051: 142 intersecting step 1 with no progress (num=154, old_num=142) 052: 154 intersecting 053: 148 intersecting step 1 with no progress (num=157, old_num=148) 054: 157 intersecting 055: 147 intersecting 056: 143 intersecting step 1 with no progress (num=146, old_num=143) 057: 146 intersecting step 2 with no progress (num=147, old_num=146) 058: 147 intersecting 059: 146 intersecting step 1 with no progress (num=146, old_num=146) 060: 146 intersecting step 2 with no progress (num=153, old_num=146) 061: 153 intersecting 062: 152 intersecting 063: 150 intersecting step 1 with no progress (num=156, old_num=150) 064: 156 intersecting step 2 with no progress (num=156, old_num=156) 065: 156 intersecting 066: 140 intersecting step 1 with no progress (num=145, old_num=140) 067: 145 intersecting step 2 with no progress (num=148, old_num=145) 068: 148 intersecting step 3 with no progress (num=165, old_num=148) 069: 165 intersecting 070: 164 intersecting 071: 158 intersecting step 1 with no progress (num=168, old_num=158) 072: 168 intersecting 073: 157 intersecting step 1 with no progress (num=157, old_num=157) 074: 157 intersecting step 2 with no progress (num=160, old_num=157) 075: 160 intersecting 076: 158 intersecting 077: 156 intersecting step 1 with no progress (num=158, old_num=156) 078: 158 intersecting 079: 155 intersecting step 1 with no progress (num=163, old_num=155) 080: 163 intersecting 081: 155 intersecting step 1 with no progress (num=168, old_num=155) 082: 168 intersecting 083: 156 intersecting step 1 with no progress (num=156, old_num=156) 084: 156 intersecting step 2 with no progress (num=161, old_num=156) 085: 161 intersecting step 3 with no progress (num=167, old_num=161) 086: 167 intersecting 087: 160 intersecting step 1 with no progress (num=162, old_num=160) 088: 162 intersecting 089: 160 intersecting step 1 with no progress (num=165, old_num=160) 090: 165 intersecting step 2 with no progress (num=169, old_num=165) 091: 169 intersecting step 3 with no progress (num=175, old_num=169) 092: 175 intersecting step 4 with no progress (num=180, old_num=175) 093: 180 intersecting step 5 with no progress (num=182, old_num=180) 094: 182 intersecting step 6 with no progress (num=187, old_num=182) 095: 187 intersecting step 7 with no progress (num=196, old_num=187) 096: 196 intersecting step 8 with no progress (num=197, old_num=196) 097: 197 intersecting 098: 196 intersecting step 1 with no progress (num=196, old_num=196) 099: 196 intersecting step 2 with no progress (num=196, old_num=196) 100: 196 intersecting step 3 with no progress (num=196, old_num=196) 101: 196 intersecting terminating search with 117 intersecting Area 224946 0.26777 0.06857 0.000000 0.5818 Corner 674838 60.00000 10.68789 0.000000 180.0000 Edge 337419 0.78955 0.12552 0.000000 1.5562 Hinge 337419 -nan -nan 0.000000 179.9877 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 MRIcopyHeader(): source has ctab removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6646, nmarked2=5, nripped=6646 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56238: xyz = (26.2108,-15.1704,71.8102) oxyz = (26.2108,-15.1704,71.8102) wxzy = (26.2108,-15.1704,71.8102) pxyz = (0,0,0) CBVO Creating mask 112475 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=6646 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6646, nmarked2=5, nripped=6646 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=2 had to be increased for 569 vertices, nripped=6646 mean border=91.0, 341 (341) missing vertices, mean dist 0.0 [0.9 (%44.5)->0.8 (%55.5))] %59 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0358 min Finding expansion regions mean absolute distance = 0.88 +- 1.15 3279 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=4106495.0, rms=10.467 001: dt: 0.5000, sse=2858564.8, rms=8.213 (21.533%) 002: dt: 0.5000, sse=2125076.0, rms=6.537 (20.404%) 003: dt: 0.5000, sse=1423061.8, rms=5.263 (19.491%) 004: dt: 0.5000, sse=1205306.4, rms=4.209 (20.024%) 005: dt: 0.5000, sse=1062854.0, rms=3.478 (17.372%) 006: dt: 0.5000, sse=696960.6, rms=3.032 (12.817%) 007: dt: 0.5000, sse=647239.2, rms=2.802 (7.601%) 008: dt: 0.5000, sse=641223.9, rms=2.677 (4.470%) 009: dt: 0.5000, sse=629734.1, rms=2.609 (2.533%) 010: dt: 0.5000, sse=612217.9, rms=2.557 (1.987%) 011: dt: 0.5000, sse=580109.8, rms=2.495 (2.433%) rms = 2.4698/2.4947, sse=598750.3/580109.7, time step reduction 1 of 3 to 0.250 0 1 1 012: dt: 0.5000, sse=598750.3, rms=2.470 (0.997%) 013: dt: 0.2500, sse=567737.7, rms=1.833 (25.795%) 014: dt: 0.2500, sse=542536.9, rms=1.738 (5.187%) rms = 1.7207/1.7377, sse=538203.4/542536.9, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=538203.4, rms=1.721 (0.976%) rms = 1.6842/1.7207, sse=538743.5/538203.4, time step reduction 3 of 3 to 0.062 0 1 1 016: dt: 0.1250, sse=538743.5, rms=1.684 (2.124%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6646 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7199, nmarked2=14, nripped=7199 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=1 had to be increased for 525 vertices, nripped=7199 mean border=92.5, 461 (147) missing vertices, mean dist -0.2 [0.5 (%63.6)->0.3 (%36.4))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0238 min Finding expansion regions mean absolute distance = 0.42 +- 0.74 3509 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=739929.1, rms=3.287 017: dt: 0.5000, sse=617496.1, rms=2.292 (30.262%) 018: dt: 0.5000, sse=611399.4, rms=2.001 (12.724%) 019: dt: 0.5000, sse=594395.0, rms=1.929 (3.565%) rms = 1.9076/1.9294, sse=597978.8/594395.0, time step reduction 1 of 3 to 0.250 0 1 1 020: dt: 0.5000, sse=597978.8, rms=1.908 (1.127%) 021: dt: 0.2500, sse=596120.0, rms=1.534 (19.591%) rms = 1.4647/1.5339, sse=599475.6/596120.0, time step reduction 2 of 3 to 0.125 0 1 0 022: dt: 0.2500, sse=599475.6, rms=1.465 (4.509%) rms = 1.4296/1.4647, sse=586456.7/599475.6, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=586456.7, rms=1.430 (2.398%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7199 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 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7240, nmarked2=19, nripped=7240 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 545 vertices, nripped=7240 mean border=93.3, 502 (117) missing vertices, mean dist -0.1 [0.4 (%57.2)->0.2 (%42.8))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0128 min Finding expansion regions mean absolute distance = 0.30 +- 0.51 3294 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=shark, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=646856.9, rms=2.165 024: dt: 0.5000, sse=622537.1, rms=1.739 (19.673%) 025: dt: 0.5000, sse=617599.2, rms=1.644 (5.474%) rms = 1.7365/1.6435, sse=628507.0/617599.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=591348.0, rms=1.452 (11.629%) rms = 1.3841/1.4524, sse=591925.0/591348.0, time step reduction 2 of 3 to 0.125 0 1 0 027: dt: 0.2500, sse=591925.0, rms=1.384 (4.705%) rms = 1.3469/1.3841, sse=576309.2/591925.0, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=576309.2, rms=1.347 (2.688%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7240 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 3 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7277, nmarked2=19, nripped=7277 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 528 vertices, nripped=7277 mean border=93.5, 608 (98) missing vertices, mean dist -0.0 [0.3 (%51.6)->0.2 (%48.4))] %83 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0082 min Finding expansion regions mean absolute distance = 0.27 +- 0.41 2718 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=shark, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=590956.4, rms=1.615 rms = 1.6052/1.6148, sse=589244.7/590956.4, time step reduction 1 of 3 to 0.250 0 0 1 029: dt: 0.5000, sse=589244.7, rms=1.605 (0.593%) rms = 1.4185/1.6052, sse=601283.0/589244.7, time step reduction 2 of 3 to 0.125 0 1 0 030: dt: 0.2500, sse=601283.0, rms=1.419 (11.632%) 031: dt: 0.1250, sse=568687.1, rms=1.321 (6.904%) rms = 1.2958/1.3206, sse=574611.0/568687.1, time step reduction 3 of 3 to 0.062 0 1 1 032: dt: 0.1250, sse=574611.0, rms=1.296 (1.879%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 85 intersecting step 1 with no progress (num=118, old_num=85) 001: 118 intersecting 002: 108 intersecting 003: 96 intersecting step 1 with no progress (num=112, old_num=96) 004: 112 intersecting 005: 109 intersecting 006: 106 intersecting 007: 98 intersecting step 1 with no progress (num=108, old_num=98) 008: 108 intersecting 009: 94 intersecting step 1 with no progress (num=107, old_num=94) 010: 107 intersecting 011: 99 intersecting step 1 with no progress (num=106, old_num=99) 012: 106 intersecting 013: 90 intersecting step 1 with no progress (num=99, old_num=90) 014: 99 intersecting 015: 94 intersecting step 1 with no progress (num=96, old_num=94) 016: 96 intersecting 017: 89 intersecting step 1 with no progress (num=105, old_num=89) 018: 105 intersecting step 2 with no progress (num=106, old_num=105) 019: 106 intersecting step 3 with no progress (num=117, old_num=106) 020: 117 intersecting 021: 115 intersecting step 1 with no progress (num=118, old_num=115) 022: 118 intersecting step 2 with no progress (num=129, old_num=118) 023: 129 intersecting step 3 with no progress (num=141, old_num=129) 024: 141 intersecting 025: 125 intersecting step 1 with no progress (num=131, old_num=125) 026: 131 intersecting step 2 with no progress (num=133, old_num=131) 027: 133 intersecting step 3 with no progress (num=141, old_num=133) 028: 141 intersecting 029: 137 intersecting 030: 126 intersecting step 1 with no progress (num=129, old_num=126) 031: 129 intersecting step 2 with no progress (num=133, old_num=129) 032: 133 intersecting 033: 122 intersecting step 1 with no progress (num=125, old_num=122) 034: 125 intersecting step 2 with no progress (num=127, old_num=125) 035: 127 intersecting step 3 with no progress (num=130, old_num=127) 036: 130 intersecting step 4 with no progress (num=137, old_num=130) 037: 137 intersecting 038: 123 intersecting step 1 with no progress (num=136, old_num=123) 039: 136 intersecting 040: 128 intersecting 041: 127 intersecting step 1 with no progress (num=131, old_num=127) 042: 131 intersecting 043: 130 intersecting 044: 126 intersecting step 1 with no progress (num=136, old_num=126) 045: 136 intersecting 046: 124 intersecting step 1 with no progress (num=125, old_num=124) 047: 125 intersecting step 2 with no progress (num=128, old_num=125) 048: 128 intersecting step 3 with no progress (num=128, old_num=128) 049: 128 intersecting step 4 with no progress (num=134, old_num=128) 050: 134 intersecting step 5 with no progress (num=142, old_num=134) 051: 142 intersecting 052: 140 intersecting 053: 137 intersecting step 1 with no progress (num=138, old_num=137) 054: 138 intersecting step 2 with no progress (num=139, old_num=138) 055: 139 intersecting 056: 131 intersecting 057: 121 intersecting step 1 with no progress (num=130, old_num=121) 058: 130 intersecting 059: 128 intersecting 060: 124 intersecting step 1 with no progress (num=124, old_num=124) 061: 124 intersecting step 2 with no progress (num=125, old_num=124) 062: 125 intersecting 063: 123 intersecting step 1 with no progress (num=124, old_num=123) 064: 124 intersecting 065: 123 intersecting step 1 with no progress (num=124, old_num=123) 066: 124 intersecting 067: 123 intersecting step 1 with no progress (num=123, old_num=123) 068: 123 intersecting step 2 with no progress (num=123, old_num=123) 069: 123 intersecting step 3 with no progress (num=123, old_num=123) 070: 123 intersecting step 4 with no progress (num=123, old_num=123) 071: 123 intersecting step 5 with no progress (num=123, old_num=123) 072: 123 intersecting step 6 with no progress (num=123, old_num=123) 073: 123 intersecting step 7 with no progress (num=123, old_num=123) 074: 123 intersecting step 8 with no progress (num=123, old_num=123) 075: 123 intersecting step 9 with no progress (num=123, old_num=123) 076: 123 intersecting step 10 with no progress (num=123, old_num=123) 077: 123 intersecting step 11 with no progress (num=123, old_num=123) 078: 123 intersecting step 12 with no progress (num=123, old_num=123) 079: 123 intersecting step 13 with no progress (num=123, old_num=123) 080: 123 intersecting step 14 with no progress (num=123, old_num=123) 081: 123 intersecting step 15 with no progress (num=123, old_num=123) 082: 123 intersecting step 16 with no progress (num=123, old_num=123) terminating search with 85 intersecting Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.91 minutes #VMPC# mris_place_surfaces VmPeak 2282044 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Mon Jan 9 12:58:03 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 12 non-cortical segments detected only using segment with 7347 vertices erasing segment 1 (vno[0] = 31623) erasing segment 2 (vno[0] = 32374) erasing segment 3 (vno[0] = 37769) erasing segment 4 (vno[0] = 38012) erasing segment 5 (vno[0] = 42052) erasing segment 6 (vno[0] = 68872) erasing segment 7 (vno[0] = 70987) erasing segment 8 (vno[0] = 71001) erasing segment 9 (vno[0] = 71626) erasing segment 10 (vno[0] = 108629) erasing segment 11 (vno[0] = 111222) #-------------------------------------------- #@# CortexLabel+HipAmyg lh Mon Jan 9 12:58:14 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 24 non-cortical segments detected only using segment with 5652 vertices erasing segment 1 (vno[0] = 31623) erasing segment 2 (vno[0] = 32374) erasing segment 3 (vno[0] = 37769) erasing segment 4 (vno[0] = 41588) erasing segment 5 (vno[0] = 42052) erasing segment 6 (vno[0] = 44802) erasing segment 7 (vno[0] = 54342) erasing segment 8 (vno[0] = 61150) erasing segment 9 (vno[0] = 68872) erasing segment 10 (vno[0] = 70987) erasing segment 11 (vno[0] = 71001) erasing segment 12 (vno[0] = 71626) erasing segment 13 (vno[0] = 92834) erasing segment 14 (vno[0] = 92923) erasing segment 15 (vno[0] = 92968) erasing segment 16 (vno[0] = 93043) erasing segment 17 (vno[0] = 93739) erasing segment 18 (vno[0] = 94728) erasing segment 19 (vno[0] = 94845) erasing segment 20 (vno[0] = 95197) erasing segment 21 (vno[0] = 108187) erasing segment 22 (vno[0] = 110321) erasing segment 23 (vno[0] = 111222) #-------------------------------------------- #@# CortexLabel rh Mon Jan 9 12:58:24 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 7 non-cortical segments detected only using segment with 7193 vertices erasing segment 1 (vno[0] = 58586) erasing segment 2 (vno[0] = 68683) erasing segment 3 (vno[0] = 69395) erasing segment 4 (vno[0] = 75593) erasing segment 5 (vno[0] = 77294) erasing segment 6 (vno[0] = 111802) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Mon Jan 9 12:58:34 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 8 non-cortical segments detected only using segment with 6040 vertices erasing segment 1 (vno[0] = 58586) erasing segment 2 (vno[0] = 68683) erasing segment 3 (vno[0] = 69395) erasing segment 4 (vno[0] = 75593) erasing segment 5 (vno[0] = 77294) erasing segment 6 (vno[0] = 104393) erasing segment 7 (vno[0] = 111802) #-------------------------------------------- #@# Smooth2 lh Mon Jan 9 12:58:44 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Mon Jan 9 12:58:44 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 324717 of (324717 324720) to complete... Waiting for PID 324720 of (324717 324720) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (324717 324720) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Mon Jan 9 12:58:46 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Mon Jan 9 12:58:46 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 324769 of (324769 324772) to complete... Waiting for PID 324772 of (324769 324772) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.6 mm, total surface area = 70679 mm^2 step 000: RMS=0.177 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 28.019339 mris_inflate stimesec 0.135822 mris_inflate ru_maxrss 182624 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29217 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9040 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1052 mris_inflate ru_nivcsw 14 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.8 mm, total surface area = 68165 mm^2 step 000: RMS=0.174 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 29.050524 mris_inflate stimesec 0.665948 mris_inflate ru_maxrss 178388 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 327403 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8792 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 945 mris_inflate ru_nivcsw 39 PIDs (324769 324772) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Mon Jan 9 12:58:57 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Mon Jan 9 12:58:57 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf reconbatchjobs /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 324856 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324859 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324862 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324865 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324868 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324871 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324874 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324877 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324880 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324883 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324886 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... Waiting for PID 324889 of (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 20.424*4pi (256.653) --> -19 handles ICI = 162.7, FI = 1440.7, variation=23326.234 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 101 vertices thresholded to be in k1 ~ [-0.56 0.44], k2 ~ [-0.23 0.10] total integrated curvature = 0.502*4pi (6.310) --> 0 handles ICI = 1.4, FI = 9.2, variation=154.578 102 vertices thresholded to be in [-0.02 0.06] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 109 vertices thresholded to be in [-0.28 0.21] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.025 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 21.252*4pi (267.062) --> -20 handles ICI = 162.9, FI = 1481.6, variation=23802.021 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 194 vertices thresholded to be in k1 ~ [-0.82 1.85], k2 ~ [-0.65 0.17] total integrated curvature = 0.537*4pi (6.743) --> 0 handles ICI = 1.5, FI = 8.2, variation=145.129 150 vertices thresholded to be in [-0.14 0.06] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.003 110 vertices thresholded to be in [-0.32 0.65] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.026 done. PIDs (324856 324859 324862 324865 324868 324871 324874 324877 324880 324883 324886 324889) completed and logs appended. #-------------------------------------------- #@# Sphere lh Mon Jan 9 12:59:27 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Mon Jan 9 12:59:27 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 324966 of (324966 324969) to complete... Waiting for PID 324969 of (324966 324969) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.322... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.10 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.97 removing remaining folds... final distance error %20.00 MRISunfold() return, current seed 1234 -01: dt=0.0000, 39 negative triangles VmPeak 770676 182: dt=0.9900, 39 negative triangles 183: dt=0.9900, 23 negative triangles 184: dt=0.9900, 14 negative triangles 185: dt=0.9900, 13 negative triangles 186: dt=0.9900, 15 negative triangles 187: dt=0.9900, 12 negative triangles 188: dt=0.9900, 10 negative triangles 189: dt=0.9900, 6 negative triangles 190: dt=0.9900, 10 negative triangles 191: dt=0.9900, 7 negative triangles 192: dt=0.9900, 7 negative triangles 193: dt=0.9900, 4 negative triangles 194: dt=0.9900, 9 negative triangles 195: dt=0.9900, 4 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 6 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 2 negative triangles 202: dt=0.9900, 2 negative triangles 203: dt=0.9900, 4 negative triangles 204: dt=0.9900, 2 negative triangles 205: dt=0.9900, 2 negative triangles 206: dt=0.9900, 2 negative triangles 207: dt=0.9900, 3 negative triangles 208: dt=0.9900, 2 negative triangles 209: dt=0.9900, 1 negative triangles 210: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0587 hours FSRUNTIME@ mris_sphere 0.0587 hours 4 threads #VMPC# mris_sphere VmPeak 770676 mris_sphere done mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.329... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.55 pass 1: epoch 2 of 3 starting distance error %20.51 unfolding complete - removing small folds... starting distance error %20.41 removing remaining folds... final distance error %20.46 MRISunfold() return, current seed 1234 -01: dt=0.0000, 452 negative triangles VmPeak 768040 233: dt=0.9900, 452 negative triangles 234: dt=0.9900, 390 negative triangles 235: dt=0.9900, 398 negative triangles 236: dt=0.9900, 398 negative triangles 237: dt=0.9900, 390 negative triangles 238: dt=0.9900, 393 negative triangles 239: dt=0.9900, 396 negative triangles 240: dt=0.9900, 396 negative triangles 241: dt=0.9900, 386 negative triangles 242: dt=0.9900, 393 negative triangles 243: dt=0.9900, 379 negative triangles 244: dt=0.9900, 386 negative triangles 245: dt=0.9900, 378 negative triangles 246: dt=0.9900, 386 negative triangles 247: dt=0.9900, 371 negative triangles 248: dt=0.9900, 381 negative triangles 249: dt=0.9900, 383 negative triangles 250: dt=0.9900, 379 negative triangles 251: dt=0.9900, 375 negative triangles 252: dt=0.9900, 377 negative triangles 253: dt=0.9900, 376 negative triangles 254: dt=0.9900, 379 negative triangles 255: dt=0.9900, 374 negative triangles 256: dt=0.9900, 376 negative triangles 257: dt=0.9405, 379 negative triangles 258: dt=0.9405, 377 negative triangles 259: dt=0.9405, 374 negative triangles 260: dt=0.9405, 376 negative triangles 261: dt=0.9405, 384 negative triangles 262: dt=0.9405, 377 negative triangles 263: dt=0.9405, 370 negative triangles 264: dt=0.9405, 369 negative triangles 265: dt=0.9405, 369 negative triangles 266: dt=0.9405, 367 negative triangles 267: dt=0.9405, 370 negative triangles 268: dt=0.9405, 371 negative triangles 269: dt=0.9405, 371 negative triangles 270: dt=0.9405, 368 negative triangles 271: dt=0.9405, 365 negative triangles 272: dt=0.9405, 371 negative triangles 273: dt=0.9405, 367 negative triangles 274: dt=0.9405, 374 negative triangles 275: dt=0.9405, 368 negative triangles 276: dt=0.9405, 371 negative triangles 277: dt=0.9405, 365 negative triangles 278: dt=0.9405, 376 negative triangles 279: dt=0.9405, 368 negative triangles 280: dt=0.9405, 374 negative triangles 281: dt=0.8935, 369 negative triangles 282: dt=0.8935, 375 negative triangles 283: dt=0.8935, 376 negative triangles 284: dt=0.8935, 377 negative triangles 285: dt=0.8935, 373 negative triangles 286: dt=0.8935, 377 negative triangles 287: dt=0.8935, 373 negative triangles 288: dt=0.8935, 376 negative triangles 289: dt=0.8935, 369 negative triangles 290: dt=0.8935, 374 negative triangles 291: dt=0.8488, 375 negative triangles 292: dt=0.8488, 373 negative triangles 293: dt=0.8488, 371 negative triangles 294: dt=0.8488, 374 negative triangles 295: dt=0.8488, 366 negative triangles 296: dt=0.8488, 378 negative triangles 297: dt=0.8488, 369 negative triangles 298: dt=0.8488, 376 negative triangles 299: dt=0.8488, 376 negative triangles 300: dt=0.8488, 371 negative triangles 301: dt=0.8064, 375 negative triangles 302: dt=0.8064, 367 negative triangles 303: dt=0.8064, 376 negative triangles 304: dt=0.8064, 379 negative triangles 305: dt=0.8064, 366 negative triangles 306: dt=0.8064, 370 negative triangles 307: dt=0.8064, 368 negative triangles 308: dt=0.8064, 368 negative triangles 309: dt=0.8064, 367 negative triangles 310: dt=0.8064, 371 negative triangles 311: dt=0.7660, 369 negative triangles 312: dt=0.7660, 370 negative triangles 313: dt=0.7660, 369 negative triangles 314: dt=0.7660, 368 negative triangles 315: dt=0.7660, 372 negative triangles 316: dt=0.7660, 372 negative triangles 317: dt=0.7660, 371 negative triangles 318: dt=0.7660, 373 negative triangles 319: dt=0.7660, 365 negative triangles 320: dt=0.7660, 370 negative triangles 321: dt=0.7277, 368 negative triangles expanding nbhd size to 1 322: dt=0.9900, 370 negative triangles 323: dt=0.9900, 366 negative triangles 324: dt=0.9900, 365 negative triangles 325: dt=0.9900, 358 negative triangles 326: dt=0.9900, 357 negative triangles 327: dt=0.9900, 352 negative triangles 328: dt=0.9900, 353 negative triangles 329: dt=0.9900, 349 negative triangles 330: dt=0.9900, 350 negative triangles 331: dt=0.9900, 350 negative triangles 332: dt=0.9900, 354 negative triangles 333: dt=0.9900, 357 negative triangles 334: dt=0.9900, 354 negative triangles 335: dt=0.9900, 355 negative triangles 336: dt=0.9900, 354 negative triangles 337: dt=0.9900, 358 negative triangles 338: dt=0.9900, 356 negative triangles 339: dt=0.9405, 359 negative triangles 340: dt=0.9405, 358 negative triangles 341: dt=0.9405, 357 negative triangles 342: dt=0.9405, 354 negative triangles 343: dt=0.9405, 355 negative triangles 344: dt=0.9405, 354 negative triangles 345: dt=0.9405, 357 negative triangles 346: dt=0.9405, 355 negative triangles 347: dt=0.9405, 359 negative triangles 348: dt=0.9405, 362 negative triangles 349: dt=0.8935, 360 negative triangles 350: dt=0.8935, 358 negative triangles 351: dt=0.8935, 359 negative triangles 352: dt=0.8935, 358 negative triangles 353: dt=0.8935, 358 negative triangles 354: dt=0.8935, 358 negative triangles 355: dt=0.8935, 356 negative triangles 356: dt=0.8935, 355 negative triangles 357: dt=0.8935, 352 negative triangles 358: dt=0.8935, 357 negative triangles 359: dt=0.8488, 356 negative triangles 360: dt=0.8488, 354 negative triangles 361: dt=0.8488, 355 negative triangles 362: dt=0.8488, 357 negative triangles 363: dt=0.8488, 355 negative triangles 364: dt=0.8488, 361 negative triangles 365: dt=0.8488, 356 negative triangles 366: dt=0.8488, 356 negative triangles 367: dt=0.8488, 357 negative triangles 368: dt=0.8488, 360 negative triangles 369: dt=0.8064, 357 negative triangles 370: dt=0.8064, 357 negative triangles 371: dt=0.8064, 356 negative triangles 372: dt=0.8064, 352 negative triangles 373: dt=0.8064, 355 negative triangles 374: dt=0.8064, 358 negative triangles 375: dt=0.8064, 359 negative triangles 376: dt=0.8064, 354 negative triangles 377: dt=0.8064, 351 negative triangles 378: dt=0.8064, 353 negative triangles 379: dt=0.7660, 360 negative triangles 380: dt=0.7660, 359 negative triangles 381: dt=0.7660, 354 negative triangles 382: dt=0.7660, 359 negative triangles 383: dt=0.7660, 354 negative triangles 384: dt=0.7660, 352 negative triangles 385: dt=0.7660, 354 negative triangles 386: dt=0.7660, 358 negative triangles 387: dt=0.7660, 350 negative triangles 388: dt=0.7660, 354 negative triangles 389: dt=0.7277, 356 negative triangles 390: dt=0.7277, 356 negative triangles 391: dt=0.7277, 358 negative triangles 392: dt=0.7277, 354 negative triangles 393: dt=0.7277, 353 negative triangles 394: dt=0.7277, 351 negative triangles 395: dt=0.7277, 350 negative triangles 396: dt=0.7277, 357 negative triangles 397: dt=0.7277, 357 negative triangles 398: dt=0.7277, 351 negative triangles 399: dt=0.6914, 352 negative triangles 400: dt=0.6914, 350 negative triangles 401: dt=0.6914, 357 negative triangles 402: dt=0.6914, 356 negative triangles 403: dt=0.6914, 360 negative triangles 404: dt=0.6914, 356 negative triangles 405: dt=0.6914, 348 negative triangles 406: dt=0.6914, 360 negative triangles 407: dt=0.6914, 356 negative triangles 408: dt=0.6914, 347 negative triangles 409: dt=0.6914, 349 negative triangles 410: dt=0.6914, 355 negative triangles 411: dt=0.6914, 354 negative triangles 412: dt=0.6914, 352 negative triangles 413: dt=0.6914, 348 negative triangles 414: dt=0.6914, 350 negative triangles 415: dt=0.6914, 351 negative triangles 416: dt=0.6914, 347 negative triangles 417: dt=0.6914, 348 negative triangles 418: dt=0.6914, 342 negative triangles 419: dt=0.6914, 340 negative triangles 420: dt=0.6914, 343 negative triangles 421: dt=0.6914, 348 negative triangles 422: dt=0.6914, 351 negative triangles 423: dt=0.6914, 341 negative triangles 424: dt=0.6914, 345 negative triangles 425: dt=0.6914, 346 negative triangles 426: dt=0.6914, 344 negative triangles 427: dt=0.6914, 343 negative triangles 428: dt=0.6914, 345 negative triangles 429: dt=0.6568, 342 negative triangles 430: dt=0.6568, 348 negative triangles 431: dt=0.6568, 351 negative triangles 432: dt=0.6568, 350 negative triangles 433: dt=0.6568, 346 negative triangles 434: dt=0.6568, 345 negative triangles 435: dt=0.6568, 343 negative triangles 436: dt=0.6568, 355 negative triangles 437: dt=0.6568, 341 negative triangles 438: dt=0.6568, 349 negative triangles 439: dt=0.6239, 347 negative triangles 440: dt=0.6239, 348 negative triangles 441: dt=0.6239, 346 negative triangles 442: dt=0.6239, 347 negative triangles 443: dt=0.6239, 351 negative triangles 444: dt=0.6239, 343 negative triangles 445: dt=0.6239, 345 negative triangles 446: dt=0.6239, 348 negative triangles 447: dt=0.6239, 352 negative triangles 448: dt=0.6239, 345 negative triangles 449: dt=0.5927, 350 negative triangles 450: dt=0.5927, 345 negative triangles 451: dt=0.5927, 342 negative triangles 452: dt=0.5927, 349 negative triangles 453: dt=0.5927, 347 negative triangles 454: dt=0.5927, 347 negative triangles 455: dt=0.5927, 348 negative triangles 456: dt=0.5927, 352 negative triangles 457: dt=0.5927, 353 negative triangles 458: dt=0.5927, 349 negative triangles 459: dt=0.5631, 354 negative triangles 460: dt=0.5631, 350 negative triangles 461: dt=0.5631, 349 negative triangles 462: dt=0.5631, 349 negative triangles 463: dt=0.5631, 351 negative triangles 464: dt=0.5631, 349 negative triangles 465: dt=0.5631, 341 negative triangles 466: dt=0.5631, 341 negative triangles 467: dt=0.5631, 350 negative triangles 468: dt=0.5631, 346 negative triangles 469: dt=0.5350, 350 negative triangles 470: dt=0.5350, 352 negative triangles 471: dt=0.5350, 346 negative triangles 472: dt=0.5350, 351 negative triangles 473: dt=0.5350, 348 negative triangles 474: dt=0.5350, 350 negative triangles 475: dt=0.5350, 354 negative triangles 476: dt=0.5350, 353 negative triangles 477: dt=0.5350, 352 negative triangles 478: dt=0.5350, 353 negative triangles 479: dt=0.5082, 353 negative triangles 480: dt=0.5082, 350 negative triangles 481: dt=0.5082, 344 negative triangles 482: dt=0.5082, 343 negative triangles 483: dt=0.5082, 345 negative triangles 484: dt=0.5082, 353 negative triangles 485: dt=0.5082, 350 negative triangles 486: dt=0.5082, 351 negative triangles 487: dt=0.5082, 352 negative triangles 488: dt=0.5082, 357 negative triangles 489: dt=0.4828, 353 negative triangles 490: dt=0.4828, 349 negative triangles 491: dt=0.4828, 347 negative triangles 492: dt=0.4828, 353 negative triangles 493: dt=0.4828, 349 negative triangles 494: dt=0.4828, 347 negative triangles 495: dt=0.4828, 347 negative triangles 496: dt=0.4828, 344 negative triangles 497: dt=0.4828, 348 negative triangles 498: dt=0.4828, 347 negative triangles 499: dt=0.4587, 347 negative triangles 500: dt=0.4587, 355 negative triangles 501: dt=0.4587, 350 negative triangles 502: dt=0.4587, 357 negative triangles 503: dt=0.4587, 347 negative triangles 504: dt=0.4587, 345 negative triangles 505: dt=0.4587, 346 negative triangles 506: dt=0.4587, 347 negative triangles 507: dt=0.4587, 350 negative triangles 508: dt=0.4587, 344 negative triangles 509: dt=0.4357, 343 negative triangles 510: dt=0.4357, 344 negative triangles 511: dt=0.4357, 355 negative triangles 512: dt=0.4357, 341 negative triangles 513: dt=0.4357, 345 negative triangles 514: dt=0.4357, 344 negative triangles 515: dt=0.4357, 346 negative triangles 516: dt=0.4357, 344 negative triangles 517: dt=0.4357, 349 negative triangles 518: dt=0.4357, 346 negative triangles 519: dt=0.4139, 346 negative triangles 520: dt=0.4139, 348 negative triangles 521: dt=0.4139, 347 negative triangles 522: dt=0.4139, 340 negative triangles 523: dt=0.4139, 350 negative triangles 524: dt=0.4139, 345 negative triangles 525: dt=0.4139, 347 negative triangles 526: dt=0.4139, 349 negative triangles 527: dt=0.4139, 340 negative triangles 528: dt=0.4139, 349 negative triangles 529: dt=0.3932, 351 negative triangles 530: dt=0.3932, 345 negative triangles 531: dt=0.3932, 340 negative triangles 532: dt=0.3932, 342 negative triangles 533: dt=0.3932, 347 negative triangles 534: dt=0.3932, 343 negative triangles 535: dt=0.3932, 346 negative triangles 536: dt=0.3932, 344 negative triangles 537: dt=0.3932, 333 negative triangles 538: dt=0.3932, 338 negative triangles 539: dt=0.3932, 342 negative triangles 540: dt=0.3932, 349 negative triangles 541: dt=0.3932, 353 negative triangles 542: dt=0.3932, 346 negative triangles 543: dt=0.3932, 344 negative triangles 544: dt=0.3932, 344 negative triangles 545: dt=0.3932, 339 negative triangles 546: dt=0.3932, 347 negative triangles 547: dt=0.3736, 346 negative triangles 548: dt=0.3736, 347 negative triangles 549: dt=0.3736, 347 negative triangles 550: dt=0.3736, 344 negative triangles 551: dt=0.3736, 350 negative triangles 552: dt=0.3736, 349 negative triangles 553: dt=0.3736, 348 negative triangles 554: dt=0.3736, 347 negative triangles 555: dt=0.3736, 340 negative triangles 556: dt=0.3736, 346 negative triangles 557: dt=0.3549, 348 negative triangles 558: dt=0.3549, 345 negative triangles 559: dt=0.3549, 343 negative triangles 560: dt=0.3549, 339 negative triangles 561: dt=0.3549, 345 negative triangles 562: dt=0.3549, 343 negative triangles 563: dt=0.3549, 348 negative triangles 564: dt=0.3549, 349 negative triangles 565: dt=0.3549, 343 negative triangles 566: dt=0.3549, 344 negative triangles 567: dt=0.3372, 336 negative triangles 568: dt=0.3372, 344 negative triangles 569: dt=0.3372, 349 negative triangles 570: dt=0.3372, 332 negative triangles 571: dt=0.3372, 343 negative triangles 572: dt=0.3372, 340 negative triangles 573: dt=0.3372, 349 negative triangles 574: dt=0.3372, 349 negative triangles 575: dt=0.3372, 344 negative triangles 576: dt=0.3372, 344 negative triangles 577: dt=0.3372, 351 negative triangles 578: dt=0.3372, 345 negative triangles 579: dt=0.3372, 338 negative triangles 580: dt=0.3203, 339 negative triangles 581: dt=0.3203, 348 negative triangles 582: dt=0.3203, 348 negative triangles 583: dt=0.3203, 348 negative triangles 584: dt=0.3203, 350 negative triangles 585: dt=0.3203, 343 negative triangles 586: dt=0.3203, 345 negative triangles 587: dt=0.3203, 345 negative triangles 588: dt=0.3203, 348 negative triangles 589: dt=0.3203, 348 negative triangles 590: dt=0.3043, 341 negative triangles 591: dt=0.3043, 342 negative triangles 592: dt=0.3043, 343 negative triangles 593: dt=0.3043, 342 negative triangles 594: dt=0.3043, 339 negative triangles 595: dt=0.3043, 342 negative triangles 596: dt=0.3043, 338 negative triangles 597: dt=0.3043, 340 negative triangles 598: dt=0.3043, 340 negative triangles 599: dt=0.3043, 353 negative triangles 600: dt=0.2891, 353 negative triangles 601: dt=0.2891, 346 negative triangles 602: dt=0.2891, 350 negative triangles 603: dt=0.2891, 343 negative triangles 604: dt=0.2891, 340 negative triangles 605: dt=0.2891, 344 negative triangles 606: dt=0.2891, 341 negative triangles 607: dt=0.2891, 339 negative triangles 608: dt=0.2891, 342 negative triangles 609: dt=0.2891, 339 negative triangles 610: dt=0.2746, 344 negative triangles 611: dt=0.2746, 338 negative triangles 612: dt=0.2746, 341 negative triangles 613: dt=0.2746, 346 negative triangles 614: dt=0.2746, 343 negative triangles 615: dt=0.2746, 343 negative triangles 616: dt=0.2746, 350 negative triangles 617: dt=0.2746, 337 negative triangles 618: dt=0.2746, 349 negative triangles 619: dt=0.2746, 353 negative triangles 620: dt=0.2609, 351 negative triangles 621: dt=0.2609, 349 negative triangles 622: dt=0.2609, 347 negative triangles 623: dt=0.2609, 345 negative triangles 624: dt=0.2609, 341 negative triangles 625: dt=0.2609, 345 negative triangles 626: dt=0.2609, 343 negative triangles 627: dt=0.2609, 349 negative triangles 628: dt=0.2609, 342 negative triangles 629: dt=0.2609, 345 negative triangles 630: dt=0.2478, 344 negative triangles 631: dt=0.2478, 341 negative triangles 632: dt=0.2478, 338 negative triangles 633: dt=0.2478, 350 negative triangles 634: dt=0.2478, 339 negative triangles 635: dt=0.2478, 349 negative triangles 636: dt=0.2478, 349 negative triangles 637: dt=0.2478, 347 negative triangles 638: dt=0.2478, 346 negative triangles 639: dt=0.2478, 346 negative triangles 640: dt=0.2354, 344 negative triangles 641: dt=0.2354, 342 negative triangles 642: dt=0.2354, 339 negative triangles 643: dt=0.2354, 345 negative triangles 644: dt=0.2354, 344 negative triangles 645: dt=0.2354, 343 negative triangles 646: dt=0.2354, 339 negative triangles 647: dt=0.2354, 344 negative triangles 648: dt=0.2354, 341 negative triangles 649: dt=0.2354, 342 negative triangles 650: dt=0.2237, 351 negative triangles 651: dt=0.2237, 360 negative triangles 652: dt=0.2237, 348 negative triangles 653: dt=0.2237, 352 negative triangles 654: dt=0.2237, 356 negative triangles 655: dt=0.2237, 352 negative triangles 656: dt=0.2237, 345 negative triangles 657: dt=0.2237, 342 negative triangles 658: dt=0.2237, 345 negative triangles 659: dt=0.2237, 357 negative triangles 660: dt=0.2125, 345 negative triangles 661: dt=0.2125, 352 negative triangles 662: dt=0.2125, 353 negative triangles 663: dt=0.2125, 342 negative triangles 664: dt=0.2125, 345 negative triangles 665: dt=0.2125, 347 negative triangles 666: dt=0.2125, 346 negative triangles 667: dt=0.2125, 343 negative triangles 668: dt=0.2125, 345 negative triangles 669: dt=0.2125, 355 negative triangles 670: dt=0.2019, 353 negative triangles 671: dt=0.2019, 340 negative triangles 672: dt=0.2019, 351 negative triangles 673: dt=0.2019, 341 negative triangles 674: dt=0.2019, 351 negative triangles 675: dt=0.2019, 346 negative triangles 676: dt=0.2019, 345 negative triangles 677: dt=0.2019, 344 negative triangles 678: dt=0.2019, 353 negative triangles 679: dt=0.2019, 354 negative triangles 680: dt=0.1918, 356 negative triangles 681: dt=0.1918, 348 negative triangles 682: dt=0.1918, 349 negative triangles 683: dt=0.1918, 340 negative triangles 684: dt=0.1918, 340 negative triangles 685: dt=0.1918, 341 negative triangles 686: dt=0.1918, 340 negative triangles 687: dt=0.1918, 338 negative triangles 688: dt=0.1918, 342 negative triangles 689: dt=0.1918, 345 negative triangles 690: dt=0.1822, 345 negative triangles 691: dt=0.1822, 349 negative triangles 692: dt=0.1822, 349 negative triangles 693: dt=0.1822, 349 negative triangles 694: dt=0.1822, 348 negative triangles 695: dt=0.1822, 347 negative triangles 696: dt=0.1822, 345 negative triangles 697: dt=0.1822, 345 negative triangles 698: dt=0.1822, 346 negative triangles 699: dt=0.1822, 353 negative triangles 700: dt=0.1731, 345 negative triangles 701: dt=0.1731, 344 negative triangles 702: dt=0.1731, 338 negative triangles 703: dt=0.1731, 338 negative triangles 704: dt=0.1731, 346 negative triangles 705: dt=0.1731, 351 negative triangles 706: dt=0.1731, 344 negative triangles 707: dt=0.1731, 347 negative triangles 708: dt=0.1731, 342 negative triangles 709: dt=0.1731, 349 negative triangles 710: dt=0.1644, 356 negative triangles 711: dt=0.1644, 348 negative triangles 712: dt=0.1644, 342 negative triangles 713: dt=0.1644, 350 negative triangles 714: dt=0.1644, 359 negative triangles 715: dt=0.1644, 353 negative triangles 716: dt=0.1644, 344 negative triangles 717: dt=0.1644, 349 negative triangles 718: dt=0.1644, 351 negative triangles 719: dt=0.1644, 344 negative triangles 720: dt=0.1562, 353 negative triangles 721: dt=0.1562, 358 negative triangles 722: dt=0.1562, 352 negative triangles 723: dt=0.1562, 349 negative triangles 724: dt=0.1562, 356 negative triangles 725: dt=0.1562, 353 negative triangles 726: dt=0.1562, 352 negative triangles 727: dt=0.1562, 350 negative triangles 728: dt=0.1562, 344 negative triangles 729: dt=0.1562, 344 negative triangles 730: dt=0.1484, 354 negative triangles 731: dt=0.1484, 353 negative triangles 732: dt=0.1484, 358 negative triangles 733: dt=0.1484, 357 negative triangles 734: dt=0.1484, 351 negative triangles 735: dt=0.1484, 341 negative triangles 736: dt=0.1484, 351 negative triangles 737: dt=0.1484, 349 negative triangles 738: dt=0.1484, 348 negative triangles 739: dt=0.1484, 349 negative triangles 740: dt=0.1410, 349 negative triangles 741: dt=0.1410, 352 negative triangles 742: dt=0.1410, 353 negative triangles 743: dt=0.1410, 345 negative triangles 744: dt=0.1410, 350 negative triangles 745: dt=0.1410, 347 negative triangles 746: dt=0.1410, 343 negative triangles 747: dt=0.1410, 344 negative triangles 748: dt=0.1410, 344 negative triangles 749: dt=0.1410, 343 negative triangles 750: dt=0.1339, 340 negative triangles 751: dt=0.1339, 342 negative triangles 752: dt=0.1339, 338 negative triangles 753: dt=0.1339, 341 negative triangles 754: dt=0.1339, 350 negative triangles 755: dt=0.1339, 339 negative triangles 756: dt=0.1339, 342 negative triangles 757: dt=0.1339, 342 negative triangles 758: dt=0.1339, 351 negative triangles 759: dt=0.1339, 359 negative triangles 760: dt=0.1272, 348 negative triangles 761: dt=0.1272, 355 negative triangles 762: dt=0.1272, 356 negative triangles 763: dt=0.1272, 353 negative triangles 764: dt=0.1272, 352 negative triangles 765: dt=0.1272, 345 negative triangles 766: dt=0.1272, 347 negative triangles 767: dt=0.1272, 339 negative triangles 768: dt=0.1272, 343 negative triangles 769: dt=0.1272, 344 negative triangles 770: dt=0.1209, 349 negative triangles 771: dt=0.1209, 342 negative triangles 772: dt=0.1209, 340 negative triangles 773: dt=0.1209, 345 negative triangles 774: dt=0.1209, 342 negative triangles 775: dt=0.1209, 351 negative triangles 776: dt=0.1209, 356 negative triangles 777: dt=0.1209, 355 negative triangles 778: dt=0.1209, 354 negative triangles 779: dt=0.1209, 351 negative triangles 780: dt=0.1148, 350 negative triangles 781: dt=0.1148, 347 negative triangles 782: dt=0.1148, 350 negative triangles 783: dt=0.1148, 342 negative triangles 784: dt=0.1148, 347 negative triangles 785: dt=0.1148, 346 negative triangles 786: dt=0.1148, 352 negative triangles 787: dt=0.1148, 348 negative triangles 788: dt=0.1148, 343 negative triangles 789: dt=0.1148, 344 negative triangles 790: dt=0.1091, 344 negative triangles 791: dt=0.1091, 348 negative triangles 792: dt=0.1091, 344 negative triangles 793: dt=0.1091, 339 negative triangles 794: dt=0.1091, 342 negative triangles 795: dt=0.1091, 343 negative triangles 796: dt=0.1091, 345 negative triangles 797: dt=0.1091, 347 negative triangles 798: dt=0.1091, 345 negative triangles 799: dt=0.1091, 351 negative triangles 800: dt=0.1036, 342 negative triangles 801: dt=0.1036, 343 negative triangles 802: dt=0.1036, 343 negative triangles 803: dt=0.1036, 345 negative triangles 804: dt=0.1036, 341 negative triangles 805: dt=0.1036, 346 negative triangles 806: dt=0.1036, 347 negative triangles 807: dt=0.1036, 347 negative triangles 808: dt=0.1036, 349 negative triangles 809: dt=0.1036, 354 negative triangles 810: dt=0.0984, 347 negative triangles 811: dt=0.0984, 358 negative triangles 812: dt=0.0984, 349 negative triangles 813: dt=0.0984, 348 negative triangles 814: dt=0.0984, 343 negative triangles 815: dt=0.0984, 340 negative triangles 816: dt=0.0984, 348 negative triangles 817: dt=0.0984, 347 negative triangles 818: dt=0.0984, 341 negative triangles 819: dt=0.0984, 348 negative triangles 820: dt=0.0935, 352 negative triangles 821: dt=0.0935, 351 negative triangles 822: dt=0.0935, 347 negative triangles 823: dt=0.0935, 342 negative triangles 824: dt=0.0935, 343 negative triangles 825: dt=0.0935, 344 negative triangles 826: dt=0.0935, 345 negative triangles 827: dt=0.0935, 348 negative triangles 828: dt=0.0935, 350 negative triangles 829: dt=0.0935, 349 negative triangles 830: dt=0.0888, 353 negative triangles 831: dt=0.0888, 348 negative triangles 832: dt=0.0888, 348 negative triangles 833: dt=0.0888, 346 negative triangles 834: dt=0.0888, 345 negative triangles 835: dt=0.0888, 352 negative triangles 836: dt=0.0888, 348 negative triangles 837: dt=0.0888, 348 negative triangles 838: dt=0.0888, 344 negative triangles 839: dt=0.0888, 342 negative triangles 840: dt=0.0844, 339 negative triangles 841: dt=0.0844, 338 negative triangles 842: dt=0.0844, 342 negative triangles 843: dt=0.0844, 343 negative triangles 844: dt=0.0844, 342 negative triangles 845: dt=0.0844, 347 negative triangles 846: dt=0.0844, 345 negative triangles 847: dt=0.0844, 344 negative triangles 848: dt=0.0844, 339 negative triangles 849: dt=0.0844, 347 negative triangles 850: dt=0.0802, 341 negative triangles 851: dt=0.0802, 340 negative triangles 852: dt=0.0802, 341 negative triangles 853: dt=0.0802, 348 negative triangles 854: dt=0.0802, 345 negative triangles 855: dt=0.0802, 342 negative triangles 856: dt=0.0802, 346 negative triangles 857: dt=0.0802, 343 negative triangles 858: dt=0.0802, 339 negative triangles 859: dt=0.0802, 350 negative triangles 860: dt=0.0762, 343 negative triangles 861: dt=0.0762, 347 negative triangles 862: dt=0.0762, 351 negative triangles 863: dt=0.0762, 345 negative triangles 864: dt=0.0762, 345 negative triangles 865: dt=0.0762, 344 negative triangles 866: dt=0.0762, 337 negative triangles 867: dt=0.0762, 337 negative triangles 868: dt=0.0762, 342 negative triangles 869: dt=0.0762, 339 negative triangles 870: dt=0.0724, 340 negative triangles 871: dt=0.0724, 336 negative triangles 872: dt=0.0724, 338 negative triangles 873: dt=0.0724, 342 negative triangles 874: dt=0.0724, 347 negative triangles 875: dt=0.0724, 356 negative triangles 876: dt=0.0724, 354 negative triangles 877: dt=0.0724, 356 negative triangles 878: dt=0.0724, 355 negative triangles 879: dt=0.0724, 351 negative triangles 880: dt=0.0687, 360 negative triangles 881: dt=0.0687, 356 negative triangles 882: dt=0.0687, 349 negative triangles 883: dt=0.0687, 353 negative triangles 884: dt=0.0687, 357 negative triangles 885: dt=0.0687, 351 negative triangles 886: dt=0.0687, 349 negative triangles 887: dt=0.0687, 351 negative triangles 888: dt=0.0687, 353 negative triangles 889: dt=0.0687, 353 negative triangles 890: dt=0.0653, 352 negative triangles 891: dt=0.0653, 346 negative triangles 892: dt=0.0653, 346 negative triangles 893: dt=0.0653, 350 negative triangles 894: dt=0.0653, 346 negative triangles 895: dt=0.0653, 351 negative triangles 896: dt=0.0653, 350 negative triangles 897: dt=0.0653, 347 negative triangles 898: dt=0.0653, 346 negative triangles 899: dt=0.0653, 349 negative triangles 900: dt=0.0620, 341 negative triangles 901: dt=0.0620, 338 negative triangles 902: dt=0.0620, 341 negative triangles 903: dt=0.0620, 335 negative triangles 904: dt=0.0620, 343 negative triangles 905: dt=0.0620, 347 negative triangles 906: dt=0.0620, 350 negative triangles 907: dt=0.0620, 353 negative triangles 908: dt=0.0620, 353 negative triangles 909: dt=0.0620, 351 negative triangles 910: dt=0.0589, 356 negative triangles 911: dt=0.0589, 351 negative triangles 912: dt=0.0589, 347 negative triangles 913: dt=0.0589, 345 negative triangles 914: dt=0.0589, 344 negative triangles 915: dt=0.0589, 347 negative triangles 916: dt=0.0589, 349 negative triangles 917: dt=0.0589, 353 negative triangles 918: dt=0.0589, 347 negative triangles 919: dt=0.0589, 346 negative triangles 920: dt=0.0560, 359 negative triangles 921: dt=0.0560, 352 negative triangles 922: dt=0.0560, 353 negative triangles 923: dt=0.0560, 348 negative triangles 924: dt=0.0560, 347 negative triangles 925: dt=0.0560, 344 negative triangles 926: dt=0.0560, 347 negative triangles 927: dt=0.0560, 340 negative triangles 928: dt=0.0560, 338 negative triangles 929: dt=0.0560, 340 negative triangles 930: dt=0.0532, 339 negative triangles 931: dt=0.0532, 340 negative triangles 932: dt=0.0532, 336 negative triangles 933: dt=0.0532, 341 negative triangles 934: dt=0.0532, 339 negative triangles 935: dt=0.0532, 338 negative triangles 936: dt=0.0532, 339 negative triangles 937: dt=0.0532, 341 negative triangles 938: dt=0.0532, 337 negative triangles 939: dt=0.0532, 338 negative triangles 940: dt=0.0505, 342 negative triangles 941: dt=0.0505, 344 negative triangles 942: dt=0.0505, 350 negative triangles 943: dt=0.0505, 348 negative triangles 944: dt=0.0505, 348 negative triangles 945: dt=0.0505, 348 negative triangles 946: dt=0.0505, 345 negative triangles 947: dt=0.0505, 346 negative triangles 948: dt=0.0505, 338 negative triangles 949: dt=0.0505, 339 negative triangles 950: dt=0.0480, 334 negative triangles 951: dt=0.0480, 339 negative triangles 952: dt=0.0480, 338 negative triangles 953: dt=0.0480, 340 negative triangles 954: dt=0.0480, 341 negative triangles 955: dt=0.0480, 342 negative triangles 956: dt=0.0480, 339 negative triangles 957: dt=0.0480, 339 negative triangles 958: dt=0.0480, 336 negative triangles 959: dt=0.0480, 344 negative triangles 960: dt=0.0456, 345 negative triangles 961: dt=0.0456, 344 negative triangles 962: dt=0.0456, 345 negative triangles 963: dt=0.0456, 340 negative triangles 964: dt=0.0456, 342 negative triangles 965: dt=0.0456, 345 negative triangles 966: dt=0.0456, 342 negative triangles 967: dt=0.0456, 338 negative triangles 968: dt=0.0456, 343 negative triangles 969: dt=0.0456, 344 negative triangles 970: dt=0.0433, 350 negative triangles 971: dt=0.0433, 346 negative triangles 972: dt=0.0433, 346 negative triangles 973: dt=0.0433, 346 negative triangles 974: dt=0.0433, 349 negative triangles 975: dt=0.0433, 351 negative triangles 976: dt=0.0433, 352 negative triangles 977: dt=0.0433, 352 negative triangles 978: dt=0.0433, 350 negative triangles 979: dt=0.0433, 355 negative triangles 980: dt=0.0412, 354 negative triangles 981: dt=0.0412, 350 negative triangles 982: dt=0.0412, 351 negative triangles 983: dt=0.0412, 354 negative triangles 984: dt=0.0412, 358 negative triangles 985: dt=0.0412, 359 negative triangles 986: dt=0.0412, 357 negative triangles 987: dt=0.0412, 357 negative triangles 988: dt=0.0412, 358 negative triangles 989: dt=0.0412, 355 negative triangles 990: dt=0.0391, 351 negative triangles 991: dt=0.0391, 358 negative triangles 992: dt=0.0391, 348 negative triangles 993: dt=0.0391, 354 negative triangles 994: dt=0.0391, 356 negative triangles 995: dt=0.0391, 359 negative triangles 996: dt=0.0391, 362 negative triangles 997: dt=0.0391, 358 negative triangles 998: dt=0.0391, 367 negative triangles 999: dt=0.0391, 362 negative triangles 1000: dt=0.0371, 361 negative triangles 1001: dt=0.0371, 365 negative triangles 1002: dt=0.0371, 363 negative triangles 1003: dt=0.0371, 366 negative triangles 1004: dt=0.0371, 364 negative triangles 1005: dt=0.0371, 366 negative triangles 1006: dt=0.0371, 367 negative triangles 1007: dt=0.0371, 365 negative triangles 1008: dt=0.0371, 358 negative triangles 1009: dt=0.0371, 359 negative triangles 1010: dt=0.0353, 361 negative triangles 1011: dt=0.0353, 363 negative triangles 1012: dt=0.0353, 360 negative triangles 1013: dt=0.0353, 360 negative triangles 1014: dt=0.0353, 356 negative triangles 1015: dt=0.0353, 357 negative triangles 1016: dt=0.0353, 356 negative triangles 1017: dt=0.0353, 353 negative triangles 1018: dt=0.0353, 355 negative triangles 1019: dt=0.0353, 349 negative triangles 1020: dt=0.0335, 353 negative triangles 1021: dt=0.0335, 349 negative triangles 1022: dt=0.0335, 349 negative triangles 1023: dt=0.0335, 349 negative triangles 1024: dt=0.0335, 355 negative triangles 1025: dt=0.0335, 348 negative triangles 1026: dt=0.0335, 342 negative triangles 1027: dt=0.0335, 339 negative triangles 1028: dt=0.0335, 339 negative triangles 1029: dt=0.0335, 343 negative triangles 1030: dt=0.0319, 345 negative triangles 1031: dt=0.0319, 353 negative triangles 1032: dt=0.0319, 350 negative triangles 1033: dt=0.0319, 345 negative triangles 1034: dt=0.0319, 344 negative triangles 1035: dt=0.0319, 348 negative triangles 1036: dt=0.0319, 347 negative triangles 1037: dt=0.0319, 351 negative triangles 1038: dt=0.0319, 347 negative triangles 1039: dt=0.0319, 349 negative triangles 1040: dt=0.0303, 350 negative triangles 1041: dt=0.0303, 351 negative triangles 1042: dt=0.0303, 355 negative triangles 1043: dt=0.0303, 351 negative triangles 1044: dt=0.0303, 348 negative triangles 1045: dt=0.0303, 352 negative triangles 1046: dt=0.0303, 350 negative triangles 1047: dt=0.0303, 355 negative triangles 1048: dt=0.0303, 353 negative triangles 1049: dt=0.0303, 354 negative triangles 1050: dt=0.0287, 357 negative triangles 1051: dt=0.0287, 356 negative triangles 1052: dt=0.0287, 354 negative triangles 1053: dt=0.0287, 355 negative triangles 1054: dt=0.0287, 353 negative triangles 1055: dt=0.0287, 352 negative triangles 1056: dt=0.0287, 354 negative triangles 1057: dt=0.0287, 354 negative triangles 1058: dt=0.0287, 352 negative triangles 1059: dt=0.0287, 352 negative triangles 1060: dt=0.0273, 351 negative triangles 1061: dt=0.0273, 348 negative triangles 1062: dt=0.0273, 353 negative triangles 1063: dt=0.0273, 358 negative triangles 1064: dt=0.0273, 359 negative triangles 1065: dt=0.0273, 356 negative triangles 1066: dt=0.0273, 358 negative triangles 1067: dt=0.0273, 363 negative triangles 1068: dt=0.0273, 358 negative triangles 1069: dt=0.0273, 357 negative triangles 1070: dt=0.0259, 354 negative triangles 1071: dt=0.0259, 357 negative triangles 1072: dt=0.0259, 358 negative triangles 1073: dt=0.0259, 354 negative triangles 1074: dt=0.0259, 355 negative triangles 1075: dt=0.0259, 358 negative triangles 1076: dt=0.0259, 356 negative triangles 1077: dt=0.0259, 357 negative triangles 1078: dt=0.0259, 355 negative triangles 1079: dt=0.0259, 353 negative triangles 1080: dt=0.0246, 350 negative triangles 1081: dt=0.0246, 347 negative triangles 1082: dt=0.0246, 353 negative triangles 1083: dt=0.0246, 354 negative triangles 1084: dt=0.0246, 356 negative triangles 1085: dt=0.0246, 355 negative triangles 1086: dt=0.0246, 354 negative triangles 1087: dt=0.0246, 350 negative triangles 1088: dt=0.0246, 350 negative triangles 1089: dt=0.0246, 353 negative triangles 1090: dt=0.0234, 353 negative triangles 1091: dt=0.0234, 353 negative triangles 1092: dt=0.0234, 351 negative triangles 1093: dt=0.0234, 355 negative triangles 1094: dt=0.0234, 348 negative triangles 1095: dt=0.0234, 347 negative triangles 1096: dt=0.0234, 345 negative triangles 1097: dt=0.0234, 341 negative triangles 1098: dt=0.0234, 346 negative triangles 1099: dt=0.0234, 352 negative triangles 1100: dt=0.0222, 349 negative triangles 1101: dt=0.0222, 349 negative triangles 1102: dt=0.0222, 346 negative triangles 1103: dt=0.0222, 344 negative triangles 1104: dt=0.0222, 350 negative triangles 1105: dt=0.0222, 347 negative triangles 1106: dt=0.0222, 346 negative triangles 1107: dt=0.0222, 347 negative triangles 1108: dt=0.0222, 346 negative triangles 1109: dt=0.0222, 345 negative triangles 1110: dt=0.0211, 349 negative triangles 1111: dt=0.0211, 347 negative triangles 1112: dt=0.0211, 350 negative triangles 1113: dt=0.0211, 351 negative triangles 1114: dt=0.0211, 352 negative triangles 1115: dt=0.0211, 346 negative triangles 1116: dt=0.0211, 346 negative triangles 1117: dt=0.0211, 349 negative triangles 1118: dt=0.0211, 351 negative triangles 1119: dt=0.0211, 350 negative triangles 1120: dt=0.0201, 354 negative triangles 1121: dt=0.0201, 354 negative triangles 1122: dt=0.0201, 349 negative triangles 1123: dt=0.0201, 352 negative triangles 1124: dt=0.0201, 347 negative triangles 1125: dt=0.0201, 346 negative triangles 1126: dt=0.0201, 348 negative triangles 1127: dt=0.0201, 346 negative triangles 1128: dt=0.0201, 344 negative triangles 1129: dt=0.0201, 350 negative triangles 1130: dt=0.0191, 349 negative triangles 1131: dt=0.0191, 350 negative triangles 1132: dt=0.0191, 352 negative triangles 1133: dt=0.0191, 350 negative triangles 1134: dt=0.0191, 350 negative triangles 1135: dt=0.0191, 353 negative triangles 1136: dt=0.0191, 353 negative triangles 1137: dt=0.0191, 356 negative triangles 1138: dt=0.0191, 356 negative triangles 1139: dt=0.0191, 357 negative triangles 1140: dt=0.0181, 357 negative triangles 1141: dt=0.0181, 358 negative triangles 1142: dt=0.0181, 355 negative triangles 1143: dt=0.0181, 354 negative triangles 1144: dt=0.0181, 349 negative triangles 1145: dt=0.0181, 353 negative triangles 1146: dt=0.0181, 354 negative triangles 1147: dt=0.0181, 353 negative triangles 1148: dt=0.0181, 348 negative triangles 1149: dt=0.0181, 348 negative triangles 1150: dt=0.0172, 356 negative triangles 1151: dt=0.0172, 358 negative triangles 1152: dt=0.0172, 356 negative triangles 1153: dt=0.0172, 356 negative triangles 1154: dt=0.0172, 353 negative triangles 1155: dt=0.0172, 353 negative triangles 1156: dt=0.0172, 354 negative triangles 1157: dt=0.0172, 356 negative triangles 1158: dt=0.0172, 351 negative triangles 1159: dt=0.0172, 353 negative triangles 1160: dt=0.0164, 351 negative triangles 1161: dt=0.0164, 350 negative triangles 1162: dt=0.0164, 348 negative triangles 1163: dt=0.0164, 350 negative triangles 1164: dt=0.0164, 345 negative triangles 1165: dt=0.0164, 345 negative triangles 1166: dt=0.0164, 346 negative triangles 1167: dt=0.0164, 348 negative triangles 1168: dt=0.0164, 346 negative triangles 1169: dt=0.0164, 349 negative triangles 1170: dt=0.0155, 346 negative triangles 1171: dt=0.0155, 347 negative triangles 1172: dt=0.0155, 343 negative triangles 1173: dt=0.0155, 345 negative triangles 1174: dt=0.0155, 343 negative triangles 1175: dt=0.0155, 346 negative triangles 1176: dt=0.0155, 346 negative triangles 1177: dt=0.0155, 344 negative triangles 1178: dt=0.0155, 346 negative triangles 1179: dt=0.0155, 344 negative triangles 1180: dt=0.0148, 347 negative triangles 1181: dt=0.0148, 346 negative triangles 1182: dt=0.0148, 348 negative triangles 1183: dt=0.0148, 345 negative triangles 1184: dt=0.0148, 350 negative triangles 1185: dt=0.0148, 347 negative triangles 1186: dt=0.0148, 351 negative triangles 1187: dt=0.0148, 352 negative triangles 1188: dt=0.0148, 351 negative triangles 1189: dt=0.0148, 351 negative triangles 1190: dt=0.0140, 350 negative triangles 1191: dt=0.0140, 351 negative triangles 1192: dt=0.0140, 352 negative triangles 1193: dt=0.0140, 354 negative triangles 1194: dt=0.0140, 353 negative triangles 1195: dt=0.0140, 353 negative triangles 1196: dt=0.0140, 350 negative triangles 1197: dt=0.0140, 354 negative triangles 1198: dt=0.0140, 354 negative triangles 1199: dt=0.0140, 353 negative triangles 1200: dt=0.0133, 352 negative triangles 1201: dt=0.0133, 357 negative triangles 1202: dt=0.0133, 354 negative triangles 1203: dt=0.0133, 353 negative triangles 1204: dt=0.0133, 346 negative triangles 1205: dt=0.0133, 349 negative triangles 1206: dt=0.0133, 347 negative triangles 1207: dt=0.0133, 345 negative triangles 1208: dt=0.0133, 345 negative triangles 1209: dt=0.0133, 342 negative triangles 1210: dt=0.0127, 347 negative triangles 1211: dt=0.0127, 344 negative triangles 1212: dt=0.0127, 341 negative triangles 1213: dt=0.0127, 344 negative triangles 1214: dt=0.0127, 345 negative triangles 1215: dt=0.0127, 350 negative triangles 1216: dt=0.0127, 352 negative triangles 1217: dt=0.0127, 348 negative triangles 1218: dt=0.0127, 348 negative triangles 1219: dt=0.0127, 350 negative triangles 1220: dt=0.0120, 347 negative triangles 1221: dt=0.0120, 344 negative triangles 1222: dt=0.0120, 344 negative triangles 1223: dt=0.0120, 339 negative triangles 1224: dt=0.0120, 341 negative triangles 1225: dt=0.0120, 340 negative triangles 1226: dt=0.0120, 342 negative triangles 1227: dt=0.0120, 339 negative triangles 1228: dt=0.0120, 343 negative triangles 1229: dt=0.0120, 347 negative triangles 1230: dt=0.0114, 344 negative triangles 1231: dt=0.0114, 344 negative triangles 1232: dt=0.0114, 347 negative triangles 1233: dt=0.0114, 350 negative triangles 1234: 345 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1118 hours FSRUNTIME@ mris_sphere 0.1118 hours 4 threads #VMPC# mris_sphere VmPeak 768040 mris_sphere done PIDs (324966 324969) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Mon Jan 9 13:06:09 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_register -curv ../surf/lh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Mon Jan 9 13:06:09 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_register -curv ../surf/rh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 325040 of (325040 325043) to complete... Waiting for PID 325043 of (325040 325043) to complete... mris_register -curv ../surf/lh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts cmdline mris_register -curv ../surf/lh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.2.0 7.2.0 reading surface from ../surf/lh.sphere... reading template parameterization from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=shark, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.333 curvature mean = 0.037, std = 0.819 curvature mean = 0.013, std = 0.877 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (3.00, -11.00, -11.50) sse = 198827.1, elapsed since starting=0.0677 min MRISrigidBodyAlignGlobal() done 0.07 min curvature mean = 0.013, std = 0.845 curvature mean = 0.005, std = 0.954 curvature mean = 0.009, std = 0.854 curvature mean = 0.002, std = 0.982 curvature mean = 0.009, std = 0.858 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.024, std = 0.284 curvature mean = 0.045, std = 0.250 curvature mean = 0.055, std = 0.370 curvature mean = 0.037, std = 0.312 curvature mean = 0.032, std = 0.560 curvature mean = 0.036, std = 0.340 curvature mean = 0.017, std = 0.697 curvature mean = 0.036, std = 0.351 curvature mean = 0.006, std = 0.803 MRISregister() return, current seed 0 -01: dt=0.0000, 24 negative triangles VmPeak 770708 108: dt=0.9900, 24 negative triangles expanding nbhd size to 1 109: dt=0.9900, 27 negative triangles 110: dt=0.9900, 23 negative triangles 111: dt=0.9900, 20 negative triangles 112: dt=0.9900, 21 negative triangles 113: dt=0.9900, 22 negative triangles 114: dt=0.9900, 22 negative triangles 115: dt=0.9900, 21 negative triangles 116: dt=0.9900, 21 negative triangles 117: dt=0.9900, 21 negative triangles 118: dt=0.9900, 20 negative triangles 119: dt=0.9900, 20 negative triangles 120: dt=0.9900, 20 negative triangles 121: dt=0.9900, 19 negative triangles 122: dt=0.9900, 18 negative triangles 123: dt=0.9900, 18 negative triangles 124: dt=0.9900, 18 negative triangles 125: dt=0.9900, 18 negative triangles 126: dt=0.9900, 18 negative triangles 127: dt=0.9900, 18 negative triangles 128: dt=0.9900, 17 negative triangles 129: dt=0.9900, 18 negative triangles 130: dt=0.9900, 17 negative triangles 131: dt=0.9900, 17 negative triangles 132: dt=0.9900, 17 negative triangles 133: dt=0.9900, 17 negative triangles 134: dt=0.9900, 16 negative triangles 135: dt=0.9900, 14 negative triangles 136: dt=0.9900, 13 negative triangles 137: dt=0.9900, 13 negative triangles 138: dt=0.9900, 12 negative triangles 139: dt=0.9900, 11 negative triangles 140: dt=0.9900, 11 negative triangles 141: dt=0.9900, 11 negative triangles 142: dt=0.9900, 11 negative triangles 143: dt=0.9900, 11 negative triangles 144: dt=0.9900, 11 negative triangles 145: dt=0.9900, 11 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 11 negative triangles 148: dt=0.9900, 10 negative triangles 149: dt=0.9900, 9 negative triangles 150: dt=0.9900, 10 negative triangles 151: dt=0.9900, 9 negative triangles 152: dt=0.9900, 9 negative triangles 153: dt=0.9900, 7 negative triangles 154: dt=0.9900, 7 negative triangles 155: dt=0.9900, 7 negative triangles 156: dt=0.9900, 7 negative triangles 157: dt=0.9900, 7 negative triangles 158: dt=0.9900, 7 negative triangles 159: dt=0.9900, 6 negative triangles 160: dt=0.9900, 6 negative triangles 161: dt=0.9900, 6 negative triangles 162: dt=0.9900, 5 negative triangles 163: dt=0.9900, 5 negative triangles 164: dt=0.9900, 4 negative triangles 165: dt=0.9900, 4 negative triangles 166: dt=0.9900, 4 negative triangles 167: dt=0.9900, 4 negative triangles 168: dt=0.9900, 3 negative triangles 169: dt=0.9900, 3 negative triangles 170: dt=0.9900, 3 negative triangles 171: dt=0.9900, 3 negative triangles 172: dt=0.9900, 3 negative triangles 173: dt=0.9900, 2 negative triangles 174: dt=0.9900, 2 negative triangles 175: dt=0.9900, 2 negative triangles 176: dt=0.9900, 2 negative triangles 177: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.05 hours #VMPC# mris_register VmPeak 770708 FSRUNTIME@ mris_register 0.0530 hours 4 threads mris_register -curv ../surf/rh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts cmdline mris_register -curv ../surf/rh.sphere /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.2.0 7.2.0 reading surface from ../surf/rh.sphere... reading template parameterization from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=shark, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=shark, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.440 curvature mean = 0.033, std = 0.809 curvature mean = 0.013, std = 0.882 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (11.50, -9.50, -6.50) sse = 187631.2, elapsed since starting=0.0659 min MRISrigidBodyAlignGlobal() done 0.07 min curvature mean = 0.015, std = 0.834 curvature mean = 0.005, std = 0.957 curvature mean = 0.014, std = 0.844 curvature mean = 0.002, std = 0.983 curvature mean = 0.014, std = 0.848 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.027, std = 4.614 curvature mean = 0.040, std = 0.239 curvature mean = 0.004, std = 0.024 curvature mean = 0.034, std = 0.300 curvature mean = 0.002, std = 0.040 curvature mean = 0.034, std = 0.327 curvature mean = 0.001, std = 0.068 curvature mean = 0.034, std = 0.338 curvature mean = -0.000, std = 0.139 MRISregister() return, current seed 0 -01: dt=0.0000, 414 negative triangles VmPeak 768204 109: dt=0.9900, 414 negative triangles 110: dt=0.9405, 428 negative triangles expanding nbhd size to 1 111: dt=0.9900, 422 negative triangles 112: dt=0.9900, 406 negative triangles 113: dt=0.9900, 407 negative triangles 114: dt=0.9900, 411 negative triangles 115: dt=0.9900, 409 negative triangles 116: dt=0.9900, 407 negative triangles 117: dt=0.9900, 400 negative triangles 118: dt=0.9900, 392 negative triangles 119: dt=0.9900, 391 negative triangles 120: dt=0.9900, 386 negative triangles 121: dt=0.9900, 385 negative triangles 122: dt=0.9900, 387 negative triangles 123: dt=0.9900, 390 negative triangles 124: dt=0.9900, 388 negative triangles 125: dt=0.9900, 385 negative triangles 126: dt=0.9900, 379 negative triangles 127: dt=0.9900, 378 negative triangles 128: dt=0.9900, 379 negative triangles 129: dt=0.9900, 380 negative triangles 130: dt=0.9900, 379 negative triangles 131: dt=0.9900, 380 negative triangles 132: dt=0.9900, 379 negative triangles 133: dt=0.9900, 373 negative triangles 134: dt=0.9900, 373 negative triangles 135: dt=0.9900, 375 negative triangles 136: dt=0.9900, 378 negative triangles 137: dt=0.9900, 377 negative triangles 138: dt=0.9900, 375 negative triangles 139: dt=0.9900, 373 negative triangles 140: dt=0.9900, 370 negative triangles 141: dt=0.9900, 373 negative triangles 142: dt=0.9900, 372 negative triangles 143: dt=0.9900, 369 negative triangles 144: dt=0.9900, 369 negative triangles 145: dt=0.9900, 373 negative triangles 146: dt=0.9900, 371 negative triangles 147: dt=0.9900, 368 negative triangles 148: dt=0.9900, 367 negative triangles 149: dt=0.9900, 369 negative triangles 150: dt=0.9900, 370 negative triangles 151: dt=0.9900, 373 negative triangles 152: dt=0.9900, 371 negative triangles 153: dt=0.9900, 368 negative triangles 154: dt=0.9900, 370 negative triangles 155: dt=0.9900, 370 negative triangles 156: dt=0.9900, 369 negative triangles 157: dt=0.9900, 369 negative triangles 158: dt=0.9405, 371 negative triangles 159: dt=0.9405, 368 negative triangles 160: dt=0.9405, 369 negative triangles 161: dt=0.9405, 370 negative triangles 162: dt=0.9405, 370 negative triangles 163: dt=0.9405, 370 negative triangles 164: dt=0.9405, 370 negative triangles 165: dt=0.9405, 367 negative triangles 166: dt=0.9405, 370 negative triangles 167: dt=0.9405, 374 negative triangles 168: dt=0.8935, 372 negative triangles 169: dt=0.8935, 371 negative triangles 170: dt=0.8935, 371 negative triangles 171: dt=0.8935, 374 negative triangles 172: dt=0.8935, 373 negative triangles 173: dt=0.8935, 375 negative triangles 174: dt=0.8935, 375 negative triangles 175: dt=0.8935, 376 negative triangles 176: dt=0.8935, 375 negative triangles 177: dt=0.8935, 377 negative triangles 178: dt=0.8488, 374 negative triangles 179: dt=0.8488, 377 negative triangles 180: dt=0.8488, 375 negative triangles 181: dt=0.8488, 378 negative triangles 182: dt=0.8488, 375 negative triangles 183: dt=0.8488, 377 negative triangles 184: dt=0.8488, 376 negative triangles 185: dt=0.8488, 378 negative triangles 186: dt=0.8488, 374 negative triangles 187: dt=0.8488, 378 negative triangles 188: dt=0.8064, 380 negative triangles 189: dt=0.8064, 379 negative triangles 190: dt=0.8064, 381 negative triangles 191: dt=0.8064, 376 negative triangles 192: dt=0.8064, 376 negative triangles 193: dt=0.8064, 383 negative triangles 194: dt=0.8064, 377 negative triangles 195: dt=0.8064, 379 negative triangles 196: dt=0.8064, 377 negative triangles 197: dt=0.8064, 378 negative triangles 198: dt=0.7660, 378 negative triangles 199: dt=0.7660, 378 negative triangles 200: dt=0.7660, 374 negative triangles 201: dt=0.7660, 373 negative triangles 202: dt=0.7660, 371 negative triangles 203: dt=0.7660, 376 negative triangles 204: dt=0.7660, 379 negative triangles 205: dt=0.7660, 378 negative triangles 206: dt=0.7660, 375 negative triangles 207: dt=0.7660, 375 negative triangles 208: dt=0.7277, 375 negative triangles 209: dt=0.7277, 372 negative triangles 210: dt=0.7277, 374 negative triangles 211: dt=0.7277, 377 negative triangles 212: dt=0.7277, 374 negative triangles 213: dt=0.7277, 372 negative triangles 214: dt=0.7277, 375 negative triangles 215: dt=0.7277, 375 negative triangles 216: dt=0.7277, 375 negative triangles 217: dt=0.7277, 371 negative triangles 218: dt=0.7277, 366 negative triangles 219: dt=0.7277, 374 negative triangles 220: dt=0.7277, 375 negative triangles 221: dt=0.7277, 377 negative triangles 222: dt=0.7277, 375 negative triangles 223: dt=0.7277, 375 negative triangles 224: dt=0.7277, 377 negative triangles 225: dt=0.7277, 377 negative triangles 226: dt=0.7277, 374 negative triangles 227: dt=0.7277, 372 negative triangles 228: dt=0.6914, 375 negative triangles 229: dt=0.6914, 374 negative triangles 230: dt=0.6914, 372 negative triangles 231: dt=0.6914, 372 negative triangles 232: dt=0.6914, 371 negative triangles 233: dt=0.6914, 370 negative triangles 234: dt=0.6914, 371 negative triangles 235: dt=0.6914, 376 negative triangles 236: dt=0.6914, 376 negative triangles 237: dt=0.6914, 370 negative triangles 238: dt=0.6568, 373 negative triangles 239: dt=0.6568, 375 negative triangles 240: dt=0.6568, 369 negative triangles 241: dt=0.6568, 375 negative triangles 242: dt=0.6568, 374 negative triangles 243: dt=0.6568, 376 negative triangles 244: dt=0.6568, 367 negative triangles 245: dt=0.6568, 373 negative triangles 246: dt=0.6568, 368 negative triangles 247: dt=0.6568, 372 negative triangles 248: dt=0.6239, 371 negative triangles 249: dt=0.6239, 368 negative triangles 250: dt=0.6239, 367 negative triangles 251: dt=0.6239, 372 negative triangles 252: dt=0.6239, 368 negative triangles 253: dt=0.6239, 367 negative triangles 254: dt=0.6239, 370 negative triangles 255: dt=0.6239, 372 negative triangles 256: dt=0.6239, 370 negative triangles 257: dt=0.6239, 371 negative triangles 258: dt=0.5927, 368 negative triangles 259: dt=0.5927, 374 negative triangles 260: dt=0.5927, 374 negative triangles 261: dt=0.5927, 371 negative triangles 262: dt=0.5927, 369 negative triangles 263: dt=0.5927, 373 negative triangles 264: dt=0.5927, 372 negative triangles 265: dt=0.5927, 369 negative triangles 266: dt=0.5927, 370 negative triangles 267: dt=0.5927, 373 negative triangles 268: dt=0.5631, 369 negative triangles 269: dt=0.5631, 368 negative triangles 270: dt=0.5631, 372 negative triangles 271: dt=0.5631, 367 negative triangles 272: dt=0.5631, 371 negative triangles 273: dt=0.5631, 368 negative triangles 274: dt=0.5631, 364 negative triangles 275: dt=0.5631, 364 negative triangles 276: dt=0.5631, 374 negative triangles 277: dt=0.5631, 362 negative triangles 278: dt=0.5631, 369 negative triangles 279: dt=0.5631, 363 negative triangles 280: dt=0.5631, 360 negative triangles 281: dt=0.5631, 362 negative triangles 282: dt=0.5631, 361 negative triangles 283: dt=0.5631, 363 negative triangles 284: dt=0.5631, 364 negative triangles 285: dt=0.5631, 367 negative triangles 286: dt=0.5631, 362 negative triangles 287: dt=0.5631, 368 negative triangles 288: dt=0.5631, 366 negative triangles 289: dt=0.5631, 362 negative triangles 290: dt=0.5350, 363 negative triangles 291: dt=0.5350, 371 negative triangles 292: dt=0.5350, 365 negative triangles 293: dt=0.5350, 366 negative triangles 294: dt=0.5350, 365 negative triangles 295: dt=0.5350, 363 negative triangles 296: dt=0.5350, 359 negative triangles 297: dt=0.5350, 367 negative triangles 298: dt=0.5350, 366 negative triangles 299: dt=0.5350, 363 negative triangles 300: dt=0.5350, 364 negative triangles 301: dt=0.5350, 361 negative triangles 302: dt=0.5350, 368 negative triangles 303: dt=0.5350, 361 negative triangles 304: dt=0.5350, 367 negative triangles 305: dt=0.5350, 364 negative triangles 306: dt=0.5082, 362 negative triangles 307: dt=0.5082, 359 negative triangles 308: dt=0.5082, 363 negative triangles 309: dt=0.5082, 359 negative triangles 310: dt=0.5082, 359 negative triangles 311: dt=0.5082, 360 negative triangles 312: dt=0.5082, 358 negative triangles 313: dt=0.5082, 356 negative triangles 314: dt=0.5082, 357 negative triangles 315: dt=0.5082, 366 negative triangles 316: dt=0.5082, 364 negative triangles 317: dt=0.5082, 365 negative triangles 318: dt=0.5082, 366 negative triangles 319: dt=0.5082, 368 negative triangles 320: dt=0.5082, 357 negative triangles 321: dt=0.5082, 366 negative triangles 322: dt=0.5082, 365 negative triangles 323: dt=0.4828, 359 negative triangles 324: dt=0.4828, 356 negative triangles 325: dt=0.4828, 359 negative triangles 326: dt=0.4828, 362 negative triangles 327: dt=0.4828, 366 negative triangles 328: dt=0.4828, 366 negative triangles 329: dt=0.4828, 364 negative triangles 330: dt=0.4828, 361 negative triangles 331: dt=0.4828, 357 negative triangles 332: dt=0.4828, 359 negative triangles 333: dt=0.4587, 364 negative triangles 334: dt=0.4587, 356 negative triangles 335: dt=0.4587, 369 negative triangles 336: dt=0.4587, 360 negative triangles 337: dt=0.4587, 359 negative triangles 338: dt=0.4587, 360 negative triangles 339: dt=0.4587, 355 negative triangles 340: dt=0.4587, 352 negative triangles 341: dt=0.4587, 352 negative triangles 342: dt=0.4587, 352 negative triangles 343: dt=0.4587, 354 negative triangles 344: dt=0.4587, 357 negative triangles 345: dt=0.4587, 354 negative triangles 346: dt=0.4587, 356 negative triangles 347: dt=0.4587, 353 negative triangles 348: dt=0.4587, 361 negative triangles 349: dt=0.4587, 355 negative triangles 350: dt=0.4357, 360 negative triangles 351: dt=0.4357, 364 negative triangles 352: dt=0.4357, 355 negative triangles 353: dt=0.4357, 361 negative triangles 354: dt=0.4357, 359 negative triangles 355: dt=0.4357, 359 negative triangles 356: dt=0.4357, 356 negative triangles 357: dt=0.4357, 357 negative triangles 358: dt=0.4357, 360 negative triangles 359: dt=0.4357, 356 negative triangles 360: dt=0.4357, 351 negative triangles 361: dt=0.4357, 355 negative triangles 362: dt=0.4357, 348 negative triangles 363: dt=0.4357, 352 negative triangles 364: dt=0.4357, 353 negative triangles 365: dt=0.4357, 352 negative triangles 366: dt=0.4357, 364 negative triangles 367: dt=0.4357, 356 negative triangles 368: dt=0.4357, 357 negative triangles 369: dt=0.4357, 355 negative triangles 370: dt=0.4357, 354 negative triangles 371: dt=0.4357, 358 negative triangles 372: dt=0.4139, 348 negative triangles 373: dt=0.4139, 355 negative triangles 374: dt=0.4139, 354 negative triangles 375: dt=0.4139, 359 negative triangles 376: dt=0.4139, 359 negative triangles 377: dt=0.4139, 349 negative triangles 378: dt=0.4139, 365 negative triangles 379: dt=0.4139, 347 negative triangles 380: dt=0.4139, 361 negative triangles 381: dt=0.4139, 348 negative triangles 382: dt=0.4139, 353 negative triangles 383: dt=0.4139, 348 negative triangles 384: dt=0.4139, 356 negative triangles 385: dt=0.4139, 358 negative triangles 386: dt=0.4139, 353 negative triangles 387: dt=0.4139, 355 negative triangles 388: dt=0.4139, 357 negative triangles 389: dt=0.3932, 348 negative triangles 390: dt=0.3932, 357 negative triangles 391: dt=0.3932, 353 negative triangles 392: dt=0.3932, 363 negative triangles 393: dt=0.3932, 360 negative triangles 394: dt=0.3932, 364 negative triangles 395: dt=0.3932, 355 negative triangles 396: dt=0.3932, 359 negative triangles 397: dt=0.3932, 354 negative triangles 398: dt=0.3932, 357 negative triangles 399: dt=0.3736, 357 negative triangles 400: dt=0.3736, 364 negative triangles 401: dt=0.3736, 361 negative triangles 402: dt=0.3736, 360 negative triangles 403: dt=0.3736, 358 negative triangles 404: dt=0.3736, 356 negative triangles 405: dt=0.3736, 358 negative triangles 406: dt=0.3736, 352 negative triangles 407: dt=0.3736, 359 negative triangles 408: dt=0.3736, 357 negative triangles 409: dt=0.3549, 353 negative triangles 410: dt=0.3549, 355 negative triangles 411: dt=0.3549, 364 negative triangles 412: dt=0.3549, 364 negative triangles 413: dt=0.3549, 355 negative triangles 414: dt=0.3549, 361 negative triangles 415: dt=0.3549, 358 negative triangles 416: dt=0.3549, 363 negative triangles 417: dt=0.3549, 356 negative triangles 418: dt=0.3549, 350 negative triangles 419: dt=0.3372, 354 negative triangles 420: dt=0.3372, 352 negative triangles 421: dt=0.3372, 352 negative triangles 422: dt=0.3372, 358 negative triangles 423: dt=0.3372, 359 negative triangles 424: dt=0.3372, 356 negative triangles 425: dt=0.3372, 356 negative triangles 426: dt=0.3372, 355 negative triangles 427: dt=0.3372, 358 negative triangles 428: dt=0.3372, 357 negative triangles 429: dt=0.3203, 361 negative triangles 430: dt=0.3203, 351 negative triangles 431: dt=0.3203, 352 negative triangles 432: dt=0.3203, 355 negative triangles 433: dt=0.3203, 356 negative triangles 434: dt=0.3203, 358 negative triangles 435: dt=0.3203, 359 negative triangles 436: dt=0.3203, 356 negative triangles 437: dt=0.3203, 347 negative triangles 438: dt=0.3203, 357 negative triangles 439: dt=0.3043, 350 negative triangles 440: dt=0.3043, 358 negative triangles 441: dt=0.3043, 355 negative triangles 442: dt=0.3043, 359 negative triangles 443: dt=0.3043, 354 negative triangles 444: dt=0.3043, 357 negative triangles 445: dt=0.3043, 353 negative triangles 446: dt=0.3043, 353 negative triangles 447: dt=0.3043, 353 negative triangles 448: dt=0.3043, 360 negative triangles 449: dt=0.2891, 360 negative triangles 450: dt=0.2891, 353 negative triangles 451: dt=0.2891, 360 negative triangles 452: dt=0.2891, 356 negative triangles 453: dt=0.2891, 358 negative triangles 454: dt=0.2891, 362 negative triangles 455: dt=0.2891, 357 negative triangles 456: dt=0.2891, 365 negative triangles 457: dt=0.2891, 362 negative triangles 458: dt=0.2891, 362 negative triangles 459: dt=0.2746, 362 negative triangles 460: dt=0.2746, 361 negative triangles 461: dt=0.2746, 368 negative triangles 462: dt=0.2746, 357 negative triangles 463: dt=0.2746, 362 negative triangles 464: dt=0.2746, 348 negative triangles 465: dt=0.2746, 358 negative triangles 466: dt=0.2746, 354 negative triangles 467: dt=0.2746, 355 negative triangles 468: dt=0.2746, 354 negative triangles 469: dt=0.2609, 355 negative triangles 470: dt=0.2609, 356 negative triangles 471: dt=0.2609, 346 negative triangles 472: dt=0.2609, 353 negative triangles 473: dt=0.2609, 361 negative triangles 474: dt=0.2609, 366 negative triangles 475: dt=0.2609, 359 negative triangles 476: dt=0.2609, 355 negative triangles 477: dt=0.2609, 357 negative triangles 478: dt=0.2609, 358 negative triangles 479: dt=0.2609, 357 negative triangles 480: dt=0.2609, 350 negative triangles 481: dt=0.2478, 352 negative triangles 482: dt=0.2478, 356 negative triangles 483: dt=0.2478, 359 negative triangles 484: dt=0.2478, 359 negative triangles 485: dt=0.2478, 368 negative triangles 486: dt=0.2478, 368 negative triangles 487: dt=0.2478, 355 negative triangles 488: dt=0.2478, 358 negative triangles 489: dt=0.2478, 354 negative triangles 490: dt=0.2478, 349 negative triangles 491: dt=0.2354, 354 negative triangles 492: dt=0.2354, 360 negative triangles 493: dt=0.2354, 360 negative triangles 494: dt=0.2354, 353 negative triangles 495: dt=0.2354, 363 negative triangles 496: dt=0.2354, 354 negative triangles 497: dt=0.2354, 360 negative triangles 498: dt=0.2354, 366 negative triangles 499: dt=0.2354, 361 negative triangles 500: dt=0.2354, 361 negative triangles 501: dt=0.2237, 368 negative triangles 502: dt=0.2237, 362 negative triangles 503: dt=0.2237, 353 negative triangles 504: dt=0.2237, 353 negative triangles 505: dt=0.2237, 350 negative triangles 506: dt=0.2237, 350 negative triangles 507: dt=0.2237, 348 negative triangles 508: dt=0.2237, 352 negative triangles 509: dt=0.2237, 360 negative triangles 510: dt=0.2237, 355 negative triangles 511: dt=0.2125, 355 negative triangles 512: dt=0.2125, 359 negative triangles 513: dt=0.2125, 360 negative triangles 514: dt=0.2125, 355 negative triangles 515: dt=0.2125, 359 negative triangles 516: dt=0.2125, 359 negative triangles 517: dt=0.2125, 349 negative triangles 518: dt=0.2125, 351 negative triangles 519: dt=0.2125, 351 negative triangles 520: dt=0.2125, 353 negative triangles 521: dt=0.2019, 352 negative triangles 522: dt=0.2019, 353 negative triangles 523: dt=0.2019, 346 negative triangles 524: dt=0.2019, 353 negative triangles 525: dt=0.2019, 351 negative triangles 526: dt=0.2019, 350 negative triangles 527: dt=0.2019, 346 negative triangles 528: dt=0.2019, 351 negative triangles 529: dt=0.2019, 356 negative triangles 530: dt=0.2019, 358 negative triangles 531: dt=0.1918, 360 negative triangles 532: dt=0.1918, 363 negative triangles 533: dt=0.1918, 346 negative triangles 534: dt=0.1918, 350 negative triangles 535: dt=0.1918, 351 negative triangles 536: dt=0.1918, 353 negative triangles 537: dt=0.1918, 358 negative triangles 538: dt=0.1918, 352 negative triangles 539: dt=0.1918, 356 negative triangles 540: dt=0.1918, 359 negative triangles 541: dt=0.1822, 353 negative triangles 542: dt=0.1822, 353 negative triangles 543: dt=0.1822, 359 negative triangles 544: dt=0.1822, 356 negative triangles 545: dt=0.1822, 352 negative triangles 546: dt=0.1822, 350 negative triangles 547: dt=0.1822, 355 negative triangles 548: dt=0.1822, 356 negative triangles 549: dt=0.1822, 359 negative triangles 550: dt=0.1822, 359 negative triangles 551: dt=0.1731, 358 negative triangles 552: dt=0.1731, 364 negative triangles 553: dt=0.1731, 361 negative triangles 554: dt=0.1731, 357 negative triangles 555: dt=0.1731, 353 negative triangles 556: dt=0.1731, 361 negative triangles 557: dt=0.1731, 356 negative triangles 558: dt=0.1731, 353 negative triangles 559: dt=0.1731, 351 negative triangles 560: dt=0.1731, 354 negative triangles 561: dt=0.1644, 352 negative triangles 562: dt=0.1644, 355 negative triangles 563: dt=0.1644, 352 negative triangles 564: dt=0.1644, 359 negative triangles 565: dt=0.1644, 355 negative triangles 566: dt=0.1644, 356 negative triangles 567: dt=0.1644, 353 negative triangles 568: dt=0.1644, 353 negative triangles 569: dt=0.1644, 353 negative triangles 570: dt=0.1644, 357 negative triangles 571: dt=0.1562, 358 negative triangles 572: dt=0.1562, 361 negative triangles 573: dt=0.1562, 358 negative triangles 574: dt=0.1562, 354 negative triangles 575: dt=0.1562, 355 negative triangles 576: dt=0.1562, 361 negative triangles 577: dt=0.1562, 355 negative triangles 578: dt=0.1562, 351 negative triangles 579: dt=0.1562, 349 negative triangles 580: dt=0.1562, 343 negative triangles 581: dt=0.1562, 348 negative triangles 582: dt=0.1562, 348 negative triangles 583: dt=0.1562, 355 negative triangles 584: dt=0.1562, 355 negative triangles 585: dt=0.1562, 350 negative triangles 586: dt=0.1562, 354 negative triangles 587: dt=0.1562, 349 negative triangles 588: dt=0.1562, 350 negative triangles 589: dt=0.1562, 347 negative triangles 590: dt=0.1484, 345 negative triangles 591: dt=0.1484, 354 negative triangles 592: dt=0.1484, 349 negative triangles 593: dt=0.1484, 356 negative triangles 594: dt=0.1484, 358 negative triangles 595: dt=0.1484, 350 negative triangles 596: dt=0.1484, 353 negative triangles 597: dt=0.1484, 358 negative triangles 598: dt=0.1484, 350 negative triangles 599: dt=0.1484, 360 negative triangles 600: dt=0.1410, 369 negative triangles 601: dt=0.1410, 360 negative triangles 602: dt=0.1410, 361 negative triangles 603: dt=0.1410, 362 negative triangles 604: dt=0.1410, 360 negative triangles 605: dt=0.1410, 366 negative triangles 606: dt=0.1410, 372 negative triangles 607: dt=0.1410, 362 negative triangles 608: dt=0.1410, 366 negative triangles 609: dt=0.1410, 363 negative triangles 610: dt=0.1339, 370 negative triangles 611: dt=0.1339, 363 negative triangles 612: dt=0.1339, 357 negative triangles 613: dt=0.1339, 347 negative triangles 614: dt=0.1339, 351 negative triangles 615: dt=0.1339, 350 negative triangles 616: dt=0.1339, 355 negative triangles 617: dt=0.1339, 358 negative triangles 618: dt=0.1339, 360 negative triangles 619: dt=0.1339, 360 negative triangles 620: dt=0.1272, 367 negative triangles 621: dt=0.1272, 365 negative triangles 622: dt=0.1272, 363 negative triangles 623: dt=0.1272, 363 negative triangles 624: dt=0.1272, 362 negative triangles 625: dt=0.1272, 358 negative triangles 626: dt=0.1272, 360 negative triangles 627: dt=0.1272, 355 negative triangles 628: dt=0.1272, 360 negative triangles 629: dt=0.1272, 353 negative triangles 630: dt=0.1209, 366 negative triangles 631: dt=0.1209, 362 negative triangles 632: dt=0.1209, 363 negative triangles 633: dt=0.1209, 361 negative triangles 634: dt=0.1209, 361 negative triangles 635: dt=0.1209, 364 negative triangles 636: dt=0.1209, 364 negative triangles 637: dt=0.1209, 365 negative triangles 638: dt=0.1209, 356 negative triangles 639: dt=0.1209, 358 negative triangles 640: dt=0.1148, 355 negative triangles 641: dt=0.1148, 352 negative triangles 642: dt=0.1148, 359 negative triangles 643: dt=0.1148, 359 negative triangles 644: dt=0.1148, 359 negative triangles 645: dt=0.1148, 349 negative triangles 646: dt=0.1148, 355 negative triangles 647: dt=0.1148, 352 negative triangles 648: dt=0.1148, 355 negative triangles 649: dt=0.1148, 350 negative triangles 650: dt=0.1091, 351 negative triangles 651: dt=0.1091, 346 negative triangles 652: dt=0.1091, 353 negative triangles 653: dt=0.1091, 354 negative triangles 654: dt=0.1091, 355 negative triangles 655: dt=0.1091, 349 negative triangles 656: dt=0.1091, 359 negative triangles 657: dt=0.1091, 353 negative triangles 658: dt=0.1091, 352 negative triangles 659: dt=0.1091, 357 negative triangles 660: dt=0.1036, 356 negative triangles 661: dt=0.1036, 356 negative triangles 662: dt=0.1036, 356 negative triangles 663: dt=0.1036, 357 negative triangles 664: dt=0.1036, 355 negative triangles 665: dt=0.1036, 364 negative triangles 666: dt=0.1036, 364 negative triangles 667: dt=0.1036, 366 negative triangles 668: dt=0.1036, 360 negative triangles 669: dt=0.1036, 360 negative triangles 670: dt=0.0984, 363 negative triangles 671: dt=0.0984, 363 negative triangles 672: dt=0.0984, 360 negative triangles 673: dt=0.0984, 359 negative triangles 674: dt=0.0984, 350 negative triangles 675: dt=0.0984, 352 negative triangles 676: dt=0.0984, 357 negative triangles 677: dt=0.0984, 352 negative triangles 678: dt=0.0984, 357 negative triangles 679: dt=0.0984, 352 negative triangles 680: dt=0.0935, 354 negative triangles 681: dt=0.0935, 352 negative triangles 682: dt=0.0935, 352 negative triangles 683: dt=0.0935, 345 negative triangles 684: dt=0.0935, 350 negative triangles 685: dt=0.0935, 351 negative triangles 686: dt=0.0935, 348 negative triangles 687: dt=0.0935, 348 negative triangles 688: dt=0.0935, 352 negative triangles 689: dt=0.0935, 346 negative triangles 690: dt=0.0888, 350 negative triangles 691: dt=0.0888, 347 negative triangles 692: dt=0.0888, 348 negative triangles 693: dt=0.0888, 358 negative triangles 694: dt=0.0888, 357 negative triangles 695: dt=0.0888, 358 negative triangles 696: dt=0.0888, 362 negative triangles 697: dt=0.0888, 358 negative triangles 698: dt=0.0888, 361 negative triangles 699: dt=0.0888, 362 negative triangles 700: dt=0.0844, 357 negative triangles 701: dt=0.0844, 360 negative triangles 702: dt=0.0844, 362 negative triangles 703: dt=0.0844, 359 negative triangles 704: dt=0.0844, 360 negative triangles 705: dt=0.0844, 363 negative triangles 706: dt=0.0844, 360 negative triangles 707: dt=0.0844, 354 negative triangles 708: dt=0.0844, 359 negative triangles 709: dt=0.0844, 360 negative triangles 710: dt=0.0802, 365 negative triangles 711: dt=0.0802, 367 negative triangles 712: dt=0.0802, 366 negative triangles 713: dt=0.0802, 362 negative triangles 714: dt=0.0802, 356 negative triangles 715: dt=0.0802, 359 negative triangles 716: dt=0.0802, 356 negative triangles 717: dt=0.0802, 366 negative triangles 718: dt=0.0802, 366 negative triangles 719: dt=0.0802, 367 negative triangles 720: dt=0.0762, 362 negative triangles 721: dt=0.0762, 367 negative triangles 722: dt=0.0762, 368 negative triangles 723: dt=0.0762, 365 negative triangles 724: dt=0.0762, 361 negative triangles 725: dt=0.0762, 361 negative triangles 726: dt=0.0762, 365 negative triangles 727: dt=0.0762, 367 negative triangles 728: dt=0.0762, 367 negative triangles 729: dt=0.0762, 369 negative triangles 730: dt=0.0724, 370 negative triangles 731: dt=0.0724, 367 negative triangles 732: dt=0.0724, 365 negative triangles 733: dt=0.0724, 362 negative triangles 734: dt=0.0724, 361 negative triangles 735: dt=0.0724, 364 negative triangles 736: dt=0.0724, 363 negative triangles 737: dt=0.0724, 364 negative triangles 738: dt=0.0724, 367 negative triangles 739: dt=0.0724, 362 negative triangles 740: dt=0.0687, 363 negative triangles 741: dt=0.0687, 360 negative triangles 742: dt=0.0687, 359 negative triangles 743: dt=0.0687, 354 negative triangles 744: dt=0.0687, 355 negative triangles 745: dt=0.0687, 358 negative triangles 746: dt=0.0687, 364 negative triangles 747: dt=0.0687, 364 negative triangles 748: dt=0.0687, 367 negative triangles 749: dt=0.0687, 364 negative triangles 750: dt=0.0653, 374 negative triangles 751: dt=0.0653, 374 negative triangles 752: dt=0.0653, 376 negative triangles 753: dt=0.0653, 366 negative triangles 754: dt=0.0653, 360 negative triangles 755: dt=0.0653, 361 negative triangles 756: dt=0.0653, 362 negative triangles 757: dt=0.0653, 356 negative triangles 758: dt=0.0653, 362 negative triangles 759: dt=0.0653, 356 negative triangles 760: dt=0.0620, 359 negative triangles 761: dt=0.0620, 359 negative triangles 762: dt=0.0620, 359 negative triangles 763: dt=0.0620, 358 negative triangles 764: dt=0.0620, 360 negative triangles 765: dt=0.0620, 359 negative triangles 766: dt=0.0620, 362 negative triangles 767: dt=0.0620, 358 negative triangles 768: dt=0.0620, 363 negative triangles 769: dt=0.0620, 359 negative triangles 770: dt=0.0589, 357 negative triangles 771: dt=0.0589, 362 negative triangles 772: dt=0.0589, 357 negative triangles 773: dt=0.0589, 359 negative triangles 774: dt=0.0589, 355 negative triangles 775: dt=0.0589, 362 negative triangles 776: dt=0.0589, 359 negative triangles 777: dt=0.0589, 365 negative triangles 778: dt=0.0589, 366 negative triangles 779: dt=0.0589, 358 negative triangles 780: dt=0.0560, 353 negative triangles 781: dt=0.0560, 356 negative triangles 782: dt=0.0560, 358 negative triangles 783: dt=0.0560, 349 negative triangles 784: dt=0.0560, 355 negative triangles 785: dt=0.0560, 357 negative triangles 786: dt=0.0560, 357 negative triangles 787: dt=0.0560, 349 negative triangles 788: dt=0.0560, 349 negative triangles 789: dt=0.0560, 355 negative triangles 790: dt=0.0532, 355 negative triangles 791: dt=0.0532, 359 negative triangles 792: dt=0.0532, 353 negative triangles 793: dt=0.0532, 349 negative triangles 794: dt=0.0532, 353 negative triangles 795: dt=0.0532, 350 negative triangles 796: dt=0.0532, 354 negative triangles 797: dt=0.0532, 350 negative triangles 798: dt=0.0532, 347 negative triangles 799: dt=0.0532, 348 negative triangles 800: dt=0.0505, 353 negative triangles 801: dt=0.0505, 356 negative triangles 802: dt=0.0505, 355 negative triangles 803: dt=0.0505, 357 negative triangles 804: dt=0.0505, 355 negative triangles 805: dt=0.0505, 359 negative triangles 806: dt=0.0505, 361 negative triangles 807: dt=0.0505, 355 negative triangles 808: dt=0.0505, 358 negative triangles 809: dt=0.0505, 359 negative triangles 810: dt=0.0480, 360 negative triangles 811: dt=0.0480, 357 negative triangles 812: dt=0.0480, 357 negative triangles 813: dt=0.0480, 356 negative triangles 814: dt=0.0480, 359 negative triangles 815: dt=0.0480, 356 negative triangles 816: dt=0.0480, 359 negative triangles 817: dt=0.0480, 357 negative triangles 818: dt=0.0480, 359 negative triangles 819: dt=0.0480, 360 negative triangles 820: dt=0.0456, 358 negative triangles 821: dt=0.0456, 359 negative triangles 822: dt=0.0456, 360 negative triangles 823: dt=0.0456, 358 negative triangles 824: dt=0.0456, 360 negative triangles 825: dt=0.0456, 358 negative triangles 826: dt=0.0456, 352 negative triangles 827: dt=0.0456, 358 negative triangles 828: dt=0.0456, 358 negative triangles 829: dt=0.0456, 356 negative triangles 830: dt=0.0433, 360 negative triangles 831: dt=0.0433, 358 negative triangles 832: dt=0.0433, 358 negative triangles 833: dt=0.0433, 361 negative triangles 834: dt=0.0433, 364 negative triangles 835: dt=0.0433, 364 negative triangles 836: dt=0.0433, 366 negative triangles 837: dt=0.0433, 362 negative triangles 838: dt=0.0433, 363 negative triangles 839: dt=0.0433, 361 negative triangles 840: dt=0.0412, 364 negative triangles 841: dt=0.0412, 361 negative triangles 842: dt=0.0412, 358 negative triangles 843: dt=0.0412, 356 negative triangles 844: dt=0.0412, 353 negative triangles 845: dt=0.0412, 357 negative triangles 846: dt=0.0412, 355 negative triangles 847: dt=0.0412, 359 negative triangles 848: dt=0.0412, 353 negative triangles 849: dt=0.0412, 354 negative triangles 850: dt=0.0391, 358 negative triangles 851: dt=0.0391, 365 negative triangles 852: dt=0.0391, 362 negative triangles 853: dt=0.0391, 360 negative triangles 854: dt=0.0391, 360 negative triangles 855: dt=0.0391, 360 negative triangles 856: dt=0.0391, 359 negative triangles 857: dt=0.0391, 359 negative triangles 858: dt=0.0391, 358 negative triangles 859: dt=0.0391, 359 negative triangles 860: dt=0.0371, 360 negative triangles 861: dt=0.0371, 357 negative triangles 862: dt=0.0371, 361 negative triangles 863: dt=0.0371, 357 negative triangles 864: dt=0.0371, 353 negative triangles 865: dt=0.0371, 357 negative triangles 866: dt=0.0371, 359 negative triangles 867: dt=0.0371, 356 negative triangles 868: dt=0.0371, 363 negative triangles 869: dt=0.0371, 357 negative triangles 870: dt=0.0353, 356 negative triangles 871: dt=0.0353, 354 negative triangles 872: dt=0.0353, 357 negative triangles 873: dt=0.0353, 357 negative triangles 874: dt=0.0353, 356 negative triangles 875: dt=0.0353, 358 negative triangles 876: dt=0.0353, 357 negative triangles 877: dt=0.0353, 358 negative triangles 878: dt=0.0353, 357 negative triangles 879: dt=0.0353, 357 negative triangles 880: dt=0.0335, 350 negative triangles 881: dt=0.0335, 351 negative triangles 882: dt=0.0335, 347 negative triangles 883: dt=0.0335, 343 negative triangles 884: dt=0.0335, 345 negative triangles 885: dt=0.0335, 350 negative triangles 886: dt=0.0335, 359 negative triangles 887: dt=0.0335, 358 negative triangles 888: dt=0.0335, 358 negative triangles 889: dt=0.0335, 353 negative triangles 890: dt=0.0319, 351 negative triangles 891: dt=0.0319, 345 negative triangles 892: dt=0.0319, 345 negative triangles 893: dt=0.0319, 343 negative triangles 894: dt=0.0319, 342 negative triangles 895: dt=0.0319, 347 negative triangles 896: dt=0.0319, 346 negative triangles 897: dt=0.0319, 355 negative triangles 898: dt=0.0319, 358 negative triangles 899: dt=0.0319, 359 negative triangles 900: dt=0.0319, 356 negative triangles 901: dt=0.0319, 354 negative triangles 902: dt=0.0319, 356 negative triangles 903: dt=0.0319, 356 negative triangles 904: dt=0.0303, 355 negative triangles 905: dt=0.0303, 358 negative triangles 906: dt=0.0303, 359 negative triangles 907: dt=0.0303, 361 negative triangles 908: dt=0.0303, 364 negative triangles 909: dt=0.0303, 362 negative triangles 910: dt=0.0303, 369 negative triangles 911: dt=0.0303, 363 negative triangles 912: dt=0.0303, 361 negative triangles 913: dt=0.0303, 363 negative triangles 914: dt=0.0287, 360 negative triangles 915: dt=0.0287, 359 negative triangles 916: dt=0.0287, 356 negative triangles 917: dt=0.0287, 359 negative triangles 918: dt=0.0287, 354 negative triangles 919: dt=0.0287, 358 negative triangles 920: dt=0.0287, 359 negative triangles 921: dt=0.0287, 366 negative triangles 922: dt=0.0287, 369 negative triangles 923: dt=0.0287, 367 negative triangles 924: dt=0.0273, 367 negative triangles 925: dt=0.0273, 371 negative triangles 926: dt=0.0273, 372 negative triangles 927: dt=0.0273, 373 negative triangles 928: dt=0.0273, 367 negative triangles 929: dt=0.0273, 364 negative triangles 930: dt=0.0273, 370 negative triangles 931: dt=0.0273, 369 negative triangles 932: dt=0.0273, 370 negative triangles 933: dt=0.0273, 370 negative triangles 934: dt=0.0259, 364 negative triangles 935: dt=0.0259, 365 negative triangles 936: dt=0.0259, 366 negative triangles 937: dt=0.0259, 364 negative triangles 938: dt=0.0259, 367 negative triangles 939: dt=0.0259, 368 negative triangles 940: dt=0.0259, 366 negative triangles 941: dt=0.0259, 359 negative triangles 942: dt=0.0259, 356 negative triangles 943: dt=0.0259, 352 negative triangles 944: dt=0.0246, 353 negative triangles 945: dt=0.0246, 355 negative triangles 946: dt=0.0246, 353 negative triangles 947: dt=0.0246, 356 negative triangles 948: dt=0.0246, 356 negative triangles 949: dt=0.0246, 354 negative triangles 950: dt=0.0246, 353 negative triangles 951: dt=0.0246, 358 negative triangles 952: dt=0.0246, 357 negative triangles 953: dt=0.0246, 356 negative triangles 954: dt=0.0234, 354 negative triangles 955: dt=0.0234, 351 negative triangles 956: dt=0.0234, 351 negative triangles 957: dt=0.0234, 351 negative triangles 958: dt=0.0234, 355 negative triangles 959: dt=0.0234, 355 negative triangles 960: dt=0.0234, 352 negative triangles 961: dt=0.0234, 353 negative triangles 962: dt=0.0234, 351 negative triangles 963: dt=0.0234, 357 negative triangles 964: dt=0.0222, 356 negative triangles 965: dt=0.0222, 354 negative triangles 966: dt=0.0222, 354 negative triangles 967: dt=0.0222, 359 negative triangles 968: dt=0.0222, 362 negative triangles 969: dt=0.0222, 358 negative triangles 970: dt=0.0222, 356 negative triangles 971: dt=0.0222, 357 negative triangles 972: dt=0.0222, 353 negative triangles 973: dt=0.0222, 358 negative triangles 974: dt=0.0211, 367 negative triangles 975: dt=0.0211, 365 negative triangles 976: dt=0.0211, 365 negative triangles 977: dt=0.0211, 363 negative triangles 978: dt=0.0211, 364 negative triangles 979: dt=0.0211, 363 negative triangles 980: dt=0.0211, 365 negative triangles 981: dt=0.0211, 362 negative triangles 982: dt=0.0211, 362 negative triangles 983: dt=0.0211, 358 negative triangles 984: dt=0.0201, 360 negative triangles 985: dt=0.0201, 362 negative triangles 986: dt=0.0201, 361 negative triangles 987: dt=0.0201, 360 negative triangles 988: dt=0.0201, 361 negative triangles 989: dt=0.0201, 356 negative triangles 990: dt=0.0201, 356 negative triangles 991: dt=0.0201, 358 negative triangles 992: dt=0.0201, 355 negative triangles 993: dt=0.0201, 361 negative triangles 994: dt=0.0191, 356 negative triangles 995: dt=0.0191, 356 negative triangles 996: dt=0.0191, 358 negative triangles 997: dt=0.0191, 360 negative triangles 998: dt=0.0191, 360 negative triangles 999: dt=0.0191, 361 negative triangles 1000: dt=0.0191, 360 negative triangles 1001: dt=0.0191, 362 negative triangles 1002: dt=0.0191, 364 negative triangles 1003: dt=0.0191, 364 negative triangles 1004: dt=0.0181, 364 negative triangles 1005: dt=0.0181, 356 negative triangles 1006: dt=0.0181, 359 negative triangles 1007: dt=0.0181, 360 negative triangles 1008: dt=0.0181, 358 negative triangles 1009: dt=0.0181, 359 negative triangles 1010: dt=0.0181, 358 negative triangles 1011: dt=0.0181, 356 negative triangles 1012: dt=0.0181, 358 negative triangles 1013: dt=0.0181, 359 negative triangles 1014: dt=0.0172, 361 negative triangles 1015: dt=0.0172, 356 negative triangles 1016: dt=0.0172, 354 negative triangles 1017: dt=0.0172, 354 negative triangles 1018: dt=0.0172, 355 negative triangles 1019: dt=0.0172, 361 negative triangles 1020: dt=0.0172, 359 negative triangles 1021: dt=0.0172, 363 negative triangles 1022: dt=0.0172, 362 negative triangles 1023: dt=0.0172, 363 negative triangles 1024: dt=0.0164, 364 negative triangles 1025: dt=0.0164, 363 negative triangles 1026: dt=0.0164, 362 negative triangles 1027: dt=0.0164, 359 negative triangles 1028: dt=0.0164, 361 negative triangles 1029: dt=0.0164, 360 negative triangles 1030: dt=0.0164, 358 negative triangles 1031: dt=0.0164, 361 negative triangles 1032: dt=0.0164, 363 negative triangles 1033: dt=0.0164, 362 negative triangles 1034: dt=0.0155, 361 negative triangles 1035: dt=0.0155, 363 negative triangles 1036: dt=0.0155, 365 negative triangles 1037: dt=0.0155, 364 negative triangles 1038: dt=0.0155, 364 negative triangles 1039: dt=0.0155, 365 negative triangles 1040: dt=0.0155, 362 negative triangles 1041: dt=0.0155, 360 negative triangles 1042: dt=0.0155, 362 negative triangles 1043: dt=0.0155, 361 negative triangles 1044: dt=0.0148, 360 negative triangles 1045: dt=0.0148, 360 negative triangles 1046: dt=0.0148, 359 negative triangles 1047: dt=0.0148, 361 negative triangles 1048: dt=0.0148, 360 negative triangles 1049: dt=0.0148, 357 negative triangles 1050: dt=0.0148, 356 negative triangles 1051: dt=0.0148, 360 negative triangles 1052: dt=0.0148, 365 negative triangles 1053: dt=0.0148, 361 negative triangles 1054: dt=0.0140, 365 negative triangles 1055: dt=0.0140, 362 negative triangles 1056: dt=0.0140, 359 negative triangles 1057: dt=0.0140, 356 negative triangles 1058: dt=0.0140, 355 negative triangles 1059: dt=0.0140, 352 negative triangles 1060: dt=0.0140, 352 negative triangles 1061: dt=0.0140, 351 negative triangles 1062: dt=0.0140, 351 negative triangles 1063: dt=0.0140, 355 negative triangles 1064: dt=0.0133, 354 negative triangles 1065: dt=0.0133, 358 negative triangles 1066: dt=0.0133, 360 negative triangles 1067: dt=0.0133, 357 negative triangles 1068: dt=0.0133, 361 negative triangles 1069: dt=0.0133, 362 negative triangles 1070: dt=0.0133, 359 negative triangles 1071: dt=0.0133, 359 negative triangles 1072: dt=0.0133, 361 negative triangles 1073: dt=0.0133, 362 negative triangles 1074: dt=0.0127, 361 negative triangles 1075: dt=0.0127, 359 negative triangles 1076: dt=0.0127, 357 negative triangles 1077: dt=0.0127, 352 negative triangles 1078: dt=0.0127, 351 negative triangles 1079: dt=0.0127, 351 negative triangles 1080: dt=0.0127, 349 negative triangles 1081: dt=0.0127, 349 negative triangles 1082: dt=0.0127, 352 negative triangles 1083: dt=0.0127, 354 negative triangles 1084: dt=0.0120, 355 negative triangles 1085: dt=0.0120, 353 negative triangles 1086: dt=0.0120, 359 negative triangles 1087: dt=0.0120, 357 negative triangles 1088: dt=0.0120, 355 negative triangles 1089: dt=0.0120, 361 negative triangles 1090: dt=0.0120, 363 negative triangles 1091: dt=0.0120, 357 negative triangles 1092: dt=0.0120, 359 negative triangles 1093: dt=0.0120, 359 negative triangles 1094: dt=0.0114, 358 negative triangles 1095: dt=0.0114, 357 negative triangles 1096: dt=0.0114, 358 negative triangles 1097: dt=0.0114, 356 negative triangles 1098: dt=0.0114, 358 negative triangles 1099: dt=0.0114, 359 negative triangles 1100: dt=0.0114, 358 negative triangles 1101: dt=0.0114, 355 negative triangles 1102: dt=0.0114, 359 negative triangles 1103: dt=0.0114, 361 negative triangles 1104: dt=0.0108, 359 negative triangles 1105: dt=0.0108, 355 negative triangles 1106: dt=0.0108, 352 negative triangles 1107: dt=0.0108, 353 negative triangles 1108: dt=0.0108, 357 negative triangles writing registered surface to ../surf/rh.sphere.reg... 1109: dt=0.0108, 357 negative triangles 1110: 354 negative triangles registration took 0.08 hours #VMPC# mris_register VmPeak 768204 FSRUNTIME@ mris_register 0.0797 hours 4 threads PIDs (325040 325043) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Mon Jan 9 13:10:56 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Mon Jan 9 13:10:56 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 326887 of (326887 326890) to complete... Waiting for PID 326890 of (326887 326890) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (326887 326890) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Mon Jan 9 13:10:56 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Mon Jan 9 13:10:56 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 326939 of (326939 326942) to complete... Waiting for PID 326942 of (326939 326942) to complete... mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (326939 326942) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Mon Jan 9 13:10:57 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Mon Jan 9 13:10:57 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 326991 of (326991 326994) to complete... Waiting for PID 326994 of (326991 326994) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 1092 labels changed using aseg relabeling using gibbs priors... 000: 2877 changed, 115656 examined... 001: 724 changed, 12018 examined... 002: 159 changed, 4005 examined... 003: 47 changed, 967 examined... 004: 20 changed, 291 examined... 005: 12 changed, 127 examined... 006: 4 changed, 60 examined... 007: 1 changed, 22 examined... 008: 1 changed, 7 examined... 009: 0 changed, 7 examined... 267 labels changed using aseg 000: 106 total segments, 64 labels (296 vertices) changed 001: 49 total segments, 5 labels (11 vertices) changed 002: 43 total segments, 1 labels (6 vertices) changed 003: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1339 vertices marked for relabeling... 1339 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 7 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 914 labels changed using aseg relabeling using gibbs priors... 000: 2353 changed, 112475 examined... 001: 575 changed, 10319 examined... 002: 119 changed, 3254 examined... 003: 41 changed, 758 examined... 004: 16 changed, 259 examined... 005: 7 changed, 84 examined... 006: 2 changed, 41 examined... 007: 2 changed, 14 examined... 008: 0 changed, 13 examined... 203 labels changed using aseg 000: 81 total segments, 38 labels (135 vertices) changed 001: 44 total segments, 1 labels (1 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1583 vertices marked for relabeling... 1583 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 6 seconds. PIDs (326991 326994) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Mon Jan 9 13:11:04 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface removing intersecting faces 000: 29 intersecting step 1 with no progress (num=31, old_num=29) 001: 31 intersecting step 2 with no progress (num=31, old_num=31) 002: 31 intersecting step 3 with no progress (num=31, old_num=31) 003: 31 intersecting step 4 with no progress (num=31, old_num=31) 004: 31 intersecting step 5 with no progress (num=31, old_num=31) 005: 31 intersecting step 6 with no progress (num=31, old_num=31) 006: 31 intersecting step 7 with no progress (num=31, old_num=31) 007: 31 intersecting step 8 with no progress (num=31, old_num=31) 008: 31 intersecting step 9 with no progress (num=31, old_num=31) 009: 31 intersecting step 10 with no progress (num=31, old_num=31) 010: 31 intersecting step 11 with no progress (num=31, old_num=31) 011: 31 intersecting step 12 with no progress (num=31, old_num=31) 012: 31 intersecting step 13 with no progress (num=31, old_num=31) 013: 31 intersecting step 14 with no progress (num=31, old_num=31) 014: 31 intersecting step 15 with no progress (num=31, old_num=31) 015: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 29 intersecting Area 231308 0.34111 0.13701 0.000541 2.5012 Corner 693924 60.00000 15.90601 0.234239 179.5104 Edge 346962 0.90160 0.22626 0.014203 4.0142 Hinge 346962 12.06279 14.65518 0.000020 179.9677 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRIcopyHeader(): source has ctab MRISripBasalGanglia(): -2 2 0.5 ripped 457 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (0,0,0) CBVO Creating mask 115656 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=2 had to be increased for 416 vertices, nripped=8648 mean border=90.4, 465 (465) missing vertices, mean dist 0.2 [0.9 (%27.9)->0.6 (%72.1))] %58 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0344 min Finding expansion regions mean absolute distance = 0.68 +- 1.10 3216 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=679868.6, rms=4.719 001: dt: 0.5000, sse=400982.0, rms=3.073 (34.890%) 002: dt: 0.5000, sse=307496.7, rms=2.383 (22.447%) 003: dt: 0.5000, sse=287128.4, rms=2.157 (9.467%) 004: dt: 0.5000, sse=284009.3, rms=2.076 (3.783%) rms = 2.0924/2.0759, sse=282684.6/284009.3, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 005: dt: 0.2500, sse=260239.1, rms=1.802 (13.203%) 006: dt: 0.2500, sse=256415.3, rms=1.686 (6.451%) rms = 1.6510/1.6856, sse=255314.1/256415.3, time step reduction 2 of 3 to 0.125 0 0 1 007: dt: 0.2500, sse=255314.1, rms=1.651 (2.051%) rms = 1.6033/1.6510, sse=257526.9/255314.1, time step reduction 3 of 3 to 0.062 0 1 1 008: dt: 0.1250, sse=257526.9, rms=1.603 (2.888%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=1 had to be increased for 344 vertices, nripped=8648 mean border=92.1, 341 (158) missing vertices, mean dist -0.2 [0.5 (%64.7)->0.3 (%35.3))] %75 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0243 min Finding expansion regions mean absolute distance = 0.39 +- 0.68 2817 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=412405.7, rms=3.089 009: dt: 0.5000, sse=296621.8, rms=2.144 (30.600%) 010: dt: 0.5000, sse=285711.5, rms=1.904 (11.165%) rms = 1.8565/1.9043, sse=279620.5/285711.5, time step reduction 1 of 3 to 0.250 0 0 1 011: dt: 0.5000, sse=279620.5, rms=1.857 (2.508%) 012: dt: 0.2500, sse=256039.6, rms=1.568 (15.523%) rms = 1.5275/1.5683, sse=254241.6/256039.6, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=254241.6, rms=1.527 (2.605%) rms = 1.4993/1.5275, sse=250067.5/254241.6, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=250067.5, rms=1.499 (1.846%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 414 vertices, nripped=8648 mean border=92.9, 365 (107) missing vertices, mean dist -0.1 [0.3 (%58.5)->0.2 (%41.5))] %83 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0131 min Finding expansion regions mean absolute distance = 0.29 +- 0.47 3110 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=shark, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=310268.8, rms=2.270 rms = 1.8784/2.2696, sse=312613.5/310268.8, time step reduction 1 of 3 to 0.250 0 1 0 015: dt: 0.5000, sse=312613.5, rms=1.878 (17.233%) 016: dt: 0.2500, sse=262126.1, rms=1.568 (16.512%) 017: dt: 0.2500, sse=249423.8, rms=1.479 (5.693%) rms = 1.4729/1.4790, sse=254068.9/249423.8, time step reduction 2 of 3 to 0.125 0 1 1 018: dt: 0.2500, sse=254068.9, rms=1.473 (0.414%) rms = 1.4241/1.4729, sse=251631.8/254068.9, time step reduction 3 of 3 to 0.062 0 0 1 019: dt: 0.1250, sse=251631.8, rms=1.424 (3.309%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 82.0000000; outside_low = 70.7672810; outside_hi = 111.7520980; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 413 vertices, nripped=8648 mean border=93.1, 416 (90) missing vertices, mean dist -0.0 [0.3 (%52.1)->0.2 (%47.9))] %85 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0084 min Finding expansion regions mean absolute distance = 0.25 +- 0.38 3003 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=shark, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=260985.7, rms=1.600 rms = 1.6195/1.6000, sse=271700.7/260985.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=245642.8, rms=1.388 (13.250%) rms = 1.3487/1.3880, sse=256445.0/245642.8, time step reduction 2 of 3 to 0.125 0 1 1 021: dt: 0.2500, sse=256445.0, rms=1.349 (2.836%) 022: dt: 0.1250, sse=240611.7, rms=1.268 (5.956%) rms = 1.2490/1.2683, sse=234586.8/240611.7, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=234586.8, rms=1.249 (1.525%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 29 intersecting step 1 with no progress (num=60, old_num=29) 001: 60 intersecting step 2 with no progress (num=73, old_num=60) 002: 73 intersecting step 3 with no progress (num=81, old_num=73) 003: 81 intersecting 004: 78 intersecting step 1 with no progress (num=79, old_num=78) 005: 79 intersecting step 2 with no progress (num=79, old_num=79) 006: 79 intersecting step 3 with no progress (num=79, old_num=79) 007: 79 intersecting step 4 with no progress (num=79, old_num=79) 008: 79 intersecting step 5 with no progress (num=79, old_num=79) 009: 79 intersecting step 6 with no progress (num=79, old_num=79) 010: 79 intersecting step 7 with no progress (num=79, old_num=79) 011: 79 intersecting step 8 with no progress (num=79, old_num=79) 012: 79 intersecting step 9 with no progress (num=79, old_num=79) 013: 79 intersecting step 10 with no progress (num=79, old_num=79) 014: 79 intersecting step 11 with no progress (num=79, old_num=79) 015: 79 intersecting step 12 with no progress (num=79, old_num=79) 016: 79 intersecting step 13 with no progress (num=79, old_num=79) 017: 79 intersecting step 14 with no progress (num=79, old_num=79) 018: 79 intersecting step 15 with no progress (num=79, old_num=79) 019: 79 intersecting step 16 with no progress (num=79, old_num=79) terminating search with 29 intersecting Writing output to ../surf/lh.white #ET# mris_place_surface 1.57 minutes #VMPC# mris_place_surfaces VmPeak 1959388 mris_place_surface done #-------------------------------------------- #@# WhiteSurfs rh Mon Jan 9 13:13:01 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface removing intersecting faces 000: 85 intersecting step 1 with no progress (num=118, old_num=85) 001: 118 intersecting 002: 108 intersecting 003: 96 intersecting step 1 with no progress (num=112, old_num=96) 004: 112 intersecting 005: 109 intersecting 006: 106 intersecting 007: 98 intersecting step 1 with no progress (num=108, old_num=98) 008: 108 intersecting 009: 94 intersecting step 1 with no progress (num=107, old_num=94) 010: 107 intersecting 011: 99 intersecting step 1 with no progress (num=106, old_num=99) 012: 106 intersecting 013: 90 intersecting step 1 with no progress (num=99, old_num=90) 014: 99 intersecting 015: 94 intersecting step 1 with no progress (num=96, old_num=94) 016: 96 intersecting 017: 89 intersecting step 1 with no progress (num=105, old_num=89) 018: 105 intersecting step 2 with no progress (num=106, old_num=105) 019: 106 intersecting step 3 with no progress (num=117, old_num=106) 020: 117 intersecting 021: 115 intersecting step 1 with no progress (num=118, old_num=115) 022: 118 intersecting step 2 with no progress (num=129, old_num=118) 023: 129 intersecting step 3 with no progress (num=141, old_num=129) 024: 141 intersecting 025: 125 intersecting step 1 with no progress (num=131, old_num=125) 026: 131 intersecting step 2 with no progress (num=133, old_num=131) 027: 133 intersecting step 3 with no progress (num=141, old_num=133) 028: 141 intersecting 029: 137 intersecting 030: 126 intersecting step 1 with no progress (num=129, old_num=126) 031: 129 intersecting step 2 with no progress (num=133, old_num=129) 032: 133 intersecting 033: 122 intersecting step 1 with no progress (num=125, old_num=122) 034: 125 intersecting step 2 with no progress (num=127, old_num=125) 035: 127 intersecting step 3 with no progress (num=130, old_num=127) 036: 130 intersecting step 4 with no progress (num=137, old_num=130) 037: 137 intersecting 038: 123 intersecting step 1 with no progress (num=136, old_num=123) 039: 136 intersecting 040: 128 intersecting 041: 127 intersecting step 1 with no progress (num=131, old_num=127) 042: 131 intersecting 043: 130 intersecting 044: 126 intersecting step 1 with no progress (num=136, old_num=126) 045: 136 intersecting 046: 124 intersecting step 1 with no progress (num=125, old_num=124) 047: 125 intersecting step 2 with no progress (num=128, old_num=125) 048: 128 intersecting step 3 with no progress (num=128, old_num=128) 049: 128 intersecting step 4 with no progress (num=134, old_num=128) 050: 134 intersecting step 5 with no progress (num=142, old_num=134) 051: 142 intersecting 052: 140 intersecting 053: 137 intersecting step 1 with no progress (num=138, old_num=137) 054: 138 intersecting step 2 with no progress (num=139, old_num=138) 055: 139 intersecting 056: 131 intersecting 057: 121 intersecting step 1 with no progress (num=130, old_num=121) 058: 130 intersecting 059: 128 intersecting 060: 124 intersecting step 1 with no progress (num=124, old_num=124) 061: 124 intersecting step 2 with no progress (num=125, old_num=124) 062: 125 intersecting 063: 123 intersecting step 1 with no progress (num=124, old_num=123) 064: 124 intersecting 065: 123 intersecting step 1 with no progress (num=124, old_num=123) 066: 124 intersecting 067: 123 intersecting step 1 with no progress (num=123, old_num=123) 068: 123 intersecting step 2 with no progress (num=123, old_num=123) 069: 123 intersecting step 3 with no progress (num=123, old_num=123) 070: 123 intersecting step 4 with no progress (num=123, old_num=123) 071: 123 intersecting step 5 with no progress (num=123, old_num=123) 072: 123 intersecting step 6 with no progress (num=123, old_num=123) 073: 123 intersecting step 7 with no progress (num=123, old_num=123) 074: 123 intersecting step 8 with no progress (num=123, old_num=123) 075: 123 intersecting step 9 with no progress (num=123, old_num=123) 076: 123 intersecting step 10 with no progress (num=123, old_num=123) 077: 123 intersecting step 11 with no progress (num=123, old_num=123) 078: 123 intersecting step 12 with no progress (num=123, old_num=123) 079: 123 intersecting step 13 with no progress (num=123, old_num=123) 080: 123 intersecting step 14 with no progress (num=123, old_num=123) 081: 123 intersecting step 15 with no progress (num=123, old_num=123) 082: 123 intersecting step 16 with no progress (num=123, old_num=123) terminating search with 85 intersecting Area 224946 0.33770 0.13288 0.000000 3.7218 Corner 674838 60.00000 15.89640 0.000000 180.0000 Edge 337419 0.89653 0.21993 0.000000 4.9952 Hinge 337419 -nan -nan 0.000000 179.9965 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRIcopyHeader(): source has ctab MRISripBasalGanglia(): -2 2 0.5 ripped 526 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56238: xyz = (26.3917,-14.905,72.1024) oxyz = (26.3917,-14.905,72.1024) wxzy = (26.3917,-14.905,72.1024) pxyz = (0,0,0) CBVO Creating mask 112475 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=2 had to be increased for 542 vertices, nripped=8236 mean border=91.0, 472 (472) missing vertices, mean dist 0.2 [0.9 (%28.2)->0.6 (%71.8))] %56 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0340 min Finding expansion regions mean absolute distance = 0.67 +- 1.10 3106 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=922129.2, rms=4.395 001: dt: 0.5000, sse=660348.3, rms=2.844 (35.286%) 002: dt: 0.5000, sse=588603.7, rms=2.206 (22.421%) rms = 2.1218/2.2065, sse=594201.6/588603.7, time step reduction 1 of 3 to 0.250 0 1 0 003: dt: 0.5000, sse=594201.6, rms=2.122 (3.839%) 004: dt: 0.2500, sse=569810.5, rms=1.786 (15.828%) rms = 1.6953/1.7859, sse=570305.5/569810.5, time step reduction 2 of 3 to 0.125 0 1 0 005: dt: 0.2500, sse=570305.4, rms=1.695 (5.073%) rms = 1.6481/1.6953, sse=536209.6/570305.5, time step reduction 3 of 3 to 0.062 0 0 1 006: dt: 0.1250, sse=536209.6, rms=1.648 (2.785%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=1 had to be increased for 420 vertices, nripped=8236 mean border=92.4, 385 (184) missing vertices, mean dist -0.2 [0.5 (%61.7)->0.3 (%38.3))] %72 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0236 min Finding expansion regions mean absolute distance = 0.39 +- 0.71 2696 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=655825.2, rms=2.867 007: dt: 0.5000, sse=568329.0, rms=1.977 (31.022%) 008: dt: 0.5000, sse=536542.0, rms=1.735 (12.281%) rms = 1.7054/1.7346, sse=548860.9/536542.0, time step reduction 1 of 3 to 0.250 0 1 1 009: dt: 0.5000, sse=548860.9, rms=1.705 (1.682%) 010: dt: 0.2500, sse=513214.8, rms=1.378 (19.217%) rms = 1.3241/1.3777, sse=523254.2/513214.8, time step reduction 2 of 3 to 0.125 0 1 0 011: dt: 0.2500, sse=523254.2, rms=1.324 (3.892%) rms = 1.2945/1.3241, sse=502395.8/523254.2, time step reduction 3 of 3 to 0.062 0 0 1 012: dt: 0.1250, sse=502395.8, rms=1.294 (2.235%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 437 vertices, nripped=8236 mean border=93.2, 476 (128) missing vertices, mean dist -0.1 [0.4 (%56.6)->0.2 (%43.4))] %80 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0128 min Finding expansion regions mean absolute distance = 0.30 +- 0.49 2997 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=shark, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=554388.7, rms=2.056 rms = 1.6224/2.0564, sse=577653.8/554388.7, time step reduction 1 of 3 to 0.250 0 1 0 013: dt: 0.5000, sse=577653.8, rms=1.622 (21.109%) 014: dt: 0.2500, sse=550348.9, rms=1.324 (18.384%) 015: dt: 0.2500, sse=536303.1, rms=1.256 (5.127%) rms = 1.2455/1.2562, sse=567453.3/536303.1, time step reduction 2 of 3 to 0.125 0 1 1 016: dt: 0.2500, sse=567453.3, rms=1.245 (0.858%) rms = 1.2121/1.2455, sse=567251.0/567453.3, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=567251.0, rms=1.212 (2.678%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.7520980; border_low = 83.0000000; outside_low = 71.7672810; outside_hi = 111.7520980; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 396 vertices, nripped=8236 mean border=93.5, 541 (109) missing vertices, mean dist -0.0 [0.3 (%51.4)->0.2 (%48.6))] %83 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0082 min Finding expansion regions mean absolute distance = 0.27 +- 0.40 2653 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=shark, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=575960.4, rms=1.405 018: dt: 0.5000, sse=557624.8, rms=1.316 (6.364%) rms = 1.3673/1.3158, sse=546372.5/557624.8, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 019: dt: 0.2500, sse=534327.0, rms=1.109 (15.739%) rms = 1.1180/1.1087, sse=530020.0/534327.0, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 1.0604/1.1087, sse=530332.2/534327.0, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=530332.1, rms=1.060 (4.358%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes removing intersecting faces 000: 87 intersecting step 1 with no progress (num=92, old_num=87) 001: 92 intersecting 002: 79 intersecting 003: 77 intersecting 004: 74 intersecting step 1 with no progress (num=75, old_num=74) 005: 75 intersecting step 2 with no progress (num=78, old_num=75) 006: 78 intersecting 007: 72 intersecting step 1 with no progress (num=80, old_num=72) 008: 80 intersecting step 2 with no progress (num=82, old_num=80) 009: 82 intersecting step 3 with no progress (num=92, old_num=82) 010: 92 intersecting 011: 89 intersecting 012: 82 intersecting step 1 with no progress (num=90, old_num=82) 013: 90 intersecting step 2 with no progress (num=100, old_num=90) 014: 100 intersecting 015: 84 intersecting step 1 with no progress (num=86, old_num=84) 016: 86 intersecting 017: 79 intersecting step 1 with no progress (num=92, old_num=79) 018: 92 intersecting 019: 84 intersecting step 1 with no progress (num=86, old_num=84) 020: 86 intersecting step 2 with no progress (num=90, old_num=86) 021: 90 intersecting 022: 77 intersecting 023: 76 intersecting 024: 75 intersecting step 1 with no progress (num=80, old_num=75) 025: 80 intersecting step 2 with no progress (num=83, old_num=80) 026: 83 intersecting 027: 75 intersecting step 1 with no progress (num=81, old_num=75) 028: 81 intersecting step 2 with no progress (num=93, old_num=81) 029: 93 intersecting 030: 81 intersecting 031: 78 intersecting step 1 with no progress (num=81, old_num=78) 032: 81 intersecting step 2 with no progress (num=86, old_num=81) 033: 86 intersecting 034: 84 intersecting step 1 with no progress (num=84, old_num=84) 035: 84 intersecting step 2 with no progress (num=84, old_num=84) 036: 84 intersecting step 3 with no progress (num=84, old_num=84) 037: 84 intersecting step 4 with no progress (num=84, old_num=84) 038: 84 intersecting step 5 with no progress (num=84, old_num=84) 039: 84 intersecting step 6 with no progress (num=84, old_num=84) 040: 84 intersecting step 7 with no progress (num=84, old_num=84) 041: 84 intersecting step 8 with no progress (num=84, old_num=84) 042: 84 intersecting step 9 with no progress (num=84, old_num=84) 043: 84 intersecting step 10 with no progress (num=84, old_num=84) 044: 84 intersecting step 11 with no progress (num=84, old_num=84) 045: 84 intersecting step 12 with no progress (num=84, old_num=84) 046: 84 intersecting step 13 with no progress (num=84, old_num=84) 047: 84 intersecting step 14 with no progress (num=84, old_num=84) 048: 84 intersecting step 15 with no progress (num=84, old_num=84) 049: 84 intersecting step 16 with no progress (num=84, old_num=84) terminating search with 72 intersecting Writing output to ../surf/rh.white #ET# mris_place_surface 1.86 minutes #VMPC# mris_place_surfaces VmPeak 2080212 mris_place_surface done #-------------------------------------------- #@# T1PialSurf lh Mon Jan 9 13:16:17 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface removing intersecting faces 000: 29 intersecting step 1 with no progress (num=31, old_num=29) 001: 31 intersecting step 2 with no progress (num=31, old_num=31) 002: 31 intersecting step 3 with no progress (num=31, old_num=31) 003: 31 intersecting step 4 with no progress (num=31, old_num=31) 004: 31 intersecting step 5 with no progress (num=31, old_num=31) 005: 31 intersecting step 6 with no progress (num=31, old_num=31) 006: 31 intersecting step 7 with no progress (num=31, old_num=31) 007: 31 intersecting step 8 with no progress (num=31, old_num=31) 008: 31 intersecting step 9 with no progress (num=31, old_num=31) 009: 31 intersecting step 10 with no progress (num=31, old_num=31) 010: 31 intersecting step 11 with no progress (num=31, old_num=31) 011: 31 intersecting step 12 with no progress (num=31, old_num=31) 012: 31 intersecting step 13 with no progress (num=31, old_num=31) 013: 31 intersecting step 14 with no progress (num=31, old_num=31) 014: 31 intersecting step 15 with no progress (num=31, old_num=31) 015: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 29 intersecting Area 231308 0.34327 0.14591 0.001039 2.7281 Corner 693924 60.00000 16.77840 0.248217 178.3999 Edge 346962 0.90552 0.23823 0.019084 4.0142 Hinge 346962 12.10726 14.72363 0.000004 179.9709 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.2749 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (-3.05528,-18.0059,9.12601) CBVO Creating mask 115656 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=2 had to be increased for 655 vertices, nripped=6179 mean border=70.9, 633 (633) missing vertices, mean dist 1.3 [2.6 (%0.0)->3.4 (%100.0))] %12 local maxima, %23 large gradients and %59 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0284 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=12007999.0, rms=23.320 001: dt: 0.5000, sse=8754423.0, rms=19.859 (14.844%) 002: dt: 0.5000, sse=6432347.0, rms=16.960 (14.595%) 003: dt: 0.5000, sse=4937740.0, rms=14.796 (12.763%) 004: dt: 0.5000, sse=4021807.8, rms=13.294 (10.146%) 005: dt: 0.5000, sse=3435274.5, rms=12.235 (7.966%) 006: dt: 0.5000, sse=3017495.0, rms=11.420 (6.665%) 007: dt: 0.5000, sse=2650916.5, rms=10.652 (6.722%) 008: dt: 0.5000, sse=2298476.8, rms=9.857 (7.461%) 009: dt: 0.5000, sse=1954841.5, rms=9.015 (8.544%) 010: dt: 0.5000, sse=1659048.0, rms=8.221 (8.812%) 011: dt: 0.5000, sse=1446838.0, rms=7.598 (7.575%) 012: dt: 0.5000, sse=1287439.2, rms=7.093 (6.644%) 013: dt: 0.5000, sse=1173536.1, rms=6.707 (5.441%) 014: dt: 0.5000, sse=1095549.5, rms=6.428 (4.158%) 015: dt: 0.5000, sse=1045492.8, rms=6.240 (2.928%) 016: dt: 0.5000, sse=1009427.8, rms=6.100 (2.242%) 017: dt: 0.5000, sse=980996.2, rms=5.986 (1.867%) rms = 5.9426/5.9864, sse=971138.9/980996.2, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=971138.9, rms=5.943 (0.733%) 019: dt: 0.2500, sse=827378.3, rms=5.340 (10.138%) 020: dt: 0.2500, sse=793743.4, rms=5.190 (2.814%) rms = 5.1546/5.1899, sse=786471.9/793743.4, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=786471.9, rms=5.155 (0.680%) 022: dt: 0.1250, sse=734018.4, rms=4.910 (4.743%) 023: dt: 0.1250, sse=718588.6, rms=4.836 (1.518%) rms = 4.8338/4.8356, sse=718502.4/718588.6, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=718502.4, rms=4.834 (0.037%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=1 had to be increased for 14001 vertices, nripped=6179 mean border=69.4, 7755 (214) missing vertices, mean dist 0.2 [0.2 (%28.1)->0.7 (%71.9))] %20 local maxima, %19 large gradients and %49 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0089 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=969434.4, rms=5.737 rms = 6.0205/5.7369, sse=1041879.4/969434.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=883120.4, rms=5.378 (6.247%) 026: dt: 0.2500, sse=848454.6, rms=5.226 (2.829%) rms = 5.3865/5.2263, sse=885090.8/848454.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 027: dt: 0.1250, sse=829474.4, rms=5.141 (1.627%) 028: dt: 0.1250, sse=815317.6, rms=5.076 (1.271%) rms = 5.0444/5.0759, sse=808424.4/815317.6, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=808424.4, rms=5.044 (0.622%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 14685 vertices, nripped=6179 mean border=68.9, 7935 (185) missing vertices, mean dist 0.1 [0.2 (%31.5)->0.6 (%68.5))] %25 local maxima, %13 large gradients and %49 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0052 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=shark, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=849586.1, rms=5.230 rms = 6.0317/5.2302, sse=1043842.8/849586.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=819025.4, rms=5.094 (2.595%) rms = 5.2374/5.0944, sse=850462.7/819025.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 5.0734/5.0944, sse=814421.0/819025.5, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=814421.1, rms=5.073 (0.414%) maximum number of reductions reached, breaking from loop positioning took 0.1 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 70.7672810; border_low = 48.3018460; outside_low = 10.0000000; outside_hi = 65.1509250; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115656 Gdiag_no=-1 vno start=0, stop=115656 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 10984 vertices, nripped=6179 mean border=68.5, 12469 (174) missing vertices, mean dist 0.1 [0.2 (%33.0)->0.4 (%67.0))] %26 local maxima, %11 large gradients and %46 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0032 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=shark, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=835280.9, rms=5.166 rms = 5.4379/5.1664, sse=892951.9/835281.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=795526.3, rms=4.989 (3.426%) 033: dt: 0.2500, sse=769570.1, rms=4.879 (2.208%) rms = 4.8848/4.8792, sse=769241.0/769570.1, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step 034: dt: 0.1250, sse=751081.4, rms=4.791 (1.805%) 035: dt: 0.1250, sse=721680.4, rms=4.650 (2.955%) 036: dt: 0.1250, sse=703251.8, rms=4.560 (1.923%) 037: dt: 0.1250, sse=691693.9, rms=4.504 (1.233%) rms = 4.4578/4.5039, sse=682244.2/691693.9, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=682244.2, rms=4.458 (1.024%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 113 intersecting 001: 64 intersecting 002: 35 intersecting 003: 29 intersecting step 1 with no progress (num=29, old_num=29) 004: 29 intersecting step 2 with no progress (num=29, old_num=29) 005: 29 intersecting step 3 with no progress (num=29, old_num=29) 006: 29 intersecting step 4 with no progress (num=29, old_num=29) 007: 29 intersecting step 5 with no progress (num=29, old_num=29) 008: 29 intersecting step 6 with no progress (num=29, old_num=29) 009: 29 intersecting step 7 with no progress (num=29, old_num=29) 010: 29 intersecting step 8 with no progress (num=29, old_num=29) 011: 29 intersecting step 9 with no progress (num=29, old_num=29) 012: 29 intersecting step 10 with no progress (num=29, old_num=29) 013: 29 intersecting step 11 with no progress (num=29, old_num=29) 014: 29 intersecting step 12 with no progress (num=29, old_num=29) 015: 29 intersecting step 13 with no progress (num=29, old_num=29) 016: 29 intersecting step 14 with no progress (num=29, old_num=29) 017: 29 intersecting step 15 with no progress (num=29, old_num=29) 018: 29 intersecting step 16 with no progress (num=29, old_num=29) terminating search with 29 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.14 minutes #VMPC# mris_place_surfaces VmPeak 1453568 mris_place_surface done #-------------------------------------------- #@# T1PialSurf rh Mon Jan 9 13:18:48 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface removing intersecting faces 000: 72 intersecting step 1 with no progress (num=80, old_num=72) 001: 80 intersecting step 2 with no progress (num=82, old_num=80) 002: 82 intersecting step 3 with no progress (num=92, old_num=82) 003: 92 intersecting 004: 89 intersecting 005: 82 intersecting step 1 with no progress (num=90, old_num=82) 006: 90 intersecting step 2 with no progress (num=100, old_num=90) 007: 100 intersecting 008: 84 intersecting step 1 with no progress (num=86, old_num=84) 009: 86 intersecting 010: 79 intersecting step 1 with no progress (num=92, old_num=79) 011: 92 intersecting 012: 84 intersecting step 1 with no progress (num=86, old_num=84) 013: 86 intersecting step 2 with no progress (num=90, old_num=86) 014: 90 intersecting 015: 77 intersecting 016: 76 intersecting 017: 75 intersecting step 1 with no progress (num=80, old_num=75) 018: 80 intersecting step 2 with no progress (num=83, old_num=80) 019: 83 intersecting 020: 75 intersecting step 1 with no progress (num=81, old_num=75) 021: 81 intersecting step 2 with no progress (num=93, old_num=81) 022: 93 intersecting 023: 81 intersecting 024: 78 intersecting step 1 with no progress (num=81, old_num=78) 025: 81 intersecting step 2 with no progress (num=86, old_num=81) 026: 86 intersecting 027: 84 intersecting step 1 with no progress (num=84, old_num=84) 028: 84 intersecting step 2 with no progress (num=84, old_num=84) 029: 84 intersecting step 3 with no progress (num=84, old_num=84) 030: 84 intersecting step 4 with no progress (num=84, old_num=84) 031: 84 intersecting step 5 with no progress (num=84, old_num=84) 032: 84 intersecting step 6 with no progress (num=84, old_num=84) 033: 84 intersecting step 7 with no progress (num=84, old_num=84) 034: 84 intersecting step 8 with no progress (num=84, old_num=84) 035: 84 intersecting step 9 with no progress (num=84, old_num=84) 036: 84 intersecting step 10 with no progress (num=84, old_num=84) 037: 84 intersecting step 11 with no progress (num=84, old_num=84) 038: 84 intersecting step 12 with no progress (num=84, old_num=84) 039: 84 intersecting step 13 with no progress (num=84, old_num=84) 040: 84 intersecting step 14 with no progress (num=84, old_num=84) 041: 84 intersecting step 15 with no progress (num=84, old_num=84) 042: 84 intersecting step 16 with no progress (num=84, old_num=84) terminating search with 72 intersecting Area 224946 0.34043 0.14329 0.000000 3.7218 Corner 674838 60.00000 16.79442 0.000441 179.9981 Edge 337419 0.90146 0.23575 0.000166 4.9952 Hinge 337419 12.25769 14.91668 0.000024 179.9625 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.7749 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 vertex 56238: xyz = (26.5169,-14.8084,72.2833) oxyz = (26.5169,-14.8084,72.2833) wxzy = (26.5169,-14.8084,72.2833) pxyz = (26.5169,-14.8084,72.2833) CBVO Creating mask 112475 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=2 had to be increased for 579 vertices, nripped=6576 mean border=71.4, 501 (501) missing vertices, mean dist 1.4 [2.2 (%0.0)->3.4 (%100.0))] %13 local maxima, %24 large gradients and %57 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0276 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=11464051.0, rms=23.155 001: dt: 0.5000, sse=9198952.0, rms=20.706 (10.578%) 002: dt: 0.5000, sse=6776970.5, rms=17.715 (14.446%) 003: dt: 0.5000, sse=5138142.5, rms=15.362 (13.280%) 004: dt: 0.5000, sse=4101902.5, rms=13.665 (11.045%) 005: dt: 0.5000, sse=3444328.2, rms=12.468 (8.762%) 006: dt: 0.5000, sse=2974339.8, rms=11.535 (7.483%) 007: dt: 0.5000, sse=2604101.8, rms=10.742 (6.873%) 008: dt: 0.5000, sse=2262915.0, rms=9.955 (7.329%) 009: dt: 0.5000, sse=1936250.2, rms=9.137 (8.212%) 010: dt: 0.5000, sse=1644439.6, rms=8.340 (8.733%) 011: dt: 0.5000, sse=1424882.2, rms=7.683 (7.876%) 012: dt: 0.5000, sse=1278776.5, rms=7.211 (6.146%) 013: dt: 0.5000, sse=1170026.8, rms=6.837 (5.187%) 014: dt: 0.5000, sse=1103162.1, rms=6.594 (3.554%) 015: dt: 0.5000, sse=1045408.8, rms=6.376 (3.299%) 016: dt: 0.5000, sse=1009629.4, rms=6.235 (2.206%) 017: dt: 0.5000, sse=981857.8, rms=6.123 (1.806%) 018: dt: 0.5000, sse=960986.8, rms=6.036 (1.419%) 019: dt: 0.5000, sse=949180.2, rms=5.984 (0.863%) 020: dt: 0.5000, sse=935661.8, rms=5.926 (0.972%) rms = 5.8946/5.9257, sse=929068.3/935661.8, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=929068.3, rms=5.895 (0.524%) 022: dt: 0.2500, sse=798812.1, rms=5.328 (9.620%) 023: dt: 0.2500, sse=765655.8, rms=5.175 (2.865%) rms = 5.1728/5.1749, sse=765783.8/765655.8, time step reduction 2 of 3 to 0.125 0 1 1 024: dt: 0.2500, sse=765783.8, rms=5.173 (0.040%) 025: dt: 0.1250, sse=713723.5, rms=4.923 (4.821%) 026: dt: 0.1250, sse=699280.5, rms=4.852 (1.454%) rms = 4.8271/4.8519, sse=694460.6/699280.5, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=694460.6, rms=4.827 (0.510%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=1 had to be increased for 13434 vertices, nripped=6576 mean border=69.9, 7875 (153) missing vertices, mean dist 0.2 [0.3 (%28.3)->0.8 (%71.7))] %21 local maxima, %19 large gradients and %47 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0098 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=970854.5, rms=5.859 rms = 6.1136/5.8586, sse=1034329.0/970854.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=886977.6, rms=5.507 (5.993%) 029: dt: 0.2500, sse=853318.6, rms=5.360 (2.680%) rms = 5.4911/5.3598, sse=882905.4/853318.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 030: dt: 0.1250, sse=834913.1, rms=5.277 (1.549%) 031: dt: 0.1250, sse=817710.7, rms=5.197 (1.503%) rms = 5.1678/5.1975, sse=811250.0/817710.7, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=811250.0, rms=5.168 (0.572%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 13991 vertices, nripped=6576 mean border=69.4, 7914 (132) missing vertices, mean dist 0.2 [0.3 (%31.1)->0.6 (%68.9))] %26 local maxima, %13 large gradients and %48 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0057 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=shark, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=862572.8, rms=5.400 rms = 6.1329/5.3996, sse=1038169.6/862572.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=832794.1, rms=5.268 (2.442%) rms = 5.4157/5.2678, sse=865288.9/832794.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 5.2482/5.2678, sse=828504.6/832794.1, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=828504.6, rms=5.248 (0.371%) maximum number of reductions reached, breaking from loop positioning took 0.1 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.2479020; border_hi = 71.7672810; border_low = 49.3018460; outside_low = 10.0000000; outside_hi = 66.1509250; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=112475 Gdiag_no=-1 vno start=0, stop=112475 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 10018 vertices, nripped=6576 mean border=68.9, 12569 (127) missing vertices, mean dist 0.1 [0.3 (%32.3)->0.5 (%67.7))] %27 local maxima, %11 large gradients and %45 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0034 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=shark, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=855117.3, rms=5.367 rms = 5.5349/5.3667, sse=888485.2/855117.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=812666.9, rms=5.179 (3.503%) 036: dt: 0.2500, sse=773703.8, rms=5.008 (3.289%) rms = 5.0088/5.0084, sse=772299.2/773703.7, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step 037: dt: 0.1250, sse=756079.0, rms=4.924 (1.687%) 038: dt: 0.1250, sse=726525.1, rms=4.781 (2.901%) 039: dt: 0.1250, sse=707223.6, rms=4.687 (1.965%) 040: dt: 0.1250, sse=694418.0, rms=4.625 (1.333%) 041: dt: 0.1250, sse=682032.9, rms=4.563 (1.333%) rms = 4.5162/4.5629, sse=672660.7/682032.9, time step reduction 3 of 3 to 0.062 0 0 1 042: dt: 0.1250, sse=672660.7, rms=4.516 (1.025%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 83 intersecting step 1 with no progress (num=92, old_num=83) 001: 92 intersecting step 2 with no progress (num=97, old_num=92) 002: 97 intersecting 003: 72 intersecting 004: 66 intersecting step 1 with no progress (num=73, old_num=66) 005: 73 intersecting 006: 70 intersecting 007: 62 intersecting 008: 59 intersecting step 1 with no progress (num=60, old_num=59) 009: 60 intersecting step 2 with no progress (num=62, old_num=60) 010: 62 intersecting step 3 with no progress (num=65, old_num=62) 011: 65 intersecting 012: 63 intersecting step 1 with no progress (num=63, old_num=63) 013: 63 intersecting step 2 with no progress (num=63, old_num=63) 014: 63 intersecting step 3 with no progress (num=63, old_num=63) 015: 63 intersecting step 4 with no progress (num=63, old_num=63) 016: 63 intersecting step 5 with no progress (num=63, old_num=63) 017: 63 intersecting step 6 with no progress (num=63, old_num=63) 018: 63 intersecting step 7 with no progress (num=63, old_num=63) 019: 63 intersecting step 8 with no progress (num=63, old_num=63) 020: 63 intersecting step 9 with no progress (num=63, old_num=63) 021: 63 intersecting step 10 with no progress (num=63, old_num=63) 022: 63 intersecting step 11 with no progress (num=63, old_num=63) 023: 63 intersecting step 12 with no progress (num=63, old_num=63) 024: 63 intersecting step 13 with no progress (num=63, old_num=63) 025: 63 intersecting step 14 with no progress (num=63, old_num=63) 026: 63 intersecting step 15 with no progress (num=63, old_num=63) 027: 63 intersecting step 16 with no progress (num=63, old_num=63) terminating search with 59 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.49 minutes #VMPC# mris_place_surfaces VmPeak 1533312 mris_place_surface done #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon Jan 9 13:22:05 CET 2023 bbregister --s Test --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz --lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask tmp /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230 Log file is /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.log Mon Jan 9 13:22:05 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/bbregister --s Test --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz --lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask bbregister 7.2.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii mri_convert /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00118486, -0.999997, 0.00188591) j_ras = (0.0980046, -0.00176071, -0.995184) k_ras = (0.995185, 0.00136398, 0.0980023) writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii... mri_coreg --s Test --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --regdat /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.init.dat --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts cmdline mri_coreg --s Test --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --regdat /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.init.dat --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname sharky machine x86_64 user brainstimmaps dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii Reading in ref /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/brainmask.mgz Setting cras translation parameters to align volume centers Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Init matrix params -1.0474 1.0278 -0.0515 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial parameters to be opt -1.0474 1.0278 -0.0515 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 4 movsat = 819.0000 mov gstd 1.8908 1.8908 1.8914 Smoothing mov refsat = 241.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0482998704 nhits = 180123 out of 16777216, Percent Overlap: 68.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -1.04744; 0.00000 1.00000 0.00000 1.02782; 0.00000 0.00000 1.00000 -0.05146; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -0.00118 -0.00188 -0.99556 350.82333; -0.09757 0.99077 -0.00175 109.84100; -0.99518 -0.09800 0.00136 226.70732; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -1.04744 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0407441 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -1.047440 1.027817 -0.051460 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0482999086 #@# 4 188 -1.04744 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0482999 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.048300 #@# 4 190 -0.04744 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0485200 #@# 4 194 -0.42941 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0486172 #@# 4 196 -0.39856 1.02782 -0.05146 0.00000 0.00000 0.00000 -1.0486178 #@# 4 205 -0.40856 0.99300 -0.05146 0.00000 0.00000 0.00000 -1.0486192 #@# 4 206 -0.40856 0.96334 -0.05146 0.00000 0.00000 0.00000 -1.0486197 #@# 4 217 -0.40856 0.95334 -0.21759 0.00000 0.00000 0.00000 -1.0486393 #@# 4 218 -0.40856 0.95334 -0.22759 0.00000 0.00000 0.00000 -1.0486394 #@# 4 219 -0.40856 0.95334 -0.23759 0.00000 0.00000 0.00000 -1.0486398 #@# 4 229 -0.40856 0.95334 -0.23759 0.38197 0.00000 0.00000 -1.0486951 #@# 4 230 -0.40856 0.95334 -0.23759 0.35166 0.00000 0.00000 -1.0486959 #@# 4 232 -0.40856 0.95334 -0.23759 0.32872 0.00000 0.00000 -1.0486960 #@# 4 240 -0.40856 0.95334 -0.23759 0.32872 -0.61803 0.00000 -1.0487163 #@# 4 242 -0.40856 0.95334 -0.23759 0.32872 -0.39161 0.00000 -1.0487279 #@# 4 253 -0.40856 0.95334 -0.23759 0.32872 -0.39161 -0.22387 -1.0487548 #@# 4 254 -0.40856 0.95334 -0.23759 0.32872 -0.39161 -0.23387 -1.0487549 powell nthiter 1: fret = -1.048755 #@# 4 272 -0.39856 0.94334 -0.23759 0.32872 -0.39161 -0.23387 -1.0487550 #@# 4 282 -0.39856 0.93334 -0.44359 0.32872 -0.39161 -0.23387 -1.0487845 #@# 4 290 -0.39856 0.93334 -0.44359 0.71069 -0.39161 -0.23387 -1.0487889 #@# 4 291 -0.39856 0.93334 -0.44359 0.53261 -0.39161 -0.23387 -1.0488014 #@# 4 300 -0.39856 0.93334 -0.44359 0.54261 -0.54299 -0.23387 -1.0488060 #@# 4 301 -0.39856 0.93334 -0.44359 0.54261 -0.53299 -0.23387 -1.0488065 #@# 4 302 -0.39856 0.93334 -0.44359 0.54261 -0.49092 -0.23387 -1.0488069 #@# 4 304 -0.39856 0.93334 -0.44359 0.54261 -0.50762 -0.23387 -1.0488071 #@# 4 305 -0.39856 0.93334 -0.44359 0.54261 -0.51762 -0.23387 -1.0488074 Powell done niters total = 1 OptTimeSec 4.0 sec OptTimeMin 0.07 min nEvals 315 Final optimized parameters -0.39855793 0.93334097 -0.44359189 0.54261124 -0.51762331 -0.23386888 Final matrix parameters -0.3986 0.9333 -0.4436 0.5426 -0.5176 -0.2439 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.048807331110246 --------------------------------- Final RefRAS-to-MovRAS 0.99995 -0.00408 -0.00903 -0.39856; 0.00417 0.99995 0.00947 0.93334; 0.00899 -0.00951 0.99991 -0.44359; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.00295 0.00756 -0.99553 349.24756; -0.08865 0.99158 0.00727 107.80823; -0.99602 -0.08902 -0.00363 227.02847; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.3986 0.9333 -0.4436 0.5426 -0.5176 -0.2339 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.3986 0.9333 -0.4436 0.5426 -0.5176 -0.2339 nhits = 179917 out of 16777216, Percent Overlap: 68.6 mri_coreg RunTimeSec 73.8 sec To check run: tkregisterfv --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --targ /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/brainmask.mgz --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/mri_coreg.lta --s Test --surfs mri_coreg done mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.init.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 7.2.0 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.init.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 sysname Linux hostname sharky machine x86_64 user brainstimmaps movvol /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii regfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.init.dat subject Test dof 6 outregfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1674045052 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00297 0.99997 0.00759 0.83787; 0.99602 -0.00363 0.08902 -0.32104; -0.08904 -0.00730 0.99600 -0.31540; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.984621 1 -25.0 -25.0 25.0 1.017466 2 -25.0 25.0 -25.0 1.038251 3 -25.0 25.0 25.0 1.012044 4 25.0 -25.0 -25.0 0.964212 5 25.0 -25.0 25.0 0.983200 6 25.0 25.0 -25.0 1.011342 7 25.0 25.0 25.0 0.972777 REL: 8 0.109127 7.983914 0.997989 rel = 0.109347 Initial costs ---------------- Number of surface hits 2114 WM Intensity 240.1715 +/- 35.1222 Ctx Intensity 334.6100 +/- 76.4379 Pct Contrast 30.9717 +/- 24.3055 Cost 0.1091 RelCost 0.1093 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9956 0.9956 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9766 0.9766 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9588 0.9588 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9504 0.9504 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.8819 0.8819 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8427 0.8427 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.7442 0.7442 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.6232 0.6232 0.0 121 -4.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6180 0.6180 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5810 0.5810 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1091 0.1091 0.0 Brute Force -------------------------- Min cost was 0.109127 Number of iterations 729 Search time 0.763804 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.109127 5 -0.618 0.000 0.000 0.000 0.000 0.000 0.0940338703 7 -0.478 0.000 0.000 0.000 0.000 0.000 0.0933509113 11 -0.477 0.000 0.000 0.000 0.000 0.000 0.0933482803 12 -0.472 0.000 0.000 0.000 0.000 0.000 0.0933448650 14 -0.473 0.000 0.000 0.000 0.000 0.000 0.0933441222 22 -0.473 -0.102 0.000 0.000 0.000 0.000 0.0928127023 23 -0.473 -0.086 0.000 0.000 0.000 0.000 0.0925635291 25 -0.473 -0.077 0.000 0.000 0.000 0.000 0.0925360332 26 -0.473 -0.078 0.000 0.000 0.000 0.000 0.0925353060 32 -0.473 -0.078 -0.618 0.000 0.000 0.000 0.0893769789 34 -0.473 -0.078 -0.350 0.000 0.000 0.000 0.0833226219 35 -0.473 -0.078 -0.341 0.000 0.000 0.000 0.0832733857 37 -0.473 -0.078 -0.326 0.000 0.000 0.000 0.0832320685 47 -0.473 -0.078 -0.326 -0.022 0.000 0.000 0.0827986433 49 -0.473 -0.078 -0.326 -0.119 0.000 0.000 0.0808924099 62 -0.473 -0.078 -0.326 -0.119 0.016 0.000 0.0808763119 63 -0.473 -0.078 -0.326 -0.119 0.013 0.000 0.0808696218 64 -0.473 -0.078 -0.326 -0.119 0.010 0.000 0.0808655179 73 -0.473 -0.078 -0.326 -0.119 0.010 0.013 0.0808416942 76 -0.473 -0.078 -0.326 -0.119 0.010 0.011 0.0808404784 powell nthiter 1: fret = 0.080840 89 -0.474 -0.078 -0.326 -0.119 0.010 0.011 0.0808401661 101 -0.474 -0.071 -0.326 -0.119 0.010 0.011 0.0808196183 102 -0.474 -0.073 -0.326 -0.119 0.010 0.011 0.0808117621 103 -0.474 -0.074 -0.326 -0.119 0.010 0.011 0.0808111888 112 -0.474 -0.074 -0.259 -0.119 0.010 0.011 0.0798570953 114 -0.474 -0.074 -0.275 -0.119 0.010 0.011 0.0798226950 115 -0.474 -0.074 -0.269 -0.119 0.010 0.011 0.0798099126 127 -0.474 -0.074 -0.269 -0.144 0.010 0.011 0.0798031545 128 -0.474 -0.074 -0.269 -0.132 0.010 0.011 0.0796682913 129 -0.474 -0.074 -0.269 -0.131 0.010 0.011 0.0796668238 139 -0.474 -0.074 -0.269 -0.131 0.011 0.011 0.0796560844 140 -0.474 -0.074 -0.269 -0.131 0.017 0.011 0.0796372610 142 -0.474 -0.074 -0.269 -0.131 0.018 0.011 0.0796372569 151 -0.474 -0.074 -0.269 -0.131 0.018 0.001 0.0794951614 155 -0.474 -0.074 -0.269 -0.131 0.018 -0.000 0.0794937584 156 -0.474 -0.074 -0.269 -0.131 0.018 -0.001 0.0794932062 powell nthiter 2: fret = 0.079493 167 -0.481 -0.074 -0.269 -0.131 0.018 -0.001 0.0794705124 168 -0.483 -0.074 -0.269 -0.131 0.018 -0.001 0.0794692361 180 -0.483 -0.076 -0.269 -0.131 0.018 -0.001 0.0794548806 181 -0.483 -0.078 -0.269 -0.131 0.018 -0.001 0.0794514553 183 -0.483 -0.077 -0.269 -0.131 0.018 -0.001 0.0794511042 194 -0.483 -0.077 -0.264 -0.131 0.018 -0.001 0.0794222954 195 -0.483 -0.077 -0.263 -0.131 0.018 -0.001 0.0794215703 207 -0.483 -0.077 -0.263 -0.134 0.018 -0.001 0.0794180277 208 -0.483 -0.077 -0.263 -0.133 0.018 -0.001 0.0794151633 219 -0.483 -0.077 -0.263 -0.133 0.020 -0.001 0.0794031835 220 -0.483 -0.077 -0.263 -0.133 0.022 -0.001 0.0794004735 222 -0.483 -0.077 -0.263 -0.133 0.021 -0.001 0.0794003094 229 -0.483 -0.077 -0.263 -0.133 0.021 -0.007 0.0793918510 231 -0.483 -0.077 -0.263 -0.133 0.021 -0.005 0.0793856403 powell nthiter 3: fret = 0.079386 244 -0.486 -0.077 -0.263 -0.133 0.021 -0.005 0.0793828026 245 -0.485 -0.077 -0.263 -0.133 0.021 -0.005 0.0793825896 257 -0.485 -0.078 -0.263 -0.133 0.021 -0.005 0.0793783500 269 -0.485 -0.078 -0.264 -0.133 0.021 -0.005 0.0793774742 292 -0.485 -0.078 -0.264 -0.133 0.022 -0.005 0.0793743973 293 -0.485 -0.078 -0.264 -0.133 0.023 -0.005 0.0793731540 303 -0.485 -0.078 -0.264 -0.133 0.023 -0.006 0.0793698189 304 -0.485 -0.078 -0.264 -0.133 0.023 -0.007 0.0793694342 305 -0.487 -0.080 -0.265 -0.133 0.025 -0.009 0.0793633489 powell nthiter 4: fret = 0.079369 340 -0.488 -0.080 -0.265 -0.133 0.023 -0.007 0.0793624220 364 -0.488 -0.080 -0.265 -0.133 0.025 -0.007 0.0793609742 powell nthiter 5: fret = 0.079361 410 -0.488 -0.080 -0.266 -0.133 0.025 -0.007 0.0793600683 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.976147 1 -25.0 -25.0 25.0 1.003093 2 -25.0 25.0 -25.0 1.040366 3 -25.0 25.0 25.0 1.020369 4 25.0 -25.0 -25.0 0.963913 5 25.0 -25.0 25.0 0.989877 6 25.0 25.0 -25.0 0.998785 7 25.0 25.0 25.0 0.991167 REL: 8 0.079360 7.983718 0.997965 rel = 0.0795219 Number of iterations 5 Min cost was 0.079360 Number of FunctionCalls 443 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.505900 sec Parameters at optimum (transmm) -0.48821 -0.07957 -0.26629 Parameters at optimum (rotdeg) -0.13317 0.02455 -0.00657 Final costs ---------------- Number of surface hits 2114 WM Intensity 238.9832 +/- 33.9690 Ctx Intensity 335.1641 +/- 72.9207 Pct Contrast 31.7115 +/- 24.3357 Cost 0.0794 RelCost 0.1093 Reg at min cost was 0.00304 0.99996 0.00803 0.34948; 0.99581 -0.00376 0.09133 -0.40145; -0.09136 -0.00772 0.99579 -0.58131; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat, type = 14 Original Reg 0.00297 0.99997 0.00759 0.83787; 0.99602 -0.00363 0.08902 -0.32104; -0.08904 -0.00730 0.99600 -0.31540; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00008 0.00000 -0.00044 0.48839; 0.00021 0.00013 -0.00231 0.08040; 0.00232 0.00042 0.00021 0.26591; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.518750 Computing change in rh position Surface-RMS-Diff-mm 0.542565 0.030012 0.618929 mri_segreg done mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 7.2.0 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mri_segreg --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii --init-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat --out-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname sharky machine x86_64 user brainstimmaps movvol /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/template.nii regfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/tmp.bbregister.327230/bbr.pass1.dat subject Test dof 6 outregfile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 1.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1673355427 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00304 0.99996 0.00803 0.34948; 0.99581 -0.00376 0.09133 -0.40145; -0.09136 -0.00772 0.99579 -0.58131; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 1.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.028982 1 -25.0 -25.0 25.0 1.014816 2 -25.0 25.0 -25.0 1.014260 3 -25.0 25.0 25.0 1.007483 4 25.0 -25.0 -25.0 0.997000 5 25.0 -25.0 25.0 1.023490 6 25.0 25.0 -25.0 1.007710 7 25.0 25.0 25.0 1.006121 REL: 8 0.082402 8.099861 1.012483 rel = 0.0813861 Initial costs ---------------- Number of surface hits 212196 WM Intensity 236.0041 +/- 31.5034 Ctx Intensity 337.0468 +/- 72.4561 Pct Contrast 33.4647 +/- 23.7419 Cost 0.0824 RelCost 0.0814 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0884 0.0884 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0867 0.0867 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0863 0.0863 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0851 0.0851 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0851 0.0851 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0846 0.0846 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0831 0.0831 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.0819 0.0819 0.0 132 -0.1000 0.0000 0.0000 0.1000 0.1000 -0.1000 0.0809 0.0809 0.0 375 0.0000 0.0000 0.0000 0.1000 0.1000 -0.1000 0.0805 0.0805 0.0 399 0.0000 0.0000 0.1000 0.1000 0.0000 -0.1000 0.0800 0.0800 0.0 Brute Force -------------------------- Min cost was 0.079969 Number of iterations 729 Search time 0.816397 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.100 0.100 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0.1 3 0.1 4 0 5 -0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.083157 9 -0.004 0.000 0.100 0.100 0.000 -0.100 0.0831562364 10 -0.003 0.000 0.100 0.100 0.000 -0.100 0.0831561407 11 -0.002 0.000 0.100 0.100 0.000 -0.100 0.0831561300 23 -0.002 -0.001 0.100 0.100 0.000 -0.100 0.0831545935 30 -0.002 -0.001 -0.142 0.100 0.000 -0.100 0.0815174314 31 -0.002 -0.001 -0.144 0.100 0.000 -0.100 0.0815174161 33 -0.002 -0.001 -0.143 0.100 0.000 -0.100 0.0815173725 40 -0.002 -0.001 -0.143 0.049 0.000 -0.100 0.0814645476 43 -0.002 -0.001 -0.143 0.040 0.000 -0.100 0.0814621267 53 -0.002 -0.001 -0.143 0.040 -0.076 -0.100 0.0810827699 54 -0.002 -0.001 -0.143 0.040 -0.114 -0.100 0.0809273206 57 -0.002 -0.001 -0.143 0.040 -0.148 -0.100 0.0808458219 58 -0.002 -0.001 -0.143 0.040 -0.149 -0.100 0.0808447258 60 -0.002 -0.001 -0.143 0.040 -0.153 -0.100 0.0808435811 61 -0.002 -0.001 -0.143 0.040 -0.152 -0.100 0.0808435337 69 -0.002 -0.001 -0.143 0.040 -0.152 -0.103 0.0808387597 70 -0.002 -0.001 -0.143 0.040 -0.152 -0.132 0.0807632107 74 -0.002 -0.001 -0.143 0.040 -0.152 -0.140 0.0807588784 76 -0.002 -0.001 -0.143 0.040 -0.152 -0.138 0.0807587929 powell nthiter 1: fret = 0.080759 86 0.117 -0.001 -0.143 0.040 -0.152 -0.138 0.0805113422 87 0.100 -0.001 -0.143 0.040 -0.152 -0.138 0.0805026802 89 0.101 -0.001 -0.143 0.040 -0.152 -0.138 0.0805024231 90 0.107 -0.001 -0.143 0.040 -0.152 -0.138 0.0805020457 91 0.105 -0.001 -0.143 0.040 -0.152 -0.138 0.0805020249 92 0.104 -0.001 -0.143 0.040 -0.152 -0.138 0.0805019436 100 0.104 -0.083 -0.143 0.040 -0.152 -0.138 0.0803387227 101 0.104 -0.074 -0.143 0.040 -0.152 -0.138 0.0803282395 102 0.104 -0.065 -0.143 0.040 -0.152 -0.138 0.0803260148 103 0.104 -0.067 -0.143 0.040 -0.152 -0.138 0.0803254894 104 0.104 -0.068 -0.143 0.040 -0.152 -0.138 0.0803253806 114 0.104 -0.068 -0.117 0.040 -0.152 -0.138 0.0803219989 116 0.104 -0.068 -0.129 0.040 -0.152 -0.138 0.0803128432 117 0.104 -0.068 -0.130 0.040 -0.152 -0.138 0.0803124584 118 0.104 -0.068 -0.135 0.040 -0.152 -0.138 0.0803124086 120 0.104 -0.068 -0.133 0.040 -0.152 -0.138 0.0803118949 122 0.104 -0.068 -0.134 0.040 -0.152 -0.138 0.0803118608 130 0.104 -0.068 -0.134 0.029 -0.152 -0.138 0.0803041333 142 0.104 -0.068 -0.134 0.030 -0.206 -0.138 0.0801965722 143 0.104 -0.068 -0.134 0.030 -0.195 -0.138 0.0801913955 144 0.104 -0.068 -0.134 0.030 -0.196 -0.138 0.0801904491 145 0.104 -0.068 -0.134 0.030 -0.199 -0.138 0.0801900183 148 0.104 -0.068 -0.134 0.030 -0.198 -0.138 0.0801899358 156 0.104 -0.068 -0.134 0.030 -0.198 -0.199 0.0801387518 158 0.104 -0.068 -0.134 0.030 -0.198 -0.182 0.0801247488 160 0.104 -0.068 -0.134 0.030 -0.198 -0.183 0.0801243360 162 0.104 -0.068 -0.134 0.030 -0.198 -0.186 0.0801236483 powell nthiter 2: fret = 0.080124 174 0.117 -0.068 -0.134 0.030 -0.198 -0.186 0.0801185787 175 0.113 -0.068 -0.134 0.030 -0.198 -0.186 0.0801182261 176 0.114 -0.068 -0.134 0.030 -0.198 -0.186 0.0801182008 177 0.115 -0.068 -0.134 0.030 -0.198 -0.186 0.0801181776 184 0.115 -0.110 -0.134 0.030 -0.198 -0.186 0.0800620260 186 0.115 -0.111 -0.134 0.030 -0.198 -0.186 0.0800620212 196 0.115 -0.111 -0.129 0.030 -0.198 -0.186 0.0800460771 197 0.115 -0.111 -0.101 0.030 -0.198 -0.186 0.0800084641 198 0.115 -0.111 -0.102 0.030 -0.198 -0.186 0.0800074370 199 0.115 -0.111 -0.106 0.030 -0.198 -0.186 0.0800071340 201 0.115 -0.111 -0.104 0.030 -0.198 -0.186 0.0800069738 210 0.115 -0.111 -0.104 0.014 -0.198 -0.186 0.0799987796 212 0.115 -0.111 -0.104 0.019 -0.198 -0.186 0.0799974044 214 0.115 -0.111 -0.104 0.018 -0.198 -0.186 0.0799973889 225 0.115 -0.111 -0.104 0.018 -0.212 -0.186 0.0799760374 227 0.115 -0.111 -0.104 0.018 -0.211 -0.186 0.0799759043 237 0.115 -0.111 -0.104 0.018 -0.211 -0.215 0.0799399436 242 0.115 -0.111 -0.104 0.018 -0.211 -0.213 0.0799393051 245 0.127 -0.154 -0.075 0.005 -0.224 -0.240 0.0798715860 powell nthiter 3: fret = 0.079939 321 0.120 -0.170 -0.068 -0.014 -0.232 -0.239 0.0798687415 326 0.120 -0.177 -0.064 -0.018 -0.234 -0.242 0.0798670716 331 0.120 -0.177 -0.064 -0.018 -0.234 -0.242 0.0798670269 powell nthiter 4: fret = 0.079867 341 0.125 -0.177 -0.064 -0.018 -0.234 -0.242 0.0798583395 342 0.136 -0.177 -0.064 -0.018 -0.234 -0.242 0.0798458656 344 0.138 -0.177 -0.064 -0.018 -0.234 -0.242 0.0798457596 346 0.137 -0.177 -0.064 -0.018 -0.234 -0.242 0.0798457026 355 0.137 -0.177 -0.064 -0.018 -0.234 -0.233 0.0798385596 356 0.137 -0.177 -0.064 -0.018 -0.234 -0.226 0.0798369524 357 0.137 -0.177 -0.064 -0.018 -0.234 -0.227 0.0798362096 358 0.137 -0.177 -0.064 -0.018 -0.234 -0.229 0.0798358346 360 0.137 -0.177 -0.064 -0.018 -0.234 -0.228 0.0798358135 379 0.137 -0.177 -0.064 -0.021 -0.234 -0.228 0.0798346995 380 0.137 -0.177 -0.064 -0.022 -0.234 -0.228 0.0798346802 391 0.137 -0.177 -0.064 -0.022 -0.242 -0.228 0.0798308176 392 0.137 -0.177 -0.064 -0.022 -0.241 -0.228 0.0798302858 393 0.137 -0.177 -0.064 -0.022 -0.240 -0.228 0.0798300143 397 0.139 -0.193 -0.054 -0.031 -0.245 -0.235 0.0798268884 401 0.138 -0.187 -0.058 -0.027 -0.243 -0.232 0.0798232679 408 0.138 -0.187 -0.058 -0.028 -0.243 -0.232 0.0798232577 powell nthiter 5: fret = 0.079823 420 0.139 -0.187 -0.058 -0.028 -0.243 -0.232 0.0798224325 421 0.143 -0.187 -0.058 -0.028 -0.243 -0.232 0.0798213092 456 0.143 -0.187 -0.058 -0.029 -0.243 -0.232 0.0798212421 467 0.143 -0.187 -0.058 -0.029 -0.244 -0.232 0.0798210763 475 0.143 -0.188 -0.057 -0.029 -0.245 -0.232 0.0798209566 476 0.143 -0.188 -0.057 -0.029 -0.245 -0.233 0.0798209176 490 0.143 -0.188 -0.057 -0.030 -0.245 -0.233 0.0798208568 491 0.144 -0.188 -0.057 -0.030 -0.245 -0.233 0.0798208038 powell nthiter 6: fret = 0.079821 524 0.144 -0.188 -0.057 -0.030 -0.245 -0.232 0.0798207452 567 0.144 -0.188 -0.057 -0.030 -0.245 -0.232 0.0798207322 569 0.144 -0.188 -0.057 -0.030 -0.245 -0.232 0.0798207301 574 0.144 -0.188 -0.057 -0.030 -0.245 -0.232 0.0798207257 powell nthiter 7: fret = 0.079821 586 0.144 -0.188 -0.057 -0.030 -0.245 -0.232 0.0798207229 591 0.144 -0.188 -0.057 -0.030 -0.245 -0.232 0.0798207011 powell nthiter 8: fret = 0.079821 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 1.029344 1 -25.0 -25.0 25.0 1.014960 2 -25.0 25.0 -25.0 1.013400 3 -25.0 25.0 25.0 1.009051 4 25.0 -25.0 -25.0 1.000354 5 25.0 -25.0 25.0 1.022247 6 25.0 25.0 -25.0 1.006341 7 25.0 25.0 25.0 1.004071 REL: 8 0.079821 8.099767 1.012471 rel = 0.0788375 Number of iterations 8 Min cost was 0.079821 Number of FunctionCalls 723 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 17.886595 sec Parameters at optimum (transmm) 0.14395 -0.18811 -0.05724 Parameters at optimum (rotdeg) -0.02974 -0.24519 -0.23158 Final costs ---------------- Number of surface hits 212193 WM Intensity 236.0671 +/- 31.4631 Ctx Intensity 336.2266 +/- 71.8606 Pct Contrast 33.2497 +/- 23.5128 Cost 0.0798 RelCost 0.0814 Reg at min cost was 0.00746 0.99996 0.00414 0.49429; 0.99574 -0.00781 0.09183 -0.59128; -0.09186 -0.00344 0.99577 -0.63683; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat, type = 14 Original Reg 0.00304 0.99996 0.00803 0.34948; 0.99581 -0.00376 0.09133 -0.40145; -0.09136 -0.00772 0.99579 -0.58131; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00442 -0.00000 0.00389 -0.14481; 0.00007 0.00405 -0.00050 0.18984; 0.00050 -0.00428 0.00002 0.05553; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.310171 Computing change in rh position Surface-RMS-Diff-mm 0.316315 0.091195 0.567566 mri_segreg done MinCost: 0.079821 236.067115 336.226555 33.249729 tkregister2_cmdl --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat --noedit --ltaout /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz reg file /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 ---- Input registration matrix -------- 0.00746 0.99996 0.00414 0.49429; 0.99574 -0.00781 0.09183 -0.59128; -0.09186 -0.00344 0.99577 -0.63683; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz Tmov: -------------------- -1.00446 0.00000 0.00000 224.99904; 0.00000 0.00000 1.00000 -88.00012; 0.00000 -1.00446 0.00000 224.99904; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.00746 0.99996 0.00414 0.49429; 0.99574 -0.00781 0.09183 -0.59128; -0.09186 -0.00344 0.99577 -0.63683; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = Test RegMat --------------------------- 0.00746 0.99996 0.00414 0.49429; 0.99574 -0.00781 0.09183 -0.59128; -0.09186 -0.00344 0.99577 -0.63683; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Mon Jan 9 13:22:05 CET 2023 Ended at Mon Jan 9 13:23:44 CET 2023 BBR-Run-Time-Sec 99 bbregister Done To check results, run: tkregisterfv --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz --reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.lta --surfs --sd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cp /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.auto.lta /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.lta mri_convert -odt float -at /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.lta -rl /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.prenorm.mgz reading from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00118486, -0.999997, 0.00188591) j_ras = (0.0980046, -0.00176071, -0.995184) k_ras = (0.995185, 0.00136398, 0.0980023) INFO: Reading transformation from file /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz... INFO: Applying transformation from file /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99994 0.00865 0.00615 0.64154; -0.00862 0.99994 -0.00607 -0.55362; -0.00621 0.00602 0.99996 0.74872; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from short to float (noscale = 0)... writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.prenorm.mgz... mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/aseg.presurf.mgz -surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white identity.nofile -surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white identity.nofile /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.prenorm.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.norm.mgz setting seed for random number genererator to 1234 using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading mri_src from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.prenorm.mgz... Copying mri_dst from mri_src computing distance transform computing distance transform min_dist = 1 Erasing Border planes 4 Removing non-wm voxels 47405 non wm control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 MRIapplyBiasCorrectionSameGeometry() writing normalized volume to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 1017928 mri_normalize done mri_mask -transfer 255 -keep_mask_deletion_edits /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.norm.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/brain.finalsurfs.mgz /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/T2.mgz...done. #-------------------------------------------- #@# MMPialSurf lh Mon Jan 9 13:24:23 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface removing intersecting faces 000: 29 intersecting step 1 with no progress (num=29, old_num=29) 001: 29 intersecting step 2 with no progress (num=29, old_num=29) 002: 29 intersecting step 3 with no progress (num=29, old_num=29) 003: 29 intersecting step 4 with no progress (num=29, old_num=29) 004: 29 intersecting step 5 with no progress (num=29, old_num=29) 005: 29 intersecting step 6 with no progress (num=29, old_num=29) 006: 29 intersecting step 7 with no progress (num=29, old_num=29) 007: 29 intersecting step 8 with no progress (num=29, old_num=29) 008: 29 intersecting step 9 with no progress (num=29, old_num=29) 009: 29 intersecting step 10 with no progress (num=29, old_num=29) 010: 29 intersecting step 11 with no progress (num=29, old_num=29) 011: 29 intersecting step 12 with no progress (num=29, old_num=29) 012: 29 intersecting step 13 with no progress (num=29, old_num=29) 013: 29 intersecting step 14 with no progress (num=29, old_num=29) 014: 29 intersecting step 15 with no progress (num=29, old_num=29) 015: 29 intersecting step 16 with no progress (num=29, old_num=29) terminating search with 29 intersecting Area 231308 0.41456 0.33635 0.000197 6.4502 Corner 693924 60.00000 32.43870 0.055483 179.8686 Edge 346962 1.03824 0.49701 0.007399 6.5232 Hinge 346962 24.72730 30.06492 0.000044 179.9979 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.2749 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume T2.mgz using multi modal weights vertex 57828: xyz = (-3.05528,-18.0059,9.12601) oxyz = (-3.05528,-18.0059,9.12601) wxzy = (-3.05528,-18.0059,9.12601) pxyz = (-3.05528,-18.0059,9.12601) CBVO Creating mask 115656 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 50, T2_max_inside 200, T2_min_outside = 10, T2_max_outside 50 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 23268 aseg cortex voxels to 0 Creating lowres distance volumes t=0.023264 Creating white distance volumes t=0.472666 (box.dx, box.dy, box.dz) = (130, 234, 308) (region->dx, region->dy, region->dz) = (130, 234, 308) (region->dx, region->dy, region->dz) = (130, 234, 308) Creating pial distance volumes t=0.892778 (box.dx, box.dy, box.dz) = (138, 242, 316) (region->dx, region->dy, region->dz) = (138, 242, 316) (region->dx, region->dy, region->dz) = (138, 242, 316) locating cortical regions not in interior range [50.0 --> 200.0], and not in exterior range [10.0 --> 50.0] t = 1.40878 Starting loop over 115656 vertices vno = 0, t = 1.40878 vno = 20000, t = 2.31067 vno = 40000, t = 3.18182 vno = 60000, t = 3.94928 vno = 80000, t = 4.71933 vno = 100000, t = 5.54569 CPTL: t = 6.19373 79095 surface locations found to contain inconsistent values (28179 in, 50916 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=4, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 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=360522.9, rms=0.753 001: dt: 0.5000, sse=318758.0, rms=0.747 (0.807%) 002: dt: 0.5000, sse=306683.6, rms=0.740 (0.969%) 003: dt: 0.5000, sse=300276.8, rms=0.737 (0.377%) 004: dt: 0.5000, sse=296658.3, rms=0.736 (0.193%) rms = 0.7367/0.7358, sse=294265.3/296658.4, time step reduction 1 of 3 to 0.250 1 0 0 005: dt: 0.5000, sse=294265.3, rms=0.737 (-0.120%) rms = 0.7375/0.7367, sse=293086.2/294265.3, time step reduction 2 of 3 to 0.125 1 0 0 006: dt: 0.2500, sse=293086.2, rms=0.738 (-0.111%) rms = 0.7377/0.7375, sse=292440.7/293086.2, time step reduction 3 of 3 to 0.062 1 0 0 007: dt: 0.1250, sse=292440.7, rms=0.738 (-0.021%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 50, T2_max_inside 200, T2_min_outside = 10, T2_max_outside 50 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 23268 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0254949 Creating white distance volumes t=0.468528 (box.dx, box.dy, box.dz) = (130, 234, 308) (region->dx, region->dy, region->dz) = (130, 234, 308) (region->dx, region->dy, region->dz) = (130, 234, 308) Creating pial distance volumes t=0.888635 (box.dx, box.dy, box.dz) = (136, 242, 316) (region->dx, region->dy, region->dz) = (136, 242, 316) (region->dx, region->dy, region->dz) = (136, 242, 316) locating cortical regions not in interior range [50.0 --> 200.0], and not in exterior range [10.0 --> 50.0] t = 1.37041 Starting loop over 115656 vertices vno = 0, t = 1.37041 vno = 20000, t = 2.27362 vno = 40000, t = 3.14502 vno = 60000, t = 3.91443 vno = 80000, t = 4.68697 vno = 100000, t = 5.52304 CPTL: t = 6.17329 80564 surface locations found to contain inconsistent values (21466 in, 59098 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=2, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 mom=0.00, dt=0.50 000: dt: 0.0000, sse=260832.3, rms=0.725 008: dt: 0.5000, sse=260389.6, rms=0.719 (0.884%) 009: dt: 0.5000, sse=258268.9, rms=0.717 (0.241%) rms = 0.7168/0.7168, sse=257931.0/258268.9, time step reduction 1 of 3 to 0.250 1 0 0 010: dt: 0.5000, sse=257931.0, rms=0.717 (0.010%) rms = 0.7168/0.7168, sse=256860.8/257931.0, time step reduction 2 of 3 to 0.125 1 0 0 011: dt: 0.2500, sse=256860.8, rms=0.717 (-0.007%) 012: dt: 0.1250, sse=256434.3, rms=0.717 (0.016%) 013: dt: 0.1250, sse=256242.1, rms=0.717 (0.027%) rms = 0.7164/0.7165, sse=256355.4/256242.1, time step reduction 3 of 3 to 0.062 1 0 0 014: dt: 0.1250, sse=256355.4, rms=0.716 (0.010%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 66 intersecting 001: 29 intersecting step 1 with no progress (num=29, old_num=29) 002: 29 intersecting step 2 with no progress (num=29, old_num=29) 003: 29 intersecting step 3 with no progress (num=29, old_num=29) 004: 29 intersecting step 4 with no progress (num=29, old_num=29) 005: 29 intersecting step 5 with no progress (num=29, old_num=29) 006: 29 intersecting step 6 with no progress (num=29, old_num=29) 007: 29 intersecting step 7 with no progress (num=29, old_num=29) 008: 29 intersecting step 8 with no progress (num=29, old_num=29) 009: 29 intersecting step 9 with no progress (num=29, old_num=29) 010: 29 intersecting step 10 with no progress (num=29, old_num=29) 011: 29 intersecting step 11 with no progress (num=29, old_num=29) 012: 29 intersecting step 12 with no progress (num=29, old_num=29) 013: 29 intersecting step 13 with no progress (num=29, old_num=29) 014: 29 intersecting step 14 with no progress (num=29, old_num=29) 015: 29 intersecting step 15 with no progress (num=29, old_num=29) 016: 29 intersecting step 16 with no progress (num=29, old_num=29) terminating search with 29 intersecting Writing output to ../surf/lh.pial.T2 #ET# mris_place_surface 13.46 minutes #VMPC# mris_place_surfaces VmPeak 2400936 mris_place_surface done #-------------------------------------------- #@# MMPialSurf rh Mon Jan 9 13:38:20 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.pial.T1 --o ../surf/rh.pial.T2 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --white-surf ../surf/rh.white --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --mmvol T2.mgz T2 --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 7.2.0 7.2.0 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.pial.T1 --o ../surf/rh.pial.T2 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --white-surf ../surf/rh.white --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --mmvol T2.mgz T2 --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 Reading in input surface ../surf/rh.pial.T1 Not smoothing input surface removing intersecting faces 000: 59 intersecting step 1 with no progress (num=60, old_num=59) 001: 60 intersecting step 2 with no progress (num=62, old_num=60) 002: 62 intersecting step 3 with no progress (num=65, old_num=62) 003: 65 intersecting 004: 63 intersecting step 1 with no progress (num=63, old_num=63) 005: 63 intersecting step 2 with no progress (num=63, old_num=63) 006: 63 intersecting step 3 with no progress (num=63, old_num=63) 007: 63 intersecting step 4 with no progress (num=63, old_num=63) 008: 63 intersecting step 5 with no progress (num=63, old_num=63) 009: 63 intersecting step 6 with no progress (num=63, old_num=63) 010: 63 intersecting step 7 with no progress (num=63, old_num=63) 011: 63 intersecting step 8 with no progress (num=63, old_num=63) 012: 63 intersecting step 9 with no progress (num=63, old_num=63) 013: 63 intersecting step 10 with no progress (num=63, old_num=63) 014: 63 intersecting step 11 with no progress (num=63, old_num=63) 015: 63 intersecting step 12 with no progress (num=63, old_num=63) 016: 63 intersecting step 13 with no progress (num=63, old_num=63) 017: 63 intersecting step 14 with no progress (num=63, old_num=63) 018: 63 intersecting step 15 with no progress (num=63, old_num=63) 019: 63 intersecting step 16 with no progress (num=63, old_num=63) terminating search with 59 intersecting Area 224946 0.41862 0.34395 0.000000 6.4232 Corner 674838 60.00000 32.31598 0.040761 179.8639 Edge 337419 1.04263 0.50550 0.000002 7.1120 Hinge 337419 24.73552 30.12783 0.000000 179.9957 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=28065, wmmin=5, clip=110 MRIfindBrightNonWM(): 26135 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 73.7749 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume T2.mgz using multi modal weights vertex 56238: xyz = (29.1926,-16.4607,72.9355) oxyz = (26.5169,-14.8084,72.2833) wxzy = (26.5169,-14.8084,72.2833) pxyz = (29.1926,-16.4607,72.9355) CBVO Creating mask 112475 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 50, T2_max_inside 200, T2_min_outside = 10, T2_max_outside 50 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 23285 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0212603 Creating white distance volumes t=0.466199 (box.dx, box.dy, box.dz) = (128, 212, 308) (region->dx, region->dy, region->dz) = (128, 212, 308) (region->dx, region->dy, region->dz) = (128, 212, 308) Creating pial distance volumes t=0.859785 (box.dx, box.dy, box.dz) = (140, 220, 316) (region->dx, region->dy, region->dz) = (140, 220, 316) (region->dx, region->dy, region->dz) = (140, 220, 316) locating cortical regions not in interior range [50.0 --> 200.0], and not in exterior range [10.0 --> 50.0] t = 1.33951 Starting loop over 112475 vertices vno = 0, t = 1.33951 vno = 20000, t = 2.30366 vno = 40000, t = 3.18631 vno = 60000, t = 3.90618 vno = 80000, t = 4.64356 vno = 100000, t = 5.47016 CPTL: t = 5.98306 75102 surface locations found to contain inconsistent values (24025 in, 51077 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=2.0, host=shark, nav=4, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 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=357417.7, rms=0.808 001: dt: 0.5000, sse=320313.8, rms=0.802 (0.742%) 002: dt: 0.5000, sse=304429.0, rms=0.795 (0.835%) 003: dt: 0.5000, sse=299880.6, rms=0.793 (0.227%) rms = 0.7936/0.7934, sse=295734.8/299880.6, time step reduction 1 of 3 to 0.250 1 0 0 004: dt: 0.5000, sse=295734.8, rms=0.794 (-0.025%) rms = 0.7941/0.7936, sse=292678.0/295734.8, time step reduction 2 of 3 to 0.125 1 0 0 005: dt: 0.2500, sse=292678.0, rms=0.794 (-0.064%) rms = 0.7944/0.7941, sse=291461.0/292678.0, time step reduction 3 of 3 to 0.062 1 0 0 006: dt: 0.1250, sse=291461.0, rms=0.794 (-0.033%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 50, T2_max_inside 200, T2_min_outside = 10, T2_max_outside 50 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 23285 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0203263 Creating white distance volumes t=0.458435 (box.dx, box.dy, box.dz) = (128, 212, 308) (region->dx, region->dy, region->dz) = (128, 212, 308) (region->dx, region->dy, region->dz) = (128, 212, 308) Creating pial distance volumes t=0.842137 (box.dx, box.dy, box.dz) = (138, 220, 316) (region->dx, region->dy, region->dz) = (138, 220, 316) (region->dx, region->dy, region->dz) = (138, 220, 316) locating cortical regions not in interior range [50.0 --> 200.0], and not in exterior range [10.0 --> 50.0] t = 1.30987 Starting loop over 112475 vertices vno = 0, t = 1.30987 vno = 20000, t = 2.28903 vno = 40000, t = 3.18241 vno = 60000, t = 3.90271 vno = 80000, t = 4.65 vno = 100000, t = 5.47383 CPTL: t = 5.98086 76429 surface locations found to contain inconsistent values (19607 in, 56822 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=1.0, host=shark, nav=2, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 mom=0.00, dt=0.50 000: dt: 0.0000, sse=261958.3, rms=0.788 007: dt: 0.5000, sse=260767.3, rms=0.781 (0.804%) 008: dt: 0.5000, sse=258738.9, rms=0.780 (0.215%) rms = 0.7795/0.7796, sse=257557.7/258738.9, time step reduction 1 of 3 to 0.250 1 0 0 009: dt: 0.5000, sse=257557.7, rms=0.780 (0.002%) rms = 0.7797/0.7795, sse=256814.4/257557.7, time step reduction 2 of 3 to 0.125 1 0 0 010: dt: 0.2500, sse=256814.4, rms=0.780 (-0.018%) rms = 0.7796/0.7797, sse=256369.6/256814.4, time step reduction 3 of 3 to 0.062 1 0 0 011: dt: 0.1250, sse=256369.6, rms=0.780 (0.009%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 57 intersecting 001: 43 intersecting step 1 with no progress (num=44, old_num=43) 002: 44 intersecting 003: 43 intersecting step 1 with no progress (num=43, old_num=43) 004: 43 intersecting step 2 with no progress (num=43, old_num=43) 005: 43 intersecting step 3 with no progress (num=43, old_num=43) 006: 43 intersecting step 4 with no progress (num=43, old_num=43) 007: 43 intersecting step 5 with no progress (num=43, old_num=43) 008: 43 intersecting step 6 with no progress (num=43, old_num=43) 009: 43 intersecting step 7 with no progress (num=43, old_num=43) 010: 43 intersecting step 8 with no progress (num=43, old_num=43) 011: 43 intersecting step 9 with no progress (num=43, old_num=43) 012: 43 intersecting step 10 with no progress (num=43, old_num=43) 013: 43 intersecting step 11 with no progress (num=43, old_num=43) 014: 43 intersecting step 12 with no progress (num=43, old_num=43) 015: 43 intersecting step 13 with no progress (num=43, old_num=43) 016: 43 intersecting step 14 with no progress (num=43, old_num=43) 017: 43 intersecting step 15 with no progress (num=43, old_num=43) 018: 43 intersecting step 16 with no progress (num=43, old_num=43) terminating search with 43 intersecting Writing output to ../surf/rh.pial.T2 #ET# mris_place_surface 12.93 minutes #VMPC# mris_place_surfaces VmPeak 2321972 mris_place_surface done #@# white curv lh Mon Jan 9 13:51:50 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv #@# white area lh Mon Jan 9 13:51:51 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area #@# pial curv lh Mon Jan 9 13:51:52 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial #@# pial area lh Mon Jan 9 13:51:53 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial #@# thickness lh Mon Jan 9 13:51:54 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 115656 vertices processed 25000 of 115656 vertices processed 50000 of 115656 vertices processed 75000 of 115656 vertices processed 100000 of 115656 vertices processed 0 of 115656 vertices processed 25000 of 115656 vertices processed 50000 of 115656 vertices processed 75000 of 115656 vertices processed 100000 of 115656 vertices processed thickness calculation complete, 319:170 truncations. 43075 vertices at 0 distance 87251 vertices at 1 distance 57942 vertices at 2 distance 24414 vertices at 3 distance 10760 vertices at 4 distance 4634 vertices at 5 distance 1865 vertices at 6 distance 754 vertices at 7 distance 312 vertices at 8 distance 120 vertices at 9 distance 61 vertices at 10 distance 33 vertices at 11 distance 21 vertices at 12 distance 18 vertices at 13 distance 8 vertices at 14 distance 7 vertices at 15 distance 3 vertices at 16 distance 9 vertices at 17 distance 12 vertices at 18 distance 6 vertices at 19 distance 7 vertices at 20 distance writing curvature file ../surf/lh.thickness #@# area and vertex vol lh Mon Jan 9 13:52:14 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume Test lh /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.volume masking with /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Total face volume 196079 Total vertex volume 195876 (mask=0) #@# Test lh 195876 vertexvol Done #@# white curv rh Mon Jan 9 13:52:15 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv #@# white area rh Mon Jan 9 13:52:16 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area #@# pial curv rh Mon Jan 9 13:52:16 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial #@# pial area rh Mon Jan 9 13:52:17 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial #@# thickness rh Mon Jan 9 13:52:18 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 112475 vertices processed 25000 of 112475 vertices processed 50000 of 112475 vertices processed 75000 of 112475 vertices processed 100000 of 112475 vertices processed 0 of 112475 vertices processed 25000 of 112475 vertices processed 50000 of 112475 vertices processed 75000 of 112475 vertices processed 100000 of 112475 vertices processed thickness calculation complete, 362:333 truncations. 41408 vertices at 0 distance 80782 vertices at 1 distance 57018 vertices at 2 distance 25670 vertices at 3 distance 11101 vertices at 4 distance 4891 vertices at 5 distance 2068 vertices at 6 distance 847 vertices at 7 distance 385 vertices at 8 distance 234 vertices at 9 distance 109 vertices at 10 distance 67 vertices at 11 distance 46 vertices at 12 distance 55 vertices at 13 distance 36 vertices at 14 distance 39 vertices at 15 distance 31 vertices at 16 distance 46 vertices at 17 distance 32 vertices at 18 distance 32 vertices at 19 distance 53 vertices at 20 distance writing curvature file ../surf/rh.thickness #@# area and vertex vol rh Mon Jan 9 13:52:37 CET 2023 cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume Test rh /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.volume masking with /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Total face volume 193538 Total vertex volume 193328 (mask=0) #@# Test rh 193328 vertexvol Done #----------------------------------------- #@# Curvature Stats lh Mon Jan 9 13:52:38 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Test lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Test/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 222 ] Gb_filter = 0 #----------------------------------------- #@# Curvature Stats rh Mon Jan 9 13:52:39 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Test rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Test/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 192 ] Gb_filter = 0 WARN: S lookup min: -0.091699 WARN: S explicit min: 0.000000 vertex = 407 #-------------------------------------------- #@# Cortical ribbon mask Mon Jan 9 13:52:41 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon Test SUBJECTS_DIR is /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects loading input data... Running hemis serially Processing left hemi MRIcopyHeader(): source has ctab computing distance to left white surface MRIcopyHeader(): source has ctab computing distance to left pial surface Processing right hemi MRIcopyHeader(): source has ctab computing distance to right white surface MRIcopyHeader(): source has ctab computing distance to right pial surface hemi masks overlap voxels = 9 MRIcopyHeader(): source has ctab writing volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/ribbon.mgz mris_volmask took 2.21 minutes writing ribbon files MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab #----------------------------------------- #@# Cortical Parc 2 lh Mon Jan 9 13:54:53 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Mon Jan 9 13:54:53 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 329488 of (329488 329491) to complete... Waiting for PID 329491 of (329488 329491) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 45 labels changed using aseg relabeling using gibbs priors... 000: 7976 changed, 115656 examined... 001: 1824 changed, 31077 examined... 002: 541 changed, 9813 examined... 003: 237 changed, 3115 examined... 004: 109 changed, 1362 examined... 005: 49 changed, 627 examined... 006: 27 changed, 296 examined... 007: 17 changed, 165 examined... 008: 9 changed, 96 examined... 009: 6 changed, 51 examined... 010: 7 changed, 37 examined... 011: 3 changed, 38 examined... 012: 6 changed, 19 examined... 013: 1 changed, 28 examined... 014: 1 changed, 7 examined... 015: 0 changed, 7 examined... 14 labels changed using aseg 000: 209 total segments, 122 labels (1321 vertices) changed 001: 91 total segments, 6 labels (57 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 990 vertices marked for relabeling... 990 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 178 labels changed using aseg relabeling using gibbs priors... 000: 7515 changed, 112475 examined... 001: 1673 changed, 29767 examined... 002: 501 changed, 9052 examined... 003: 219 changed, 2888 examined... 004: 95 changed, 1265 examined... 005: 53 changed, 535 examined... 006: 39 changed, 284 examined... 007: 24 changed, 208 examined... 008: 10 changed, 132 examined... 009: 12 changed, 63 examined... 010: 8 changed, 55 examined... 011: 5 changed, 40 examined... 012: 1 changed, 22 examined... 013: 0 changed, 7 examined... 80 labels changed using aseg 000: 219 total segments, 132 labels (1573 vertices) changed 001: 92 total segments, 6 labels (64 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1250 vertices marked for relabeling... 1250 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 8 seconds. PIDs (329488 329491) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Mon Jan 9 13:55:02 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Mon Jan 9 13:55:02 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 329542 of (329542 329545) to complete... Waiting for PID 329545 of (329542 329545) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test lh ../surf/lh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 1520 labels changed using aseg relabeling using gibbs priors... 000: 1770 changed, 115656 examined... 001: 417 changed, 8403 examined... 002: 160 changed, 2309 examined... 003: 69 changed, 899 examined... 004: 30 changed, 385 examined... 005: 21 changed, 173 examined... 006: 14 changed, 118 examined... 007: 11 changed, 76 examined... 008: 12 changed, 68 examined... 009: 9 changed, 62 examined... 010: 6 changed, 45 examined... 011: 7 changed, 38 examined... 012: 6 changed, 35 examined... 013: 1 changed, 26 examined... 014: 1 changed, 8 examined... 015: 1 changed, 6 examined... 016: 0 changed, 8 examined... 356 labels changed using aseg 000: 44 total segments, 11 labels (352 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 502 vertices marked for relabeling... 502 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 7 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Test rh ../surf/rh.sphere.reg /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 1740 labels changed using aseg relabeling using gibbs priors... 000: 1691 changed, 112475 examined... 001: 408 changed, 7997 examined... 002: 127 changed, 2318 examined... 003: 58 changed, 718 examined... 004: 40 changed, 315 examined... 005: 22 changed, 209 examined... 006: 16 changed, 112 examined... 007: 12 changed, 84 examined... 008: 10 changed, 68 examined... 009: 6 changed, 57 examined... 010: 5 changed, 33 examined... 011: 6 changed, 30 examined... 012: 5 changed, 30 examined... 013: 4 changed, 31 examined... 014: 1 changed, 26 examined... 015: 2 changed, 7 examined... 016: 1 changed, 11 examined... 017: 0 changed, 7 examined... 369 labels changed using aseg 000: 40 total segments, 7 labels (250 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 821 vertices marked for relabeling... 821 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 6 seconds. PIDs (329542 329545) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Mon Jan 9 13:55:09 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts pctsurfcon --s Test --lh-only #----------------------------------------- #@# WM/GM Contrast rh Mon Jan 9 13:55:09 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts pctsurfcon --s Test --rh-only Waiting for PID 329594 of (329594 329597) to complete... Waiting for PID 329597 of (329594 329597) to complete... pctsurfcon --s Test --lh-only Log file is /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts/pctsurfcon.log Mon Jan 9 13:55:09 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/pctsurfcon pctsurfcon 7.2.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer mri_vol2surf --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329594/lh.wm.mgh --regheader Test --cortex srcvol = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00130 1.00000 -0.00069 -0.00003; 0.99519 0.00136 0.09800 0.00000; -0.09800 0.00056 0.99519 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Reading surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 67341 Masking with /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329594/lh.wm.mgh Dim: 115656 1 1 mri_vol2surf --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329594/lh.gm.mgh --projfrac 0.3 --regheader Test --cortex srcvol = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00130 1.00000 -0.00069 -0.00003; 0.99519 0.00136 0.09800 0.00000; -0.09800 0.00056 0.99519 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Reading surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Done reading source surface Reading thickness /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 76319 Masking with /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329594/lh.gm.mgh Dim: 115656 1 1 mri_concat /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329594/lh.wm.mgh /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329594/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.w-g.pct.mgh mri_segstats --in /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.w-g.pct.mgh --annot Test lh aparc --sum /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/stats/lh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.w-g.pct.mgh --annot Test lh aparc --sum /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/stats/lh.w-g.pct.stats --snr sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.annot Seg base 1000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.w-g.pct.mgh Vertex Area is 0.686525 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s Test --rh-only Log file is /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts/pctsurfcon.log Mon Jan 9 13:55:09 CET 2023 setenv SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects cd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/bin/pctsurfcon pctsurfcon 7.2.0 Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer mri_vol2surf --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329597/rh.wm.mgh --regheader Test --cortex srcvol = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00130 1.00000 -0.00069 -0.00003; 0.99519 0.00136 0.09800 0.00000; -0.09800 0.00056 0.99519 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Reading surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 65452 Masking with /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329597/rh.wm.mgh Dim: 112475 1 1 mri_vol2surf --mov /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329597/rh.gm.mgh --projfrac 0.3 --regheader Test --cortex srcvol = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/orig.mgz as target reference. -------- original matrix ----------- -0.00130 1.00000 -0.00069 -0.00003; 0.99519 0.00136 0.09800 0.00000; -0.09800 0.00056 0.99519 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Reading surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Done reading source surface Reading thickness /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 74104 Masking with /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329597/rh.gm.mgh Dim: 112475 1 1 mri_concat /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329597/rh.wm.mgh /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/tmp.pctsurfcon.329597/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.w-g.pct.mgh mri_segstats --in /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.w-g.pct.mgh --annot Test rh aparc --sum /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/stats/rh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.w-g.pct.mgh --annot Test rh aparc --sum /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/stats/rh.w-g.pct.stats --snr sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.annot Seg base 2000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.w-g.pct.mgh Vertex Area is 0.680842 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (329594 329597) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Mon Jan 9 13:55:12 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... MRIcopyHeader(): source has ctab 3119 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... MRIcopyHeader(): source has ctab 2159 voxels changed to hypointensity... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 4886 hypointense voxels neighboring cortex changed #----------------------------------------- #@# APas-to-ASeg Mon Jan 9 13:55:24 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/ribbon.mgz --threads 4 --lh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label --lh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white --lh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial --rh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label --rh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white --rh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects outvol aseg.mgz 64 avail.processors, using 4 Loading aseg.presurf.hypos.mgz MRIcopyHeader(): source has ctab Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/ribbon.mgz Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Done loading 0 128 64 192 1 65 193 2 66 194 3 67 195 129 4 68 196 5 69 197 6 7 198 70 8 199 71 130 9 200 72 10 201 73 11 202 74 12 203 131 75 13 204 76 14 205 77 15 206 78 132 16 207 79 17 208 80 18 209 19 81 210 133 20 211 82 21 212 83 22 213 134 84 214 23 85 215 24 216 135 86 25 217 26 87 218 27 88 219 28 136 220 29 89 221 30 90 222 31 223 91 32 137 224 33 92 225 34 226 35 93 227 36 138 94 228 37 229 38 95 39 230 139 40 231 96 41 232 140 42 233 97 43 234 44 235 98 141 45 236 46 237 99 142 47 238 48 100 239 49 143 240 50 101 241 51 144 242 52 102 53 243 145 54 103 244 55 146 245 56 104 246 57 147 247 105 58 248 148 59 249 106 60 250 149 61 107 251 62 150 108 252 63 253 151 109 254 255 110 152 111 153 112 154 113 155 156 114 157 115 158 116 159 160 117 161 118 162 119 163 164 120 165 121 166 167 122 168 123 169 170 124 171 125 172 173 126 174 175 127 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 225343 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 983104 mri_surf2volseg done mri_brainvol_stats Test ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1304106.0 #CBVS2 BrainSegVol 982594.0 #CBVS2 BrainSegVolNotVent 967625.0 #CBVS2 SupraTentVol 848107.0 #CBVS2 SupraTentVolNotVent 833138.0 #CBVS2 lhCtxGM 195718.3 #CBVS2 rhCtxGM 193155.3 #CBVS2 lhCerebralWM 198451.5 #CBVS2 rhCerebralWM 193771.5 #CBVS2 SubCortGMVol 52973.0 #CBVS2 CerebellumVol 134487.0 #CBVS2 CerebellumGMVol 107949.0 #CBVS2 VentChorVol 12523.0 #CBVS2 3rd4th5thCSF 2446.0 #CBVS2 AllCSF 14969.0 #CBVS2 CCVol 6469.0 #----------------------------------------- #@# AParc-to-ASeg aparc Mon Jan 9 13:55:30 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.annot 1000 --lh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label --lh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white --lh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial --rh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.annot 2000 --rh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label --rh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white --rh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects outvol aparc+aseg.mgz 64 avail.processors, using 4 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8224 vertices from lh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.annot Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7710 vertices from rh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.annot Done loading 0 192 64 128 1 65 2 66 193 3 67 194 4 68 195 5 69 6 196 7 197 70 8 198 9 199 71 10 200 11 201 72 12 202 13 203 14 204 15 205 16 206 17 207 18 208 73 19 209 20 210 21 211 22 212 23 213 24 214 25 215 26 216 27 217 28 218 74 29 219 30 220 31 221 32 222 33 223 34 224 35 225 36 226 37 227 38 228 39 229 40 230 41 231 75 42 232 43 233 44 234 45 235 46 236 47 237 48 238 49 239 50 240 51 241 52 242 53 243 54 244 55 245 56 246 76 57 247 58 248 59 249 60 250 61 251 62 252 63 253 254 255 129 77 78 79 130 80 81 131 82 83 132 84 133 85 134 86 135 87 136 88 137 89 138 90 91 139 92 140 93 94 141 95 142 96 97 143 144 98 145 99 146 100 147 101 148 149 102 150 103 151 152 104 153 105 154 106 155 107 156 108 157 109 158 110 159 111 112 160 113 161 114 115 162 116 163 117 118 164 119 165 120 121 166 122 123 167 124 168 125 169 126 170 127 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 387941 ndotcheck = 12038 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 967148 mri_surf2volseg done #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Mon Jan 9 13:55:59 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label --lh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white --lh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial --rh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label --rh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white --rh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects outvol aparc.a2009s+aseg.mgz 64 avail.processors, using 4 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8224 vertices from lh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.a2009s.annot Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7710 vertices from rh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.a2009s.annot Done loading 0 64 192 128 1 65 2 66 193 3 67 4 194 68 5 195 69 6 196 7 70 197 8 198 9 71 199 10 200 11 72 201 12 202 13 203 14 204 15 205 16 206 17 207 18 208 73 19 209 20 210 21 211 22 212 23 213 24 214 25 215 26 216 27 217 28 218 29 74 219 30 220 31 221 32 222 33 223 34 224 35 225 36 37 226 38 227 228 39 229 40 230 41 75 231 42 232 43 233 44 234 45 235 46 236 47 237 48 238 49 239 50 240 51 241 52 242 53 243 54 244 55 245 56 246 57 76 247 58 248 59 249 60 250 61 251 62 252 63 253 254 129 255 77 78 79 130 80 81 131 82 132 83 84 133 85 134 86 135 136 87 88 137 89 138 90 91 139 92 140 93 94 141 95 142 96 97 143 98 144 99 145 146 100 147 101 148 149 102 150 103 151 152 104 153 105 154 106 155 107 156 108 157 109 110 158 111 159 112 160 113 114 161 115 162 116 163 117 118 164 119 120 165 121 122 166 123 167 124 125 168 126 169 127 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 387941 ndotcheck = 12038 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 967236 mri_surf2volseg done #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Mon Jan 9 13:56:29 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label --lh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white --lh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial --rh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label --rh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white --rh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects outvol aparc.DKTatlas+aseg.mgz 64 avail.processors, using 4 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8224 vertices from lh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.DKTatlas.annot Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7710 vertices from rh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.DKTatlas.annot Done loading 0 64 128 192 1 65 2 66 193 3 67 4 68 194 5 69 195 6 7 196 70 8 197 9 198 71 10 199 11 200 72 12 201 13 202 14 203 15 204 16 205 17 206 18 207 19 73 208 20 209 21 210 22 211 23 212 24 213 25 214 26 215 27 216 28 217 29 74 218 30 219 31 220 32 221 33 222 34 223 35 224 36 225 37 226 38 227 39 228 40 229 41 230 42 75 231 43 232 44 233 45 234 46 235 47 236 48 237 49 238 50 239 51 240 52 241 53 242 54 243 55 244 56 245 57 246 76 58 247 59 248 60 249 61 250 62 251 63 252 253 129 254 255 77 78 79 130 80 81 131 82 83 132 84 133 85 134 86 135 87 136 88 137 89 138 90 91 139 92 140 93 94 141 95 142 96 97 143 98 144 99 145 146 100 147 101 148 149 102 150 103 151 152 104 153 105 154 106 155 107 156 108 157 109 158 110 111 159 112 160 113 161 114 115 162 116 163 117 118 164 119 120 165 121 166 122 123 167 124 168 125 169 126 127 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 387941 ndotcheck = 12038 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 967140 mri_surf2volseg done #----------------------------------------- #@# WMParc Mon Jan 9 13:56:58 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 4 --lh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.annot 3000 --lh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label --lh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white --lh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial --rh-annot /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.annot 4000 --rh-cortex-mask /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label --rh-white /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white --rh-pial /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects outvol wmparc.mgz 64 avail.processors, using 4 Loading aparc+aseg.mgz MRIcopyHeader(): source has ctab Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8224 vertices from lh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.aparc.annot Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7710 vertices from rh hemi Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.aparc.annot Done loading 0 128 192 64 1 193 65 2 194 66 3 195 67 4 196 68 5 197 69 6 198 70 7 199 8 71 9 200 72 10 201 73 11 202 74 12 203 13 204 75 14 205 15 206 16 207 76 17 208 18 209 19 210 77 20 211 129 21 212 22 213 78 23 214 215 24 216 25 217 26 79 218 27 219 28 220 29 221 30 222 31 80 223 32 33 224 34 225 130 35 226 36 227 81 37 228 38 229 39 230 40 231 232 41 82 233 42 234 43 235 44 236 45 131 237 46 238 47 83 239 48 240 49 241 50 242 132 51 243 52 244 53 84 245 54 133 246 55 247 56 248 57 249 58 250 59 85 251 60 252 61 253 62 254 63 255 134 86 87 135 88 89 136 90 91 137 92 138 93 94 139 95 140 96 97 141 98 142 99 100 143 101 144 102 103 145 104 146 105 106 147 107 148 108 109 149 110 111 150 112 113 151 114 152 115 116 153 117 154 118 155 119 156 120 121 157 122 123 158 124 125 159 126 127 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 385754 ndotcheck = 4943 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 967148 mri_surf2volseg done mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Test --surf-wm-vol --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.2.0 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Test --surf-wm-vol --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Reporting on 70 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# Parcellation Stats lh Mon Jan 9 14:00:24 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Test lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Test lh pial #----------------------------------------- #@# Parcellation Stats rh Mon Jan 9 14:00:24 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Test rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Test rh pial Waiting for PID 330256 of (330256 330259 330262 330265) to complete... Waiting for PID 330259 of (330256 330259 330262 330265) to complete... Waiting for PID 330262 of (330256 330259 330262 330265) to complete... Waiting for PID 330265 of (330256 330259 330262 330265) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Test lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 196079 Total vertex volume 195876 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 1218 823 1858 2.464 0.539 0.102 0.019 6 1.0 bankssts 886 630 1176 2.093 0.447 0.140 0.029 10 1.2 caudalanteriorcingulate 2376 1604 4602 2.788 0.445 0.107 0.020 19 1.9 caudalmiddlefrontal 1943 1340 2435 1.956 0.558 0.166 0.057 36 4.9 cuneus 390 273 795 2.444 0.889 0.125 0.035 3 0.6 entorhinal 3560 2590 6533 2.605 0.720 0.133 0.032 44 4.7 fusiform 5543 3767 9594 2.600 0.557 0.127 0.028 65 6.9 inferiorparietal 3433 2459 7732 2.969 0.589 0.124 0.026 41 3.5 inferiortemporal 1322 803 1704 2.094 0.713 0.145 0.055 31 3.5 isthmuscingulate 6714 4619 10889 2.290 0.683 0.151 0.044 106 12.8 lateraloccipital 3364 2401 7039 2.971 0.707 0.125 0.029 42 3.9 lateralorbitofrontal 3506 2705 5301 2.071 0.648 0.171 0.049 64 7.6 lingual 2416 1745 5342 2.837 0.790 0.130 0.033 40 3.4 medialorbitofrontal 3763 2684 8011 2.649 0.572 0.123 0.024 43 3.6 middletemporal 529 373 625 1.700 0.636 0.141 0.046 7 1.1 parahippocampal 2298 1442 3220 2.329 0.615 0.115 0.035 22 3.4 paracentral 2173 1567 4248 2.561 0.515 0.125 0.027 27 2.4 parsopercularis 785 596 2162 3.064 0.673 0.157 0.042 15 1.4 parsorbitalis 1599 1143 3389 2.835 0.507 0.117 0.026 15 1.5 parstriangularis 1322 991 1505 1.846 0.510 0.158 0.058 23 3.2 pericalcarine 5121 3318 7750 2.205 0.607 0.117 0.030 52 6.1 postcentral 1230 877 1531 2.054 0.636 0.137 0.034 17 1.8 posteriorcingulate 6176 4145 11335 2.722 0.640 0.123 0.034 61 8.5 precentral 4789 3369 7299 2.362 0.517 0.126 0.029 57 5.6 precuneus 835 592 1544 2.618 0.635 0.126 0.031 9 1.1 rostralanteriorcingulate 5997 4314 12687 2.789 0.489 0.136 0.032 80 7.9 rostralmiddlefrontal 9762 6650 20300 2.911 0.511 0.118 0.024 98 9.5 superiorfrontal 8303 5307 12397 2.333 0.583 0.122 0.034 106 11.5 superiorparietal 5931 4056 12509 2.836 0.676 0.113 0.025 60 6.3 superiortemporal 5464 3818 10276 2.633 0.489 0.113 0.023 54 4.8 supramarginal 316 238 945 3.244 0.569 0.158 0.062 8 0.7 frontalpole 557 413 2135 3.623 0.766 0.135 0.037 8 0.9 temporalpole 704 494 1074 2.196 0.606 0.142 0.049 9 1.3 transversetemporal 3107 2101 5935 2.943 0.797 0.122 0.040 36 5.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Test lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 196079 Total vertex volume 195876 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 1218 680 1858 2.464 0.539 0.087 0.022 14 0.9 bankssts 886 578 1176 2.093 0.447 0.103 0.020 22 0.6 caudalanteriorcingulate 2376 1658 4602 2.788 0.445 0.113 0.026 64 1.9 caudalmiddlefrontal 1943 1251 2435 1.956 0.558 0.089 0.022 22 1.3 cuneus 390 373 795 2.444 0.889 0.178 0.039 8 0.6 entorhinal 3560 2549 6533 2.605 0.720 0.107 0.025 59 3.0 fusiform 5543 3687 9594 2.600 0.557 0.107 0.024 98 4.7 inferiorparietal 3433 2781 7732 2.969 0.589 0.114 0.023 66 2.9 inferiortemporal 1322 856 1704 2.094 0.713 0.111 0.037 228 2.1 isthmuscingulate 6714 4740 10889 2.290 0.683 0.105 0.024 154 5.6 lateraloccipital 3364 2413 7039 2.971 0.707 0.107 0.025 66 3.1 lateralorbitofrontal 3506 2573 5301 2.071 0.648 0.117 0.030 72 3.6 lingual 2416 1970 5342 2.837 0.790 0.108 0.020 34 1.5 medialorbitofrontal 3763 3267 8011 2.649 0.572 0.119 0.024 53 3.2 middletemporal 529 408 625 1.700 0.636 0.125 0.035 7 0.5 parahippocampal 2298 1388 3220 2.329 0.615 0.079 0.014 28 1.3 paracentral 2173 1786 4248 2.561 0.515 0.114 0.020 21 1.7 parsopercularis 785 796 2162 3.064 0.673 0.132 0.021 16 0.7 parsorbitalis 1599 1251 3389 2.835 0.507 0.116 0.022 32 1.2 parstriangularis 1322 683 1505 1.846 0.510 0.093 0.031 22 1.0 pericalcarine 5121 3717 7750 2.205 0.607 0.091 0.015 37 2.6 postcentral 1230 715 1531 2.054 0.636 0.103 0.031 35 1.2 posteriorcingulate 6176 4124 11335 2.722 0.640 0.092 0.019 113 3.9 precentral 4789 2958 7299 2.362 0.517 0.097 0.019 66 3.4 precuneus 835 613 1544 2.618 0.635 0.097 0.022 7 0.5 rostralanteriorcingulate 5997 4664 12687 2.789 0.489 0.124 0.026 127 6.4 rostralmiddlefrontal 9762 7293 20300 2.911 0.511 0.107 0.021 137 7.2 superiorfrontal 8303 5221 12397 2.333 0.583 0.092 0.018 122 5.2 superiorparietal 5931 4662 12509 2.836 0.676 0.103 0.018 82 4.0 superiortemporal 5464 4019 10276 2.633 0.489 0.102 0.018 58 3.4 supramarginal 316 347 945 3.244 0.569 0.143 0.030 3 0.3 frontalpole 557 770 2135 3.623 0.766 0.168 0.021 4 0.6 temporalpole 704 495 1074 2.196 0.606 0.079 0.017 3 0.3 transversetemporal 3107 1789 5935 2.943 0.797 0.094 0.028 81 2.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Test rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 193538 Total vertex volume 193328 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 1117 774 1796 2.699 0.483 0.111 0.021 7 0.9 bankssts 916 614 1434 2.273 0.556 0.134 0.028 14 1.1 caudalanteriorcingulate 2443 1675 5136 2.855 0.482 0.099 0.017 21 1.8 caudalmiddlefrontal 2588 1708 3107 1.854 0.511 0.159 0.061 48 6.8 cuneus 358 257 896 2.978 0.780 0.123 0.029 3 0.4 entorhinal 2899 2081 6414 2.953 0.747 0.132 0.031 46 3.9 fusiform 5760 4061 10518 2.548 0.527 0.125 0.026 62 6.1 inferiorparietal 3117 2162 7686 3.212 0.643 0.111 0.024 33 3.1 inferiortemporal 1042 688 1309 2.086 0.572 0.153 0.055 20 2.6 isthmuscingulate 6739 4607 11031 2.416 0.660 0.149 0.041 101 12.3 lateraloccipital 3124 2152 6564 2.896 0.767 0.129 0.037 47 5.1 lateralorbitofrontal 3995 2775 5778 2.121 0.774 0.172 0.062 100 10.2 lingual 2265 1598 4910 2.954 0.732 0.126 0.035 30 3.0 medialorbitofrontal 3672 2663 8677 2.922 0.757 0.123 0.026 44 4.1 middletemporal 854 558 1619 2.737 0.792 0.088 0.019 4 0.6 parahippocampal 2320 1387 3107 2.315 0.652 0.135 0.051 47 5.2 paracentral 1547 1043 2964 2.851 0.421 0.106 0.021 14 1.3 parsopercularis 918 669 2299 2.856 0.634 0.137 0.036 15 1.3 parsorbitalis 1785 1222 3659 2.769 0.571 0.116 0.023 16 1.6 parstriangularis 1648 1311 1919 1.767 0.539 0.185 0.064 28 5.0 pericalcarine 5205 3537 8223 2.213 0.610 0.123 0.032 59 7.0 postcentral 1026 696 1282 2.111 0.631 0.128 0.029 12 1.3 posteriorcingulate 5963 4015 11129 2.702 0.638 0.120 0.031 59 7.9 precentral 5839 3879 8416 2.326 0.631 0.126 0.037 83 8.2 precuneus 619 425 1205 2.957 0.794 0.138 0.031 8 0.9 rostralanteriorcingulate 5749 4042 12460 2.870 0.541 0.127 0.030 75 6.8 rostralmiddlefrontal 8203 5591 17236 2.895 0.490 0.116 0.025 88 8.7 superiorfrontal 8246 5413 12652 2.321 0.577 0.123 0.031 103 11.2 superiorparietal 5159 3513 10703 2.816 0.600 0.113 0.026 52 6.0 superiortemporal 4813 3344 9411 2.722 0.550 0.124 0.029 52 5.7 supramarginal 371 255 1099 3.273 0.493 0.150 0.049 7 0.8 frontalpole 576 408 2287 3.885 0.725 0.136 0.036 8 0.9 temporalpole 521 325 652 2.094 0.524 0.150 0.045 8 1.0 transversetemporal 3368 2204 5751 2.693 0.858 0.119 0.037 38 4.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Test rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 193538 Total vertex volume 193328 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 1117 562 1796 2.699 0.483 0.096 0.025 28 0.7 bankssts 916 662 1434 2.273 0.556 0.104 0.025 22 0.6 caudalanteriorcingulate 2443 1861 5136 2.855 0.482 0.101 0.020 42 1.8 caudalmiddlefrontal 2588 1747 3107 1.854 0.511 0.095 0.022 34 2.1 cuneus 358 333 896 2.978 0.780 0.152 0.044 6 0.4 entorhinal 2899 2289 6414 2.953 0.747 0.123 0.029 78 3.3 fusiform 5760 4219 10518 2.548 0.527 0.106 0.025 89 4.3 inferiorparietal 3117 2652 7686 3.212 0.643 0.118 0.024 57 2.6 inferiortemporal 1042 670 1309 2.086 0.572 0.100 0.032 12 1.0 isthmuscingulate 6739 4627 11031 2.416 0.660 0.100 0.022 90 5.1 lateraloccipital 3124 2318 6564 2.896 0.767 0.116 0.030 58 3.3 lateralorbitofrontal 3995 2856 5778 2.121 0.774 0.136 0.050 107 7.8 lingual 2265 1712 4910 2.954 0.732 0.096 0.020 32 1.3 medialorbitofrontal 3672 3206 8677 2.922 0.757 0.116 0.022 93 2.7 middletemporal 854 630 1619 2.737 0.792 0.097 0.019 8 0.6 parahippocampal 2320 1325 3107 2.315 0.652 0.101 0.036 56 2.3 paracentral 1547 1074 2964 2.851 0.421 0.094 0.019 19 1.1 parsopercularis 918 910 2299 2.856 0.634 0.139 0.024 14 0.8 parsorbitalis 1785 1405 3659 2.769 0.571 0.114 0.021 26 1.5 parstriangularis 1648 967 1919 1.767 0.539 0.099 0.027 23 1.3 pericalcarine 5205 3942 8223 2.213 0.610 0.096 0.017 66 2.9 postcentral 1026 616 1282 2.111 0.631 0.098 0.032 15 0.7 posteriorcingulate 5963 4140 11129 2.702 0.638 0.093 0.020 90 4.4 precentral 5839 3485 8416 2.326 0.631 0.102 0.034 122 7.3 precuneus 619 427 1205 2.957 0.794 0.108 0.024 17 0.4 rostralanteriorcingulate 5749 4539 12460 2.870 0.541 0.120 0.026 121 5.1 rostralmiddlefrontal 8203 6314 17236 2.895 0.490 0.111 0.023 118 5.8 superiorfrontal 8246 5524 12652 2.321 0.577 0.091 0.017 84 4.8 superiorparietal 5159 4013 10703 2.816 0.600 0.099 0.017 52 3.3 superiortemporal 4813 3516 9411 2.722 0.550 0.106 0.022 62 3.7 supramarginal 371 427 1099 3.273 0.493 0.131 0.028 2 0.4 frontalpole 576 764 2287 3.885 0.725 0.155 0.022 4 0.6 temporalpole 521 327 652 2.094 0.524 0.084 0.019 4 0.3 transversetemporal 3368 1944 5751 2.693 0.858 0.103 0.030 87 2.8 insula PIDs (330256 330259 330262 330265) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Jan 9 14:00:29 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Test lh white #----------------------------------------- #@# Parcellation Stats 2 rh Mon Jan 9 14:00:29 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Test rh white Waiting for PID 330325 of (330325 330328) to complete... Waiting for PID 330328 of (330325 330328) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Test lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 196079 Total vertex volume 195876 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 1039 772 2359 2.977 0.624 0.152 0.037 15 1.6 G_and_S_frontomargin 1430 1128 3724 2.928 0.531 0.144 0.032 20 1.9 G_and_S_occipital_inf 1848 1091 2588 2.152 0.676 0.126 0.043 27 3.4 G_and_S_paracentral 1286 918 2453 2.610 0.506 0.137 0.037 15 2.0 G_and_S_subcentral 648 455 1635 2.874 0.501 0.144 0.045 14 1.2 G_and_S_transv_frontopol 1971 1414 3689 2.790 0.547 0.115 0.023 16 1.8 G_and_S_cingul-Ant 1036 705 1531 2.576 0.641 0.108 0.019 8 0.9 G_and_S_cingul-Mid-Ant 1221 848 1695 2.422 0.687 0.124 0.028 11 1.4 G_and_S_cingul-Mid-Post 454 339 875 2.338 0.725 0.152 0.034 7 0.5 G_cingul-Post-dorsal 420 207 524 2.153 0.639 0.161 0.091 18 2.0 G_cingul-Post-ventral 1846 1220 2326 1.878 0.555 0.165 0.062 35 5.0 G_cuneus 1134 830 2571 2.611 0.474 0.131 0.034 16 1.3 G_front_inf-Opercular 444 328 1223 2.830 0.412 0.144 0.037 8 0.7 G_front_inf-Orbital 945 678 2373 2.903 0.566 0.133 0.030 13 1.2 G_front_inf-Triangul 2704 1921 7201 2.958 0.458 0.137 0.032 40 3.2 G_front_middle 6779 4638 15328 2.921 0.556 0.127 0.029 85 7.6 G_front_sup 671 463 1411 2.965 0.903 0.151 0.061 12 1.6 G_Ins_lg_and_S_cent_ins 551 394 1734 3.545 0.786 0.135 0.046 8 1.2 G_insular_short 1719 1099 3081 2.442 0.567 0.148 0.040 31 3.2 G_occipital_middle 1882 1130 1962 1.829 0.515 0.153 0.057 36 4.5 G_occipital_sup 1535 1158 2993 2.436 0.745 0.149 0.043 25 2.6 G_oc-temp_lat-fusifor 2278 1810 3687 2.009 0.671 0.181 0.053 48 5.2 G_oc-temp_med-Lingual 698 489 1248 2.130 0.870 0.134 0.040 9 1.2 G_oc-temp_med-Parahip 2030 1550 5560 3.005 0.790 0.150 0.042 42 3.3 G_orbital 2366 1603 4973 2.639 0.596 0.142 0.037 43 3.8 G_pariet_inf-Angular 2377 1714 5405 2.690 0.518 0.122 0.027 30 2.4 G_pariet_inf-Supramar 3081 1916 5678 2.417 0.614 0.123 0.037 55 4.8 G_parietal_sup 1861 1075 3253 2.357 0.648 0.110 0.029 20 2.1 G_postcentral 2251 1377 5231 2.937 0.573 0.117 0.031 26 2.6 G_precentral 2533 1783 4240 2.257 0.505 0.140 0.035 41 3.5 G_precuneus 737 551 2106 2.879 0.543 0.136 0.035 17 1.1 G_rectus 576 380 1102 2.584 1.079 0.121 0.054 7 1.0 G_subcallosal 481 334 782 2.094 0.519 0.121 0.043 5 0.6 G_temp_sup-G_T_transv 2123 1483 6095 3.132 0.698 0.141 0.034 39 2.8 G_temp_sup-Lateral 775 530 1729 2.698 0.696 0.080 0.019 3 0.6 G_temp_sup-Plan_polar 830 572 1718 2.829 0.642 0.099 0.021 5 0.6 G_temp_sup-Plan_tempo 1746 1293 4672 2.975 0.582 0.133 0.032 29 1.9 G_temporal_inf 2042 1484 5286 2.808 0.584 0.130 0.027 28 2.1 G_temporal_middle 243 173 385 2.659 0.371 0.101 0.021 1 0.2 Lat_Fis-ant-Horizont 328 257 647 2.468 0.666 0.123 0.029 4 0.3 Lat_Fis-ant-Vertical 1115 743 1379 2.368 0.658 0.113 0.029 9 1.4 Lat_Fis-post 1739 1140 2341 1.974 0.598 0.154 0.053 30 3.7 Pole_occipital 1302 975 3938 3.278 0.697 0.135 0.033 17 1.8 Pole_temporal 1669 1268 2088 1.972 0.564 0.160 0.053 28 3.7 S_calcarine 2636 1945 3203 2.040 0.651 0.137 0.041 25 4.5 S_central 1129 783 1530 2.427 0.510 0.111 0.025 9 1.3 S_cingul-Marginalis 481 324 895 3.387 0.444 0.083 0.014 2 0.3 S_circular_insula_ant 1457 970 2073 2.710 0.582 0.100 0.025 9 1.7 S_circular_insula_inf 1573 1057 2194 2.737 0.491 0.111 0.024 8 1.7 S_circular_insula_sup 553 373 923 3.124 0.622 0.106 0.015 3 0.4 S_collat_transv_ant 480 333 601 2.143 0.726 0.123 0.032 4 0.7 S_collat_transv_post 1683 1126 2287 2.449 0.393 0.099 0.018 10 1.2 S_front_inf 1389 999 2506 2.741 0.447 0.131 0.030 16 1.8 S_front_middle 2371 1625 3926 2.699 0.374 0.103 0.020 15 2.1 S_front_sup 470 314 584 2.326 0.268 0.094 0.012 2 0.3 S_interm_prim-Jensen 3493 2351 4678 2.470 0.437 0.102 0.017 20 2.5 S_intrapariet_and_P_trans 837 619 1221 2.304 0.518 0.159 0.039 12 1.6 S_oc_middle_and_Lunatus 1502 1031 1941 2.332 0.559 0.126 0.035 13 2.1 S_oc_sup_and_transversal 462 347 715 2.394 0.741 0.158 0.033 5 0.7 S_occipital_ant 884 625 1465 2.964 0.450 0.114 0.019 6 0.8 S_oc-temp_lat 1896 1319 2497 2.311 0.675 0.123 0.031 17 2.5 S_oc-temp_med_and_Lingual 196 148 322 2.620 0.329 0.152 0.024 2 0.3 S_orbital_lateral 632 421 900 2.421 0.731 0.131 0.039 14 1.1 S_orbital_med-olfact 1181 819 2239 3.124 0.522 0.117 0.024 10 1.2 S_orbital-H_Shaped 1603 1106 2049 2.298 0.555 0.118 0.028 13 2.0 S_parieto_occipital 944 599 716 1.709 0.468 0.152 0.045 18 2.0 S_pericallosal 2536 1716 3614 2.490 0.456 0.107 0.021 16 2.1 S_postcentral 1265 851 1972 2.693 0.408 0.106 0.019 8 1.1 S_precentral-inf-part 1342 902 2098 2.966 0.332 0.094 0.014 6 0.9 S_precentral-sup-part 488 352 877 2.977 0.865 0.120 0.017 4 0.4 S_suborbital 810 560 1243 2.698 0.433 0.118 0.022 6 0.8 S_subparietal 893 614 1330 2.595 0.419 0.117 0.016 7 0.7 S_temporal_inf 5049 3454 7784 2.609 0.565 0.111 0.022 36 4.7 S_temporal_sup 453 321 674 2.422 0.480 0.127 0.023 4 0.5 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Test rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 193538 Total vertex volume 193328 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 584 420 1412 3.345 0.521 0.137 0.031 8 0.7 G_and_S_frontomargin 1092 788 2335 2.780 0.724 0.146 0.030 15 1.5 G_and_S_occipital_inf 1478 838 2187 2.280 0.724 0.147 0.056 40 3.7 G_and_S_paracentral 1296 922 2695 2.694 0.581 0.127 0.031 13 1.7 G_and_S_subcentral 795 566 2217 3.064 0.505 0.130 0.039 10 1.4 G_and_S_transv_frontopol 2088 1490 3928 2.897 0.648 0.118 0.026 19 2.4 G_and_S_cingul-Ant 1212 823 2014 2.662 0.577 0.111 0.025 12 1.2 G_and_S_cingul-Mid-Ant 1135 777 1589 2.308 0.649 0.120 0.029 13 1.5 G_and_S_cingul-Mid-Post 379 253 606 2.382 0.770 0.149 0.043 7 0.6 G_cingul-Post-dorsal 265 150 394 2.138 0.548 0.117 0.047 3 0.4 G_cingul-Post-ventral 2266 1521 2756 1.785 0.514 0.164 0.065 44 6.2 G_cuneus 1124 781 2686 2.782 0.431 0.115 0.026 14 1.2 G_front_inf-Opercular 219 153 602 2.932 0.529 0.131 0.027 2 0.2 G_front_inf-Orbital 624 433 1625 2.903 0.548 0.128 0.029 10 0.7 G_front_inf-Triangul 2517 1809 6966 2.944 0.515 0.132 0.031 45 2.9 G_front_middle 5351 3596 12442 2.916 0.522 0.128 0.030 73 6.7 G_front_sup 512 347 1110 2.895 0.977 0.137 0.047 7 1.1 G_Ins_lg_and_S_cent_ins 641 435 1637 2.950 0.974 0.131 0.040 9 0.9 G_insular_short 1838 1280 3869 2.505 0.585 0.140 0.033 28 2.4 G_occipital_middle 1826 1117 2365 2.000 0.610 0.142 0.049 31 3.8 G_occipital_sup 1105 808 2926 3.110 0.785 0.156 0.044 28 2.1 G_oc-temp_lat-fusifor 2654 1790 3982 2.032 0.752 0.171 0.069 77 7.1 G_oc-temp_med-Lingual 1303 848 2706 2.746 0.838 0.119 0.036 18 1.7 G_oc-temp_med-Parahip 2323 1635 6278 3.021 0.750 0.140 0.042 51 3.8 G_orbital 2495 1819 5820 2.655 0.471 0.140 0.029 38 2.8 G_pariet_inf-Angular 2206 1570 5021 2.783 0.599 0.132 0.033 30 3.0 G_pariet_inf-Supramar 2997 1894 5067 2.298 0.535 0.121 0.030 42 3.6 G_parietal_sup 2008 1260 3521 2.279 0.619 0.125 0.035 28 2.6 G_postcentral 2035 1246 4791 2.872 0.615 0.108 0.027 21 2.0 G_precentral 2862 1861 4415 2.191 0.659 0.137 0.046 60 4.6 G_precuneus 702 482 1840 2.983 0.680 0.123 0.039 11 1.0 G_rectus 413 286 803 2.742 0.899 0.151 0.066 8 1.0 G_subcallosal 447 273 627 2.144 0.574 0.175 0.051 9 1.1 G_temp_sup-G_T_transv 1677 1176 4774 3.121 0.564 0.133 0.036 23 2.6 G_temp_sup-Lateral 657 444 1429 2.949 0.796 0.075 0.016 2 0.4 G_temp_sup-Plan_polar 746 524 1525 2.689 0.514 0.130 0.033 9 1.0 G_temp_sup-Plan_tempo 1608 1118 4527 3.182 0.660 0.122 0.029 23 2.0 G_temporal_inf 2072 1568 5768 2.979 0.804 0.141 0.031 34 2.8 G_temporal_middle 412 276 710 2.542 0.570 0.108 0.022 3 0.4 Lat_Fis-ant-Horizont 187 130 315 2.731 0.419 0.096 0.014 1 0.1 Lat_Fis-ant-Vertical 1323 884 1772 2.657 0.601 0.102 0.021 7 1.2 Lat_Fis-post 3307 2287 4587 2.084 0.636 0.178 0.064 68 9.7 Pole_occipital 1389 1039 5010 3.571 0.675 0.138 0.035 26 2.0 Pole_temporal 1755 1321 2081 1.907 0.578 0.167 0.052 26 4.2 S_calcarine 2561 1920 3143 2.061 0.648 0.148 0.045 32 5.5 S_central 1058 724 1389 2.385 0.510 0.123 0.035 12 1.6 S_cingul-Marginalis 638 425 869 2.456 0.770 0.121 0.036 5 1.2 S_circular_insula_ant 1116 718 1391 2.295 0.588 0.082 0.016 5 0.8 S_circular_insula_inf 1183 772 1755 2.866 0.692 0.097 0.024 5 1.1 S_circular_insula_sup 739 514 1398 2.961 0.678 0.096 0.014 3 0.5 S_collat_transv_ant 502 339 668 2.754 0.498 0.124 0.026 4 0.7 S_collat_transv_post 1382 947 2030 2.523 0.411 0.108 0.019 10 1.1 S_front_inf 1713 1194 3459 2.924 0.501 0.120 0.027 16 1.8 S_front_middle 2338 1594 3922 2.763 0.362 0.094 0.017 14 1.7 S_front_sup 448 296 624 2.469 0.468 0.104 0.023 2 0.4 S_interm_prim-Jensen 2962 2057 4456 2.604 0.526 0.119 0.024 27 3.2 S_intrapariet_and_P_trans 740 519 936 2.368 0.577 0.115 0.024 5 0.8 S_oc_middle_and_Lunatus 1146 810 1484 2.400 0.449 0.126 0.028 10 1.4 S_oc_sup_and_transversal 449 296 672 2.858 0.414 0.099 0.023 2 0.4 S_occipital_ant 705 484 1197 3.367 0.532 0.109 0.022 4 0.7 S_oc-temp_lat 1357 934 2103 2.624 0.729 0.105 0.019 9 1.1 S_oc-temp_med_and_Lingual 358 248 636 2.740 0.494 0.108 0.024 4 0.4 S_orbital_lateral 580 403 1034 2.888 0.766 0.129 0.036 6 0.7 S_orbital_med-olfact 1098 750 1948 2.901 0.693 0.120 0.026 9 1.4 S_orbital-H_Shaped 2287 1525 2926 2.391 0.500 0.108 0.020 15 2.3 S_parieto_occipital 743 455 608 1.924 0.486 0.173 0.054 18 2.0 S_pericallosal 2354 1626 3311 2.324 0.507 0.113 0.024 18 2.6 S_postcentral 1497 1008 2274 2.764 0.441 0.102 0.017 8 1.1 S_precentral-inf-part 1136 746 1636 2.856 0.391 0.086 0.013 4 0.7 S_precentral-sup-part 341 241 574 2.927 0.599 0.133 0.020 3 0.3 S_suborbital 1165 832 1603 2.407 0.663 0.150 0.049 16 2.6 S_subparietal 780 546 1381 2.959 0.636 0.117 0.020 5 0.8 S_temporal_inf 5197 3501 7804 2.629 0.559 0.101 0.018 30 4.1 S_temporal_sup 267 190 367 2.423 0.432 0.167 0.045 6 0.6 S_temporal_transverse PIDs (330325 330328) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Jan 9 14:00:34 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Test lh white #----------------------------------------- #@# Parcellation Stats 3 rh Mon Jan 9 14:00:34 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Test rh white Waiting for PID 330382 of (330382 330385) to complete... Waiting for PID 330385 of (330382 330385) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Test lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 196079 Total vertex volume 195876 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 1534 1045 2225 2.407 0.592 0.126 0.027 16 1.8 caudalanteriorcingulate 2473 1678 4808 2.797 0.451 0.107 0.020 19 2.0 caudalmiddlefrontal 2674 1768 3296 1.993 0.574 0.153 0.053 43 6.2 cuneus 385 264 802 2.425 0.852 0.126 0.039 4 0.7 entorhinal 3328 2399 5764 2.558 0.718 0.128 0.031 38 4.3 fusiform 5765 3943 10367 2.634 0.537 0.126 0.027 69 7.0 inferiorparietal 3392 2453 7851 3.004 0.599 0.125 0.027 42 3.6 inferiortemporal 1272 775 1629 2.108 0.724 0.146 0.056 30 3.4 isthmuscingulate 6901 4721 10985 2.263 0.685 0.153 0.046 116 13.5 lateraloccipital 3842 2710 8157 2.909 0.769 0.136 0.038 62 5.6 lateralorbitofrontal 3555 2749 5427 2.077 0.647 0.171 0.048 65 7.6 lingual 2041 1472 4712 2.832 0.770 0.132 0.036 39 2.9 medialorbitofrontal 4898 3475 9806 2.594 0.586 0.121 0.024 51 4.5 middletemporal 546 381 637 1.697 0.605 0.139 0.046 7 1.1 parahippocampal 2705 1706 4064 2.370 0.646 0.117 0.035 30 4.1 paracentral 2032 1467 3871 2.544 0.513 0.128 0.027 26 2.4 parsopercularis 843 624 1944 2.901 0.561 0.128 0.033 10 1.1 parsorbitalis 1859 1327 3949 2.832 0.491 0.113 0.023 16 1.7 parstriangularis 1281 964 1432 1.816 0.502 0.157 0.059 22 3.1 pericalcarine 5921 3852 9035 2.259 0.613 0.118 0.030 61 7.1 postcentral 1403 999 1779 2.112 0.656 0.135 0.033 18 2.0 posteriorcingulate 6043 4060 11135 2.736 0.623 0.121 0.033 55 7.9 precentral 4722 3315 7231 2.326 0.535 0.128 0.030 58 5.8 precuneus 1327 934 2364 2.760 0.687 0.128 0.030 14 1.9 rostralanteriorcingulate 4158 2983 8981 2.798 0.513 0.136 0.031 55 5.3 rostralmiddlefrontal 10250 7087 21858 2.906 0.502 0.122 0.026 113 10.9 superiorfrontal 6704 4313 10331 2.393 0.564 0.120 0.032 83 9.0 superiorparietal 7378 5062 15969 2.854 0.709 0.114 0.026 73 8.1 superiortemporal 4919 3433 9025 2.606 0.485 0.112 0.023 46 4.2 supramarginal 710 497 1093 2.212 0.611 0.143 0.049 10 1.4 transversetemporal 2571 1789 5350 3.119 0.739 0.116 0.033 24 3.8 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Test rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 193538 Total vertex volume 193328 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 996 666 1553 2.285 0.574 0.132 0.028 15 1.1 caudalanteriorcingulate 2535 1731 5234 2.853 0.482 0.100 0.017 22 1.9 caudalmiddlefrontal 2986 1969 3617 1.908 0.527 0.155 0.058 53 7.4 cuneus 336 240 808 2.892 0.723 0.122 0.029 3 0.3 entorhinal 2569 1840 5538 2.922 0.778 0.131 0.030 40 3.3 fusiform 5801 4074 10602 2.551 0.521 0.126 0.026 62 6.2 inferiorparietal 3407 2377 8462 3.210 0.617 0.116 0.025 39 3.8 inferiortemporal 1042 689 1307 2.086 0.573 0.156 0.057 20 2.8 isthmuscingulate 6861 4680 11081 2.390 0.660 0.149 0.042 105 12.6 lateraloccipital 3599 2458 7708 2.904 0.820 0.137 0.042 64 6.4 lateralorbitofrontal 3878 2683 5644 2.138 0.773 0.168 0.060 96 9.5 lingual 1734 1218 4014 3.044 0.673 0.132 0.039 25 2.5 medialorbitofrontal 4517 3256 10112 2.888 0.736 0.123 0.025 51 4.9 middletemporal 910 597 1725 2.761 0.803 0.092 0.020 4 0.7 parahippocampal 2340 1400 3139 2.307 0.651 0.132 0.051 47 5.2 paracentral 1714 1156 3275 2.837 0.439 0.107 0.021 15 1.5 parsopercularis 826 597 1898 2.786 0.651 0.129 0.031 9 1.0 parsorbitalis 1824 1248 3837 2.818 0.525 0.117 0.025 19 1.8 parstriangularis 1723 1371 2020 1.747 0.533 0.185 0.065 30 5.3 pericalcarine 5823 3949 9221 2.241 0.601 0.123 0.031 64 7.9 postcentral 1076 742 1392 2.176 0.665 0.129 0.029 12 1.3 posteriorcingulate 5778 3877 10805 2.693 0.633 0.120 0.031 58 7.8 precentral 5954 3895 8545 2.311 0.634 0.126 0.038 86 8.8 precuneus 830 576 1596 2.935 0.903 0.136 0.032 11 1.2 rostralanteriorcingulate 4237 2991 9025 2.774 0.507 0.131 0.031 60 5.1 rostralmiddlefrontal 10205 6994 21574 2.903 0.501 0.117 0.026 112 11.2 superiorfrontal 6940 4623 10899 2.339 0.583 0.122 0.029 87 8.9 superiorparietal 6519 4438 14115 2.867 0.702 0.114 0.027 65 7.7 superiortemporal 4599 3208 8923 2.721 0.561 0.124 0.029 49 5.5 supramarginal 514 322 651 2.105 0.522 0.146 0.043 7 0.9 transversetemporal 2692 1786 5005 2.855 0.845 0.108 0.029 22 3.1 insula PIDs (330382 330385) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Mon Jan 9 14:00:39 CET 2023 /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/ASegStatsLUT.txt --subject Test setting seed for random number genererator to 1234 7.2.0 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/ASegStatsLUT.txt --subject Test sysname Linux hostname sharky machine x86_64 user brainstimmaps whitesurfname white UseRobust 0 atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) Computing euler number orig.nofix lheno = -224, rheno = -246 orig.nofix lhholes = 113, rhholes = 124 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Reporting on 45 segmentations Using PrintSegStat mri_segstats done /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon Jan 9 14:01:39 CET 2023 mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject Test --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject Test --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject Test --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject Test --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject Test --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 330471 of (330471 330474 330477 330480 330483) to complete... Waiting for PID 330474 of (330471 330474 330477 330480 330483) to complete... Waiting for PID 330477 of (330471 330474 330477 330480 330483) to complete... Waiting for PID 330480 of (330471 330474 330477 330480 330483) to complete... Waiting for PID 330483 of (330471 330474 330477 330480 330483) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject Test --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4181 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject Test --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8010 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject Test --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4197 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject Test --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6110 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject Test --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5986 mri_label2label: Done PIDs (330471 330474 330477 330480 330483) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject Test --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject Test --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject Test --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject Test --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 330525 of (330525 330528 330531 330534) to complete... Waiting for PID 330528 of (330525 330528 330531 330534) to complete... Waiting for PID 330531 of (330525 330528 330531 330534) to complete... Waiting for PID 330534 of (330525 330528 330531 330534) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject Test --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4218 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject Test --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 409 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13998 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject Test --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject Test --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3543 mri_label2label: Done PIDs (330525 330528 330531 330534) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject Test --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject Test --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject Test --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject Test --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject Test --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 330581 of (330581 330584 330587 330590 330593) to complete... Waiting for PID 330584 of (330581 330584 330587 330590 330593) to complete... Waiting for PID 330587 of (330581 330584 330587 330590 330593) to complete... Waiting for PID 330590 of (330581 330584 330587 330590 330593) to complete... Waiting for PID 330593 of (330581 330584 330587 330590 330593) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject Test --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 535 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5176 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject Test --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 1848 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9962 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject Test --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2149 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject Test --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1321 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject Test --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1203 mri_label2label: Done PIDs (330581 330584 330587 330590 330593) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 330647 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330650 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330653 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330656 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330659 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330662 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330665 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... Waiting for PID 330668 of (330647 330650 330653 330656 330659 330662 330665 330668) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 519 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 783 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1980 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject Test --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2186 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 438 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 858 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3777 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 228 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject Test --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 219 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1225 mri_label2label: Done PIDs (330647 330650 330653 330656 330659 330662 330665 330668) completed and logs appended. mris_label2annot --s Test --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label cmdline mris_label2annot --s Test --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname sharky machine x86_64 user brainstimmaps subject Test hemi lh SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects ColorTable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 102736 unhit vertices Writing annot to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.mpm.vpnl.annot mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 330793 of (330793 330796 330799 330802 330805) to complete... Waiting for PID 330796 of (330793 330796 330799 330802 330805) to complete... Waiting for PID 330799 of (330793 330796 330799 330802 330805) to complete... Waiting for PID 330802 of (330793 330796 330799 330802 330805) to complete... Waiting for PID 330805 of (330793 330796 330799 330802 330805) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1017 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2122 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1548 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2002 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2392 mri_label2label: Done PIDs (330793 330796 330799 330802 330805) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 330847 of (330847 330850 330853 330856) to complete... Waiting for PID 330850 of (330847 330850 330853 330856) to complete... Waiting for PID 330853 of (330847 330850 330853 330856) to complete... Waiting for PID 330856 of (330847 330850 330853 330856) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1569 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1951 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject Test --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1209 mri_label2label: Done PIDs (330847 330850 330853 330856) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject Test --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject Test --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject Test --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject Test --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject Test --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 330896 of (330896 330899 330902 330905 330908) to complete... Waiting for PID 330899 of (330896 330899 330902 330905 330908) to complete... Waiting for PID 330902 of (330896 330899 330902 330905 330908) to complete... Waiting for PID 330905 of (330896 330899 330902 330905 330908) to complete... Waiting for PID 330908 of (330896 330899 330902 330905 330908) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject Test --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 337 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3742 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject Test --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 818 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4152 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject Test --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject Test --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 477 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject Test --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 115656 Number of reverse mapping hits = 1 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 451 mri_label2label: Done PIDs (330896 330899 330902 330905 330908) completed and logs appended. mris_label2annot --s Test --hemi lh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label cmdline mris_label2annot --s Test --hemi lh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname sharky machine x86_64 user brainstimmaps subject Test hemi lh SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects ColorTable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 81175 unhit vertices Writing annot to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.BA_exvivo.annot mris_label2annot --s Test --hemi lh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label cmdline mris_label2annot --s Test --hemi lh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname sharky machine x86_64 user brainstimmaps subject Test hemi lh SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects ColorTable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 95327 unhit vertices Writing annot to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab Test lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 196079 Total vertex volume 195876 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 926 536 1678 2.356 0.557 0.126 0.035 13 1.2 BA1_exvivo 3256 2125 5243 2.525 0.506 0.106 0.021 24 2.9 BA2_exvivo 1003 752 975 1.837 0.521 0.182 0.072 16 3.0 BA3a_exvivo 1842 1233 2588 1.973 0.587 0.116 0.032 18 2.2 BA3b_exvivo 1613 956 2589 2.482 0.673 0.110 0.036 17 2.2 BA4a_exvivo 1121 819 1604 2.235 0.824 0.140 0.041 12 2.1 BA4p_exvivo 8501 5681 18430 3.005 0.442 0.114 0.023 76 7.9 BA6_exvivo 1838 1309 3534 2.649 0.467 0.121 0.027 20 1.9 BA44_exvivo 2335 1700 5136 2.750 0.534 0.124 0.026 28 2.4 BA45_exvivo 2526 1925 2905 1.696 0.550 0.189 0.068 59 7.4 V1_exvivo 7073 4885 10261 2.103 0.598 0.157 0.048 121 14.5 V2_exvivo 1568 1145 3037 2.547 0.617 0.160 0.040 26 2.7 MT_exvivo 433 341 742 2.243 0.955 0.155 0.045 7 1.0 perirhinal_exvivo 446 320 602 1.536 1.349 0.183 0.070 9 1.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab Test lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 196079 Total vertex volume 195876 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 561 309 1093 2.507 0.541 0.121 0.031 6 0.6 BA1_exvivo 1278 794 2129 2.494 0.565 0.093 0.017 8 0.9 BA2_exvivo 830 650 798 1.830 0.512 0.192 0.073 13 2.5 BA3a_exvivo 1148 777 1328 1.714 0.432 0.106 0.027 9 1.3 BA3b_exvivo 1491 896 2492 2.606 0.650 0.099 0.031 11 1.7 BA4a_exvivo 879 677 1205 2.102 0.778 0.151 0.043 10 1.8 BA4p_exvivo 4936 3290 10923 3.031 0.430 0.113 0.023 46 4.5 BA6_exvivo 1214 870 2413 2.645 0.481 0.129 0.031 15 1.4 BA44_exvivo 976 723 2450 2.958 0.528 0.135 0.028 14 1.1 BA45_exvivo 2679 2036 3245 1.753 0.599 0.187 0.068 61 7.7 V1_exvivo 3500 2435 4781 2.035 0.570 0.164 0.054 65 8.2 V2_exvivo 391 294 640 2.477 0.593 0.151 0.037 5 0.6 MT_exvivo 184 148 338 2.198 1.018 0.157 0.048 2 0.5 perirhinal_exvivo 262 177 460 2.092 1.371 0.134 0.038 3 0.5 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Mon Jan 9 14:02:10 CET 2023 mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject Test --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject Test --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject Test --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject Test --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject Test --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 331054 of (331054 331057 331060 331063 331066) to complete... Waiting for PID 331057 of (331054 331057 331060 331063 331066) to complete... Waiting for PID 331060 of (331054 331057 331060 331063 331066) to complete... Waiting for PID 331063 of (331054 331057 331060 331063 331066) to complete... Waiting for PID 331066 of (331054 331057 331060 331063 331066) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject Test --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4034 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject Test --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6796 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject Test --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4042 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject Test --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4587 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject Test --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5821 mri_label2label: Done PIDs (331054 331057 331060 331063 331066) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject Test --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject Test --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject Test --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject Test --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 331108 of (331108 331111 331114 331117) to complete... Waiting for PID 331111 of (331108 331111 331114 331117) to complete... Waiting for PID 331114 of (331108 331111 331114 331117) to complete... Waiting for PID 331117 of (331108 331111 331114 331117) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject Test --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject Test --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12378 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject Test --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 6988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject Test --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5550 mri_label2label: Done PIDs (331108 331111 331114 331117) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject Test --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject Test --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject Test --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject Test --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject Test --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 331157 of (331157 331160 331163 331166 331169) to complete... Waiting for PID 331160 of (331157 331160 331163 331166 331169) to complete... Waiting for PID 331163 of (331157 331160 331163 331166 331169) to complete... Waiting for PID 331166 of (331157 331160 331163 331166 331169) to complete... Waiting for PID 331169 of (331157 331160 331163 331166 331169) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject Test --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 1037 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5764 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject Test --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 2359 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10375 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject Test --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 1991 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject Test --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1041 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject Test --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 759 mri_label2label: Done PIDs (331157 331160 331163 331166 331169) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 331228 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331231 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331234 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331237 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331240 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331243 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331246 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... Waiting for PID 331249 of (331228 331231 331234 331237 331240 331243 331246 331249) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 608 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 806 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject Test --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 726 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 861 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3580 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 620 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1848 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject Test --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 262 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1287 mri_label2label: Done PIDs (331228 331231 331234 331237 331240 331243 331246 331249) completed and logs appended. mris_label2annot --s Test --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label cmdline mris_label2annot --s Test --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname sharky machine x86_64 user brainstimmaps subject Test hemi rh SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects ColorTable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 99672 unhit vertices Writing annot to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.mpm.vpnl.annot mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 331331 of (331331 331334 331337 331340 331343) to complete... Waiting for PID 331334 of (331331 331334 331337 331340 331343) to complete... Waiting for PID 331337 of (331331 331334 331337 331340 331343) to complete... Waiting for PID 331340 of (331331 331334 331337 331340 331343) to complete... Waiting for PID 331343 of (331331 331334 331337 331340 331343) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 906 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2725 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1731 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2193 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1394 mri_label2label: Done PIDs (331331 331334 331337 331340 331343) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 331386 of (331386 331389 331392 331395) to complete... Waiting for PID 331389 of (331386 331389 331392 331395) to complete... Waiting for PID 331392 of (331386 331389 331392 331395) to complete... Waiting for PID 331395 of (331386 331389 331392 331395) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1525 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7005 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject Test --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1189 mri_label2label: Done PIDs (331386 331389 331392 331395) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject Test --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject Test --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject Test --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject Test --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject Test --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 331435 of (331435 331438 331441 331444 331447) to complete... Waiting for PID 331438 of (331435 331438 331441 331444 331447) to complete... Waiting for PID 331441 of (331435 331438 331441 331444 331447) to complete... Waiting for PID 331444 of (331435 331438 331441 331444 331447) to complete... Waiting for PID 331447 of (331435 331438 331441 331444 331447) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject Test --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 620 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3852 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject Test --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 1105 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4542 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject Test --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 278 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject Test --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 1 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 695 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject Test --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Test trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects FREESURFER_HOME /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white Reading target registration /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 112475 Number of reverse mapping hits = 2 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 293 mri_label2label: Done PIDs (331435 331438 331441 331444 331447) completed and logs appended. mris_label2annot --s Test --hemi rh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label cmdline mris_label2annot --s Test --hemi rh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname sharky machine x86_64 user brainstimmaps subject Test hemi rh SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects ColorTable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 78492 unhit vertices Writing annot to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.BA_exvivo.annot mris_label2annot --s Test --hemi rh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label cmdline mris_label2annot --s Test --hemi rh --ctab /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname sharky machine x86_64 user brainstimmaps subject Test hemi rh SUBJECTS_DIR /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects ColorTable /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 93418 unhit vertices Writing annot to /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab Test rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 193538 Total vertex volume 193328 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 812 491 1612 2.475 0.622 0.137 0.046 14 1.3 BA1_exvivo 2921 1987 4705 2.370 0.554 0.117 0.025 27 3.1 BA2_exvivo 941 744 1005 1.890 0.474 0.177 0.058 14 2.6 BA3a_exvivo 1674 1118 2217 1.878 0.463 0.130 0.039 25 3.2 BA3b_exvivo 1266 728 2056 2.600 0.575 0.103 0.036 19 1.6 BA4a_exvivo 1099 757 1558 2.325 0.744 0.133 0.040 13 1.9 BA4p_exvivo 6125 4036 12972 2.946 0.456 0.107 0.022 55 5.7 BA6_exvivo 2853 1944 5379 2.810 0.439 0.112 0.023 27 2.7 BA44_exvivo 3156 2224 6954 2.775 0.550 0.123 0.028 36 3.4 BA45_exvivo 3309 2428 4374 1.896 0.583 0.180 0.064 63 9.7 V1_exvivo 7740 5230 10422 2.058 0.680 0.162 0.058 160 18.8 V2_exvivo 1404 969 2194 2.441 0.642 0.119 0.025 11 1.4 MT_exvivo 259 195 776 3.356 0.950 0.122 0.024 3 0.3 perirhinal_exvivo 424 291 1061 2.954 0.845 0.123 0.034 5 0.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab Test rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/mri/wm.mgz... reading input surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... reading input pial surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.pial... reading input white surface /home/brainstimmaps/RESEARCH/04_Codebase/testing/Freesurfer_7.2_testingT2/freesurfer/subjects/Test/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 193538 Total vertex volume 193328 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 866062 mm^3 (det: 2.249384 ) 539 309 992 2.380 0.630 0.132 0.049 10 0.9 BA1_exvivo 1648 1122 2636 2.291 0.568 0.116 0.025 15 1.9 BA2_exvivo 857 699 869 1.859 0.472 0.190 0.063 14 2.6 BA3a_exvivo 1271 882 1528 1.775 0.421 0.124 0.032 14 1.9 BA3b_exvivo 752 443 1290 2.787 0.455 0.114 0.033 7 1.0 BA4a_exvivo 893 646 1263 2.267 0.722 0.132 0.037 10 1.5 BA4p_exvivo 3777 2477 8065 2.944 0.471 0.107 0.023 34 3.5 BA6_exvivo 706 486 1453 2.773 0.394 0.108 0.024 8 0.7 BA44_exvivo 744 526 1914 2.977 0.483 0.121 0.024 8 0.7 BA45_exvivo 3126 2290 4050 1.881 0.578 0.178 0.064 57 9.1 V1_exvivo 4091 2851 5586 2.043 0.639 0.173 0.064 87 11.5 V2_exvivo 222 163 548 2.742 0.433 0.111 0.015 2 0.2 MT_exvivo 24 19 92 4.085 0.763 0.105 0.019 0 0.0 perirhinal_exvivo 407 295 986 3.089 0.701 0.122 0.026 3 0.4 entorhinal_exvivo Started at Mon Jan 9 11:06:45 CET 2023 Ended at Mon Jan 9 14:02:39 CET 2023 #@#%# recon-all-run-time-hours 2.932 recon-all -s Test finished without error at Mon Jan 9 14:02:39 CET 2023