Tue Aug 29 17:33:24 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01 setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects /usr/local/freesurfer/7.4.1/bin/recon-all -s EP01 -i /home/bsherma/EP01/3d.nii.gz -all -localGI subjid EP01 setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Actual FREESURFER_HOME /usr/local/freesurfer/7.4.1 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 513608 maxlocks unlimited maxsignal 513608 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 38Gi 53Gi 260Mi 34Gi 85Gi Swap: 975Mi 614Mi 361Mi ######################################## program versions used 7.4.1 (freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-00:33:24-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: bsherma Machine: rnet-lambda-vector Platform: Linux PlatformVersion: 5.15.0-78-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/7.4.1/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/7.4.1/subjects/EP01 mri_convert /home/bsherma/EP01/3d.nii.gz /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig/001.mgz mri_convert /home/bsherma/EP01/3d.nii.gz /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig/001.mgz reading from /home/bsherma/EP01/3d.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-0, 1, -0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig/001.mgz... @#@FSTIME 2023:08:29:17:33:24 mri_convert N 2 e 5.62 S 0.05 U 5.56 P 99% M 95796 F 0 R 22550 W 0 c 525 w 2 I 0 O 95928 L 14.06 13.18 9.87 @#@FSLOADPOST 2023:08:29:17:33:29 mri_convert N 2 13.25 13.03 9.84 #-------------------------------------------- #@# MotionCor Tue Aug 29 17:33:31 PDT 2023 Found 1 runs /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig/001.mgz /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz mri_info /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz type: MGH dimensions: 512 x 512 x 172 voxel sizes: 0.468800, 0.468800, 1.000001 type: SHORT (4) fov: 240.026 dof: 1 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -86.0, zend: 86.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -2.5868 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 29.8410 : x_s = 0.0000, y_s = -0.0000, z_s = 1.0000, c_s = 88.9819 talairach xfm : Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -0.4688 -0.0000 0.0000 117.4260 0.0000 0.4688 0.0000 -90.1718 0.0000 -0.0000 1.0000 2.9818 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.219774 ras to voxel transform: -2.1331 -0.0000 -0.0000 250.4821 -0.0000 2.1331 -0.0000 192.3460 -0.0000 -0.0000 1.0000 -2.9818 -0.0000 -0.0000 -0.0000 1.0000 /usr/local/freesurfer/7.4.1/subjects/EP01 mri_convert /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz --conform reading from /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-0, 1, -0) k_ras = (0, 0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 11743 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz... @#@FSTIME 2023:08:29:17:33:34 mri_convert N 3 e 13.14 S 0.05 U 13.05 P 99% M 140096 F 0 R 41992 W 0 c 2077 w 1 I 0 O 9792 L 13.95 13.18 9.90 @#@FSLOADPOST 2023:08:29:17:33:48 mri_convert N 3 18.38 14.20 10.29 mri_add_xform_to_header -c /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/talairach.xfm /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2023:08:29:17:33:48 mri_add_xform_to_header N 4 e 0.85 S 0.00 U 0.84 P 99% M 23356 F 0 R 4567 W 0 c 86 w 2 I 8 O 9792 L 18.38 14.20 10.29 @#@FSLOADPOST 2023:08:29:17:33:48 mri_add_xform_to_header N 4 18.38 14.20 10.29 mri_info /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz orig.mgz ======================================== Volume information for /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -2.5868 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 29.8410 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 88.9819 talairach xfm : /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 125.4132 0.0000 0.0000 1.0000 -98.1590 0.0000 -1.0000 0.0000 216.9819 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 125.4132 -0.0000 -0.0000 -1.0000 216.9819 -0.0000 1.0000 -0.0000 98.1590 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Tue Aug 29 17:33:49 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/mri /usr/local/freesurfer/7.4.1/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 7.4.1 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Aug 29 17:33:49 PDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.866799 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.866799/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.866799/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.866799/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.866799/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Aug 29 17:36:18 PDT 2023 mri_nu_correct.mni done @#@FSTIME 2023:08:29:17:33:49 mri_nu_correct.mni N 12 e 149.14 S 0.15 U 148.85 P 99% M 519528 F 0 R 145644 W 0 c 17337 w 91 I 0 O 17056 L 18.38 14.20 10.29 @#@FSLOADPOST 2023:08:29:17:36:18 mri_nu_correct.mni N 12 21.75 16.74 11.80 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /usr/local/freesurfer/7.4.1/subjects/EP01/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Tue Aug 29 17:36:18 PDT 2023 Ended at Tue Aug 29 17:36:36 PDT 2023 talairach_avi done @#@FSTIME 2023:08:29:17:36:18 talairach_avi N 4 e 17.96 S 0.83 U 11.13 P 66% M 255596 F 0 R 398381 W 0 c 1196 w 182 I 0 O 295272 L 21.75 16.74 11.80 @#@FSLOADPOST 2023:08:29:17:36:36 talairach_avi N 4 19.78 16.52 11.80 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/7.4.1/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.4.1 --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/7.4.1/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 1.07596 -0.04561 0.07750 -2.40933; 0.04487 1.09263 0.23366 -50.08385; -0.09998 -0.13122 1.12654 -83.02803; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Tue Aug 29 17:36:38 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7516, pval=0.6675 >= threshold=0.0050) @#@FSTIME 2023:08:29:17:36:38 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 5964 F 0 R 227 W 0 c 0 w 1 I 0 O 0 L 19.00 16.41 11.79 @#@FSLOADPOST 2023:08:29:17:36:38 talairach_afd N 4 19.00 16.41 11.79 awk -f /usr/local/freesurfer/7.4.1/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/talairach_avi.log TalAviQA: 0.97749 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Aug 29 17:36:38 PDT 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /usr/local/freesurfer/7.4.1/subjects/EP01/mri /usr/local/freesurfer/7.4.1/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 7.4.1 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Aug 29 17:36:38 PDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.867383 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.867383/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.867383/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.867383/ones.mgz 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.867383/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.867383/ones.mgz sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma input ./tmp.mri_nu_correct.mni.867383/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.867383/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.867383/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.867383/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.867383/sum.junk --avgwf ./tmp.mri_nu_correct.mni.867383/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.867383/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.867383/sum.junk --avgwf ./tmp.mri_nu_correct.mni.867383/input.mean.dat sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.867383/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.867383/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.867383/ones.mgz --i ./tmp.mri_nu_correct.mni.867383/nu0.mgz --sum ./tmp.mri_nu_correct.mni.867383/sum.junk --avgwf ./tmp.mri_nu_correct.mni.867383/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.867383/ones.mgz --i ./tmp.mri_nu_correct.mni.867383/nu0.mgz --sum ./tmp.mri_nu_correct.mni.867383/sum.junk --avgwf ./tmp.mri_nu_correct.mni.867383/output.mean.dat sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.867383/ones.mgz Loading ./tmp.mri_nu_correct.mni.867383/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.867383/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.867383/nu0.mgz ./tmp.mri_nu_correct.mni.867383/nu0.mgz mul 1.50342332172572102422 Saving result to './tmp.mri_nu_correct.mni.867383/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.867383/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.867383/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.867383/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 3, i2 = 44 #mri_make_uchar# mapping 8 113 to 3 110 : b -5.3122 m 1.01746 : thresh 5.22103 maxsat 255.845 : nzero 11282463 nsat 1936 Tue Aug 29 17:39:27 PDT 2023 mri_nu_correct.mni done @#@FSTIME 2023:08:29:17:36:38 mri_nu_correct.mni N 9 e 169.12 S 0.85 U 168.13 P 99% M 614272 F 0 R 515140 W 0 c 18919 w 158 I 0 O 49200 L 19.00 16.41 11.79 @#@FSLOADPOST 2023:08:29:17:39:27 mri_nu_correct.mni N 9 17.17 17.50 13.03 mri_add_xform_to_header -c /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2023:08:29:17:39:27 mri_add_xform_to_header N 4 e 0.88 S 0.00 U 0.87 P 99% M 23584 F 0 R 4574 W 0 c 88 w 1 I 0 O 8000 L 17.17 17.50 13.03 @#@FSLOADPOST 2023:08:29:17:39:28 mri_add_xform_to_header N 4 17.17 17.50 13.03 #-------------------------------------------- #@# Intensity Normalization Tue Aug 29 17:39:28 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 1.07596 -0.04561 0.07750 -2.40933; 0.04487 1.09263 0.23366 -50.08385; -0.09998 -0.13122 1.12654 -83.02803; 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 = 20 Starting OpenSpline(): npoints = 20 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 73 (73), valley at 51 (51) csf peak at 37, 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 74 (74), valley at 52 (52) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 16 seconds. @#@FSTIME 2023:08:29:17:39:28 mri_normalize N 7 e 76.47 S 0.31 U 76.03 P 99% M 583780 F 0 R 263278 W 0 c 10099 w 1 I 0 O 8240 L 17.17 17.50 13.03 @#@FSLOADPOST 2023:08:29:17:40:44 mri_normalize N 7 15.26 17.06 13.24 #-------------------------------------------- #@# Skull Stripping Tue Aug 29 17:40:44 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/7.4.1/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/7.4.1/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=5.0 skull bounding box = (46, 50, 15) --> (209, 216, 214) finding center of left hemi white matter using (100, 105, 115) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (80,85,90) --> (120, 125,139) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 5.9 after smoothing, mri peak at 109, scaling input intensities by 0.991 scaling channel 0 by 0.990826 initial log_p = -4.676 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.602840 @ (-10.526, -31.579, -10.526) max log p = -4.450531 @ (5.263, 15.789, 15.789) max log p = -4.372415 @ (2.632, -7.895, -7.895) max log p = -4.372415 @ (0.000, 0.000, 0.000) max log p = -4.338926 @ (0.658, -0.658, 1.974) max log p = -4.338926 @ (0.000, 0.000, 0.000) max log p = -4.338926 @ (0.000, 0.000, 0.000) max log p = -4.338926 @ (0.000, 0.000, 0.000) Found translation: (-2.0, -24.3, -0.7): log p = -4.339 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.068, old_max_log_p =-4.339 (thresh=-4.3) 1.05465 0.13885 0.00000 -30.21872; -0.16136 1.22567 0.00000 -25.41356; 0.00000 0.00000 1.07500 -9.04480; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 58 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.068, old_max_log_p =-4.068 (thresh=-4.1) 1.05465 0.13885 0.00000 -30.21872; -0.16136 1.22567 0.00000 -25.41356; 0.00000 0.00000 1.07500 -9.04480; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 58 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.975, old_max_log_p =-4.068 (thresh=-4.1) 1.09871 0.10133 0.03033 -31.45256; -0.12897 1.25092 0.03728 -35.77222; -0.02850 -0.03665 1.01452 5.20783; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 56 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.975, old_max_log_p =-3.975 (thresh=-4.0) 1.09871 0.10133 0.03033 -31.45256; -0.12897 1.25092 0.03728 -35.77222; -0.02850 -0.03665 1.01452 5.20783; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 55 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.951, old_max_log_p =-3.975 (thresh=-4.0) 1.09719 0.10048 0.03872 -32.55210; -0.12987 1.24693 0.07853 -39.24775; -0.03245 -0.08873 1.01543 13.51015; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 54 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.942, old_max_log_p =-3.951 (thresh=-3.9) 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 56 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.942, old_max_log_p =-3.942 (thresh=-3.9) 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 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 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 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: 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.942 (old=-4.676) transform before final EM align: 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 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 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 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) = 4.3 tol 0.000000 final transform: 1.09462 0.10024 0.03863 -32.18260; -0.12942 1.24255 0.07826 -38.61067; -0.03245 -0.08873 1.01543 13.51015; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 795052 FSRUNTIME@ mri_em_register 0.1224 hours 1 threads registration took 7 minutes and 21 seconds. @#@FSTIME 2023:08:29:17:40:44 mri_em_register N 4 e 440.78 S 0.65 U 439.75 P 99% M 629312 F 0 R 166629 W 0 c 48869 w 1 I 0 O 16 L 15.26 17.06 13.24 @#@FSLOADPOST 2023:08:29:17:48:05 mri_em_register N 4 13.31 15.85 14.22 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/7.4.1/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=130 z=111 r=69 first estimation of the main basin volume: 1419558 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=111, y=114, z=79, Imax=255 CSF=21, 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=1700643096747934 voxels, voxel volume =1.000 = 1700643096747934 mmm3 = 1700643035152.384 cm3 done. PostAnalyze...Basin Prior 32 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=136, z=106, r=9555 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=4, CSF_MAX=23 , nb = 45630 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = 3582 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=28 , nb = 3636 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 18972 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=23 , nb = 18936 OTHER CSF_MIN=0, CSF_intensity=14, CSF_MAX=39 , nb = 504 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 23, 34, 48, 70 after analyzing : 23, 43, 48, 49 RIGHT_CER before analyzing : 18, 30, 49, 73 after analyzing : 18, 42, 49, 49 LEFT_CER before analyzing : 28, 38, 49, 73 after analyzing : 28, 45, 49, 52 RIGHT_BRAIN before analyzing : 22, 33, 48, 69 after analyzing : 22, 43, 48, 49 LEFT_BRAIN before analyzing : 23, 35, 49, 70 after analyzing : 23, 44, 49, 50 OTHER before analyzing : 39, 51, 65, 91 after analyzing : 39, 60, 65, 67 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 67.272, std = 7.771 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.72, sigma = 3.93 after rotation: sse = 2.72, sigma = 3.93 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.76, its var is 3.29 before Erosion-Dilatation 0.19% 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...50 iterations mri_strip_skull: done peeling brain Brain Size = 1533498 voxels, voxel volume = 1.000 mm3 = 1533498 mmm3 = 1533.498 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done @#@FSTIME 2023:08:29:17:48:05 mri_watershed N 6 e 12.99 S 0.25 U 12.73 P 99% M 811412 F 0 R 205607 W 0 c 1297 w 1 I 0 O 2512 L 13.31 15.85 14.22 @#@FSLOADPOST 2023:08:29:17:48:18 mri_watershed N 6 16.39 16.42 14.44 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Aug 29 17:48:19 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/7.4.1/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/7.4.1/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=23.0 skull bounding box = (61, 73, 29) --> (194, 199, 195) finding center of left hemi white matter using (105, 115, 112) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (89,100,92) --> (121, 130,132) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 109 +- 4.7 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.248 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.169374 @ (-10.526, -10.526, -10.526) max log p = -3.857445 @ (5.263, -5.263, 5.263) max log p = -3.822995 @ (2.632, -7.895, 2.632) max log p = -3.795205 @ (1.316, 1.316, 3.947) max log p = -3.784139 @ (0.658, 0.658, 0.658) max log p = -3.784139 @ (0.000, 0.000, 0.000) max log p = -3.784139 @ (0.000, 0.000, 0.000) max log p = -3.784139 @ (0.000, 0.000, 0.000) Found translation: (-0.7, -21.7, 2.0): log p = -3.784 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.609, old_max_log_p =-3.784 (thresh=-3.8) 1.06580 0.15927 0.02372 -33.95592; -0.13053 1.12538 0.16757 -32.58755; 0.00000 -0.11999 1.07125 11.52104; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 52 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.600, old_max_log_p =-3.609 (thresh=-3.6) 1.06580 0.15927 0.02372 -33.95592; -0.12941 1.13142 0.02631 -19.03183; -0.01704 0.02793 1.08396 -14.99967; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 51 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.585, old_max_log_p =-3.600 (thresh=-3.6) 1.06580 0.15927 0.02372 -33.95592; -0.14032 1.20979 0.18014 -45.03078; 0.00000 -0.11999 1.07125 11.58519; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 49 seconds. **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.579, old_max_log_p =-3.585 (thresh=-3.6) 1.06580 0.15927 0.02372 -33.95592; -0.12979 1.11905 0.16663 -32.70671; 0.00000 -0.11999 1.07125 11.58519; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 50 seconds. **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.578, old_max_log_p =-3.579 (thresh=-3.6) 1.06580 0.15927 0.02372 -33.95592; -0.13953 1.20298 0.17913 -44.10649; 0.00000 -0.11999 1.07125 11.58519; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 50 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.447, old_max_log_p =-3.578 (thresh=-3.6) 1.05167 0.07710 0.04963 -23.79922; -0.06922 1.21608 0.11000 -47.79762; -0.04387 -0.04210 1.03905 8.10508; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 49 seconds. **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.447, old_max_log_p =-3.447 (thresh=-3.4) 1.05167 0.07710 0.04963 -23.79922; -0.06922 1.21608 0.11000 -47.79762; -0.04387 -0.04210 1.03905 8.10508; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 49 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.411, old_max_log_p =-3.447 (thresh=-3.4) 1.05160 0.11746 0.04549 -29.29278; -0.10469 1.21291 0.13435 -45.83950; -0.03339 -0.07137 1.03518 10.18554; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 47 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.404, old_max_log_p =-3.411 (thresh=-3.4) 1.05194 0.12752 0.04672 -30.82934; -0.11342 1.20987 0.14227 -45.13761; -0.03249 -0.08120 1.03283 11.18094; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 48 seconds. **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.401, old_max_log_p =-3.404 (thresh=-3.4) 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 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 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.401 (old=-4.248) transform before final EM align: 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 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 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 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: 014: -log(p) = 3.9 tol 0.000000 final transform: 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 782504 FSRUNTIME@ mri_em_register 0.1516 hours 1 threads registration took 9 minutes and 6 seconds. @#@FSTIME 2023:08:29:17:48:19 mri_em_register N 7 e 545.85 S 0.84 U 544.70 P 99% M 616652 F 0 R 166618 W 0 c 54869 w 1 I 0 O 16 L 16.39 16.42 14.44 @#@FSLOADPOST 2023:08:29:17:57:25 mri_em_register N 7 17.69 17.56 16.01 #-------------------------------------- #@# CA Normalize Tue Aug 29 17:57:25 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/7.4.1/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/7.4.1/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=23.0 skull bounding box = (61, 73, 29) --> (194, 199, 195) finding center of left hemi white matter using (105, 115, 112) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (89,100,92) --> (121, 130,132) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 109 +- 4.7 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246437 sample points... INFO: compute sample coordinates transform 1.05317 0.12767 0.04677 -31.01363; -0.11329 1.20845 0.14210 -44.94492; -0.03253 -0.08129 1.03404 11.07050; 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, 81, 31) --> (192, 178, 192) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 570 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 81, 29) --> (133, 173, 191) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 388 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 151, 54) --> (171, 192, 106) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (82, 151, 51) --> (127, 186, 106) Right_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (108, 144, 88) --> (143, 202, 117) Brain_Stem: limiting intensities to 97.0 --> 132.0 0 of 17 (0.0%) samples deleted using 996 total control points for intensity normalization... bias field = 0.983 +- 0.059 7 of 996 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 81, 31) --> (192, 178, 192) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 715 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 81, 29) --> (133, 173, 191) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 491 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 151, 54) --> (171, 192, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 72 (2.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (82, 151, 51) --> (127, 186, 106) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 74 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (108, 144, 88) --> (143, 202, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 9 of 104 (8.7%) samples deleted using 1456 total control points for intensity normalization... bias field = 1.003 +- 0.070 1 of 1424 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 81, 31) --> (192, 178, 192) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 730 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (66, 81, 29) --> (133, 173, 191) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 558 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 151, 54) --> (171, 192, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 44 of 113 (38.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (82, 151, 51) --> (127, 186, 106) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 73 (12.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (108, 144, 88) --> (143, 202, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 69 of 171 (40.4%) samples deleted using 1645 total control points for intensity normalization... bias field = 1.010 +- 0.053 1 of 1495 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 46 seconds. @#@FSTIME 2023:08:29:17:57:25 mri_ca_normalize N 8 e 45.88 S 0.42 U 45.43 P 99% M 685020 F 0 R 408182 W 0 c 4501 w 1 I 0 O 3504 L 17.69 17.56 16.01 @#@FSLOADPOST 2023:08:29:17:58:11 mri_ca_normalize N 8 20.68 18.31 16.33 #-------------------------------------- #@# CA Reg Tue Aug 29 17:58:11 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/7.4.1/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/7.4.1/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 0.801411 #GCAMreg# pass 0 level1 5 level2 1 tsec 230.274 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 0.684487 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 0.691018 #GCAMreg# pass 0 level1 4 level2 1 tsec 106.359 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 0.660842 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 0.686505 #GCAMreg# pass 0 level1 3 level2 1 tsec 29.278 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 0.686505 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 0.763436 #GCAMreg# pass 0 level1 2 level2 1 tsec 44.426 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 0.733864 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 0.789336 #GCAMreg# pass 0 level1 1 level2 1 tsec 48.127 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 0.779905 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 0.721121 #GCAMreg# pass 0 level1 0 level2 1 tsec 28.351 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 0.715991 GCAMregister done in 11.5389 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.09937 (27) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (910 voxels, overlap=0.486) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (910 voxels, peak = 22), gca=21.7 gca peak = 0.17690 (16) mri peak = 0.08101 (26) Right_Lateral_Ventricle (43): linear fit = 1.53 x + 0.0 (658 voxels, overlap=0.400) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (658 voxels, peak = 25), gca=24.0 gca peak = 0.28275 (96) mri peak = 0.11213 (101) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (769 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (769 voxels, peak = 100), gca=100.3 gca peak = 0.18948 (93) mri peak = 0.09692 (99) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (679 voxels, overlap=0.909) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (679 voxels, peak = 95), gca=95.3 gca peak = 0.20755 (55) mri peak = 0.10610 (70) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (688 voxels, overlap=0.122) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (688 voxels, peak = 66), gca=66.3 gca peak = 0.31831 (58) mri peak = 0.07956 (75) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (615 voxels, overlap=0.012) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (615 voxels, peak = 73), gca=72.8 gca peak = 0.11957 (102) mri peak = 0.11006 (107) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (52409 voxels, overlap=0.645) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (52409 voxels, peak = 107), gca=106.6 gca peak = 0.11429 (102) mri peak = 0.10608 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (52436 voxels, overlap=0.521) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (52436 voxels, peak = 108), gca=107.6 gca peak = 0.14521 (59) mri peak = 0.04842 (71) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (14154 voxels, overlap=0.080) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (14154 voxels, peak = 71), gca=70.5 gca peak = 0.14336 (58) mri peak = 0.05212 (67) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (13739 voxels, overlap=0.279) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (13739 voxels, peak = 66), gca=66.4 gca peak = 0.13305 (70) mri peak = 0.12251 (76) Right_Caudate (50): linear fit = 1.12 x + 0.0 (730 voxels, overlap=0.292) Right_Caudate (50): linear fit = 1.12 x + 0.0 (730 voxels, peak = 78), gca=78.1 gca peak = 0.15761 (71) mri peak = 0.12114 (80) Left_Caudate (11): linear fit = 1.11 x + 0.0 (859 voxels, overlap=0.381) Left_Caudate (11): linear fit = 1.11 x + 0.0 (859 voxels, peak = 78), gca=78.5 gca peak = 0.13537 (57) mri peak = 0.05585 (65) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (16616 voxels, overlap=0.210) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (16616 voxels, peak = 69), gca=69.3 gca peak = 0.13487 (56) mri peak = 0.05391 (64) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (17561 voxels, overlap=0.239) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (17561 voxels, peak = 66), gca=66.4 gca peak = 0.19040 (84) mri peak = 0.08203 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8526 voxels, overlap=0.668) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8526 voxels, peak = 89), gca=89.5 gca peak = 0.18871 (83) mri peak = 0.08789 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7188 voxels, overlap=0.496) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7188 voxels, peak = 88), gca=88.4 gca peak = 0.24248 (57) mri peak = 0.09189 (76) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (370 voxels, overlap=0.050) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (370 voxels, peak = 72), gca=71.5 gca peak = 0.35833 (56) mri peak = 0.11931 (73) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (483 voxels, overlap=0.040) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (483 voxels, peak = 71), gca=71.4 gca peak = 0.12897 (85) mri peak = 0.08067 (93) Left_Thalamus (10): linear fit = 1.09 x + 0.0 (4767 voxels, overlap=0.822) Left_Thalamus (10): linear fit = 1.09 x + 0.0 (4767 voxels, peak = 92), gca=92.2 gca peak = 0.13127 (83) mri peak = 0.06694 (93) Right_Thalamus (49): linear fit = 1.11 x + 0.0 (4155 voxels, overlap=0.672) Right_Thalamus (49): linear fit = 1.11 x + 0.0 (4155 voxels, peak = 92), gca=91.7 gca peak = 0.12974 (78) mri peak = 0.07454 (90) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1882 voxels, overlap=0.576) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1882 voxels, peak = 88), gca=87.8 gca peak = 0.17796 (79) mri peak = 0.09743 (87) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2001 voxels, overlap=0.447) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2001 voxels, peak = 88), gca=88.1 gca peak = 0.10999 (80) mri peak = 0.08703 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10798 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10798 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.09836 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1161 voxels, overlap=0.259) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1161 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.09243 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1218 voxels, overlap=0.617) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1218 voxels, peak = 97), gca=97.5 gca peak = 0.20775 (25) mri peak = 0.11771 (23) gca peak = 0.13297 (21) mri peak = 0.09241 (27) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (317 voxels, overlap=0.471) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (317 voxels, peak = 27), gca=27.4 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) 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 1.22 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.39 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 2.89842 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 0.73095 #GCAMreg# pass 0 level1 5 level2 1 tsec 911.153 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 0.628103 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 0.627464 #GCAMreg# pass 0 level1 4 level2 1 tsec 665.206 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 0.557268 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 0.555711 #GCAMreg# pass 0 level1 3 level2 1 tsec 423.663 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 0.512321 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 0.536289 #GCAMreg# pass 0 level1 2 level2 1 tsec 28.77 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 0.536289 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 0.590279 #GCAMreg# pass 0 level1 1 level2 1 tsec 30.293 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 0.583061 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 0.532824 #GCAMreg# pass 0 level1 0 level2 1 tsec 191.687 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 0.501719 GCAMregister done in 46.5625 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 0.492555 #GCAMreg# pass 0 level1 5 level2 1 tsec 34.701 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 0.492555 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 0.490212 #GCAMreg# pass 0 level1 4 level2 1 tsec 45.758 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 0.489168 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.480622 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 15 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 20 after 16 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 15 after 15 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 185.891 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 0.460999 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, 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 0.455155 #GCAMreg# pass 0 level1 2 level2 1 tsec 27.588 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 0.455155 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 0.466895 #GCAMreg# pass 0 level1 1 level2 1 tsec 30.774 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 0.466263 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 0.452997 iter 0, gcam->neg = 851 after 16 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 36.119 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 0.42121 label assignment complete, 0 changed (0.00%) GCAMregister done in 11.9748 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 0.405931 #GCAMreg# pass 0 level1 5 level2 1 tsec 16.877 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 0.405931 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 0.406103 #GCAMreg# pass 0 level1 4 level2 1 tsec 15.584 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 0.406103 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 0.406183 #GCAMreg# pass 0 level1 3 level2 1 tsec 33.528 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 0.405999 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 5 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.399231 #GCAMreg# pass 0 level1 2 level2 1 tsec 15.027 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 0.399231 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 0.406847 #GCAMreg# pass 0 level1 1 level2 1 tsec 14.605 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 0.406847 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 0.393832 iter 0, gcam->neg = 606 after 21 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 41.23 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 0.383898 GCAMregister done in 7.31882 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4465 tmin = 11.1411 Calls to gcamLabelEnergy 3934 tmin = 0.77945 Calls to gcamJacobianEnergy 4465 tmin = 7.52978 Calls to gcamSmoothnessEnergy 4465 tmin = 7.331 Calls to gcamLogLikelihoodTerm 646 tmin = 3.54722 Calls to gcamLabelTerm 595 tmin = 3.82205 Calls to gcamJacobianTerm 646 tmin = 6.7703 Calls to gcamSmoothnessTerm 646 tmin = 1.60557 Calls to gcamComputeGradient 646 tmin = 33.9855 Calls to gcamComputeMetricProperties 6317 tmin = 10.5452 mri_ca_register took 1 hours, 20 minutes and 29 seconds. #VMPC# mri_ca_register VmPeak 2022080 FSRUNTIME@ mri_ca_register 1.3415 hours 1 threads @#@FSTIME 2023:08:29:17:58:11 mri_ca_register N 9 e 4829.28 S 1.15 U 4823.20 P 99% M 1323508 F 0 R 974770 W 0 c 478873 w 2 I 0 O 62872 L 20.68 18.31 16.33 @#@FSLOADPOST 2023:08:29:19:18:40 mri_ca_register N 9 1.54 1.43 1.52 #-------------------------------------- #@# SubCort Seg Tue Aug 29 19:18:40 PDT 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/7.4.1/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname rnet-lambda-vector machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/7.4.1/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 1 == reading 1 input volumes reading classifier array from /usr/local/freesurfer/7.4.1/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 5.95 Atlas used for the 3D morph was /usr/local/freesurfer/7.4.1/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 = 0.09836 (26) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (1344 voxels, overlap=0.398) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (1344 voxels, peak = 28), gca=27.5 gca peak = 0.20380 (13) mri peak = 0.09490 (24) Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (966 voxels, overlap=0.307) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (966 voxels, peak = 23), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.12825 (99) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (611 voxels, overlap=0.805) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (611 voxels, peak = 100), gca=100.3 gca peak = 0.15814 (97) mri peak = 0.13044 (99) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (545 voxels, overlap=0.781) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (545 voxels, peak = 102), gca=102.3 gca peak = 0.27624 (56) mri peak = 0.11139 (70) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (797 voxels, overlap=0.073) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (797 voxels, peak = 67), gca=67.5 gca peak = 0.28723 (59) mri peak = 0.09495 (73) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (831 voxels, overlap=0.023) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (831 voxels, peak = 72), gca=72.3 gca peak = 0.07623 (103) mri peak = 0.12345 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (34328 voxels, overlap=0.569) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (34328 voxels, peak = 107), gca=106.6 gca peak = 0.07837 (105) mri peak = 0.12681 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (32420 voxels, overlap=0.525) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (32420 voxels, peak = 108), gca=107.6 gca peak = 0.10165 (58) mri peak = 0.05739 (71) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (19982 voxels, overlap=0.283) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (19982 voxels, peak = 70), gca=70.5 gca peak = 0.11113 (58) mri peak = 0.06112 (67) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (17801 voxels, overlap=0.559) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (17801 voxels, peak = 66), gca=66.4 gca peak = 0.27796 (67) mri peak = 0.11439 (76) Right_Caudate (50): linear fit = 1.17 x + 0.0 (795 voxels, overlap=0.055) Right_Caudate (50): linear fit = 1.17 x + 0.0 (795 voxels, peak = 79), gca=78.7 gca peak = 0.14473 (69) mri peak = 0.14547 (80) Left_Caudate (11): linear fit = 1.12 x + 0.0 (880 voxels, overlap=0.365) Left_Caudate (11): linear fit = 1.12 x + 0.0 (880 voxels, peak = 78), gca=77.6 gca peak = 0.14301 (56) mri peak = 0.05772 (68) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (19787 voxels, overlap=0.154) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (19787 voxels, peak = 69), gca=68.6 gca peak = 0.14610 (55) mri peak = 0.05931 (68) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (19258 voxels, overlap=0.267) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (19258 voxels, peak = 66), gca=65.7 gca peak = 0.16309 (85) mri peak = 0.10551 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4540 voxels, overlap=0.661) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4540 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.11109 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5146 voxels, overlap=0.588) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5146 voxels, peak = 89), gca=89.5 gca peak = 0.30461 (58) mri peak = 0.13719 (73) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (452 voxels, overlap=0.041) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (452 voxels, peak = 75), gca=74.5 gca peak = 0.32293 (57) mri peak = 0.11641 (73) Right_Amygdala (54): linear fit = 1.28 x + 0.0 (505 voxels, overlap=0.050) Right_Amygdala (54): linear fit = 1.28 x + 0.0 (505 voxels, peak = 73), gca=73.2 gca peak = 0.11083 (90) mri peak = 0.08510 (93) Left_Thalamus (10): linear fit = 1.04 x + 0.0 (3975 voxels, overlap=0.841) Left_Thalamus (10): linear fit = 1.04 x + 0.0 (3975 voxels, peak = 94), gca=94.0 gca peak = 0.11393 (83) mri peak = 0.07607 (90) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3863 voxels, overlap=0.667) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3863 voxels, peak = 88), gca=88.4 gca peak = 0.08575 (81) mri peak = 0.08105 (90) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1589 voxels, overlap=0.507) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1589 voxels, peak = 89), gca=88.7 gca peak = 0.08618 (78) mri peak = 0.10466 (84) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1652 voxels, overlap=0.426) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1652 voxels, peak = 87), gca=87.0 gca peak = 0.08005 (78) mri peak = 0.08454 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10449 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10449 voxels, peak = 85), gca=85.4 gca peak = 0.12854 (88) mri peak = 0.09321 (98) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1467 voxels, overlap=0.425) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1467 voxels, peak = 95), gca=95.5 gca peak = 0.15703 (87) mri peak = 0.10125 (98) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1433 voxels, overlap=0.516) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1433 voxels, peak = 94), gca=93.5 gca peak = 0.17522 (25) mri peak = 0.20000 (29) gca peak = 0.17113 (14) mri peak = 0.14841 (24) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (234 voxels, overlap=0.580) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (234 voxels, peak = 21), gca=20.5 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 1.23 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.45 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11873 (25) mri peak = 0.09836 (26) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1344 voxels, overlap=0.753) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1344 voxels, peak = 23), gca=23.4 gca peak = 0.16944 (19) mri peak = 0.09490 (24) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (966 voxels, overlap=0.570) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (966 voxels, peak = 23), gca=22.5 gca peak = 0.21728 (100) mri peak = 0.12825 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (611 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (611 voxels, peak = 100), gca=100.5 gca peak = 0.16048 (100) mri peak = 0.13044 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (545 voxels, overlap=0.838) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (545 voxels, peak = 100), gca=100.5 gca peak = 0.27313 (67) mri peak = 0.11139 (70) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (797 voxels, overlap=1.001) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (797 voxels, peak = 66), gca=66.0 gca peak = 0.31098 (69) mri peak = 0.09495 (73) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (831 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (831 voxels, peak = 71), gca=70.7 gca peak = 0.07636 (107) mri peak = 0.12345 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34328 voxels, overlap=0.723) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34328 voxels, peak = 107), gca=107.0 gca peak = 0.07733 (107) mri peak = 0.12681 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32420 voxels, overlap=0.642) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32420 voxels, peak = 107), gca=107.0 gca peak = 0.08003 (69) mri peak = 0.05739 (71) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (19982 voxels, overlap=0.960) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (19982 voxels, peak = 68), gca=68.0 gca peak = 0.10021 (67) mri peak = 0.06112 (67) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (17801 voxels, overlap=0.949) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (17801 voxels, peak = 67), gca=67.0 gca peak = 0.21888 (78) mri peak = 0.11439 (76) Right_Caudate (50): linear fit = 0.96 x + 0.0 (795 voxels, overlap=0.686) Right_Caudate (50): linear fit = 0.96 x + 0.0 (795 voxels, peak = 75), gca=75.3 gca peak = 0.14147 (77) mri peak = 0.14547 (80) Left_Caudate (11): linear fit = 0.94 x + 0.0 (880 voxels, overlap=0.581) Left_Caudate (11): linear fit = 0.94 x + 0.0 (880 voxels, peak = 72), gca=72.0 gca peak = 0.11353 (69) mri peak = 0.05772 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (19787 voxels, overlap=0.979) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (19787 voxels, peak = 68), gca=68.0 gca peak = 0.13127 (66) mri peak = 0.05931 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (19258 voxels, overlap=0.983) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (19258 voxels, peak = 66), gca=66.0 gca peak = 0.15248 (90) mri peak = 0.10551 (87) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4540 voxels, overlap=0.952) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4540 voxels, peak = 89), gca=88.7 gca peak = 0.16966 (90) mri peak = 0.11109 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5146 voxels, overlap=0.916) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5146 voxels, peak = 90), gca=89.6 gca peak = 0.26177 (73) mri peak = 0.13719 (73) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (452 voxels, overlap=0.667) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (452 voxels, peak = 72), gca=71.9 gca peak = 0.28196 (73) mri peak = 0.11641 (73) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (505 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (505 voxels, peak = 74), gca=74.1 gca peak = 0.10860 (94) mri peak = 0.08510 (93) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3975 voxels, overlap=0.895) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3975 voxels, peak = 94), gca=93.5 gca peak = 0.09922 (86) mri peak = 0.07607 (90) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3863 voxels, overlap=0.937) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3863 voxels, peak = 86), gca=85.6 gca peak = 0.07732 (87) mri peak = 0.08105 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1589 voxels, overlap=0.865) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1589 voxels, peak = 87), gca=86.6 gca peak = 0.08076 (86) mri peak = 0.10466 (84) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1652 voxels, overlap=0.829) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1652 voxels, peak = 85), gca=84.7 gca peak = 0.08438 (86) mri peak = 0.08454 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10449 voxels, overlap=0.731) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10449 voxels, peak = 86), gca=85.6 gca peak = 0.11740 (97) mri peak = 0.09321 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1467 voxels, overlap=0.805) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1467 voxels, peak = 97), gca=96.5 gca peak = 0.14874 (93) mri peak = 0.10125 (98) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1433 voxels, overlap=0.866) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1433 voxels, peak = 95), gca=95.3 gca peak = 0.13112 (36) mri peak = 0.20000 (29) gca peak = 0.12908 (21) mri peak = 0.14841 (24) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (234 voxels, overlap=0.740) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (234 voxels, peak = 21), gca=20.7 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.17357 (34) gca peak Third_Ventricle = 0.13112 (36) gca peak CSF = 0.16418 (52) gca peak Left_Accumbens_area = 0.75365 (70) gca peak Left_undetermined = 0.99358 (32) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11426 (35) gca peak Right_Inf_Lat_Vent = 0.26261 (28) gca peak Right_Accumbens_area = 0.30854 (76) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13918 (38) gca peak Fifth_Ventricle = 0.59466 (46) gca peak WM_hypointensities = 0.10283 (79) gca peak non_WM_hypointensities = 0.14678 (42) gca peak Optic_Chiasm = 0.51654 (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 1.03 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 63112 voxels changed in iteration 0 of unlikely voxel relabeling 176 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 43384 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 394 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 66363 changed. image ll: -2.086, PF=0.500 pass 2: 16193 changed. image ll: -2.086, PF=0.500 pass 3: 4069 changed. 42542 voxels changed in iteration 0 of unlikely voxel relabeling 174 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6293 voxels changed in iteration 0 of unlikely voxel relabeling 87 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5132 voxels changed in iteration 0 of unlikely voxel relabeling 29 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4437 voxels changed in iteration 0 of unlikely voxel relabeling 29 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 1 with volume 6173 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 4 with volume 5297 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 132 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1569.050185 mri_ca_label stimesec 1.031367 mri_ca_label ru_maxrss 2087608 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1073452 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 664 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 0 mri_ca_label ru_nivcsw 153325 mri_ca_label took 26 minutes and 11 seconds. mri_ca_label done @#@FSTIME 2023:08:29:19:18:40 mri_ca_label N 10 e 1571.14 S 1.13 U 1569.05 P 99% M 2087608 F 0 R 1073456 W 0 c 153335 w 1 I 0 O 664 L 1.54 1.43 1.52 @#@FSLOADPOST 2023:08:29:19:44:52 mri_ca_label N 10 1.14 1.25 1.31 #-------------------------------------- #@# CC Seg Tue Aug 29 19:44:52 PDT 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/cc_up.lta EP01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/7.4.1/subjects/EP01/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/7.4.1/subjects/EP01/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/7.4.1/subjects/EP01/mri/norm.mgz 28886 voxels in left wm, 49700 in right wm, xrange [123, 133] searching rotation angles z=[-12 2], y=[-6 8] searching scale 1 Z rot -11.6 searching scale 1 Z rot -11.4 searching scale 1 Z rot -11.1 searching scale 1 Z rot -10.9 searching scale 1 Z rot -10.6 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 global minimum found at slice 129.0, rotations (1.71, -4.40) final transformation (x=129.0, yr=1.712, zr=-4.397): 0.99661 0.07666 0.02979 -13.16217; -0.07662 0.99706 -0.00229 16.49313; -0.02988 0.00000 0.99955 22.90261; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 min_x_fornix = 139 min_x_fornix = 141 WARNING: min_x_fornix not set min_x_fornix = 146 min_x_fornix = 134 cc center is found at 128 122 109 eigenvectors: 0.00161 -0.00307 0.99999; -0.00666 -0.99997 -0.00306; 0.99998 -0.00666 -0.00163; writing aseg with callosum to /usr/local/freesurfer/7.4.1/subjects/EP01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #VMPC# mri_cc VmPeak 445760 mri_cc done @#@FSTIME 2023:08:29:19:44:52 mri_cc N 7 e 24.33 S 0.24 U 24.07 P 99% M 345320 F 0 R 277535 W 0 c 2418 w 1 I 0 O 656 L 1.14 1.25 1.31 @#@FSLOADPOST 2023:08:29:19:45:16 mri_cc N 7 1.21 1.26 1.31 #-------------------------------------- #@# Merge ASeg Tue Aug 29 19:45:16 PDT 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Aug 29 19:45:16 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 aseg read with width 256 (src width 256) ************** resampling aseg to account for mismatch with source image *************** normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 515 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 75 (75), valley at 35 (35) csf peak at 13, setting threshold to 54 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 74 (74), valley at 35 (35) csf peak at 13, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 44 seconds. @#@FSTIME 2023:08:29:19:45:16 mri_normalize N 9 e 108.13 S 0.81 U 107.15 P 99% M 1202900 F 0 R 665921 W 0 c 12278 w 1 I 0 O 2528 L 1.21 1.26 1.31 @#@FSLOADPOST 2023:08:29:19:47:04 mri_normalize N 9 1.35 1.31 1.32 #-------------------------------------------- #@# Mask BFS Tue Aug 29 19:47:04 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1482351 voxels in mask (pct= 8.84) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2023:08:29:19:47:04 mri_mask N 5 e 1.15 S 0.01 U 1.14 P 99% M 74224 F 0 R 17259 W 0 c 112 w 1 I 0 O 2472 L 1.35 1.31 1.32 @#@FSLOADPOST 2023:08:29:19:47:05 mri_mask N 5 1.35 1.31 1.32 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Tue Aug 29 19:47:05 PDT 2023 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2023:08:29:19:47:05 AntsDenoiseImageFs N 4 e 30.55 S 0.09 U 30.43 P 99% M 350980 F 0 R 86504 W 0 c 2987 w 1 I 0 O 2536 L 1.35 1.31 1.32 @#@FSLOADPOST 2023:08:29:19:47:36 AntsDenoiseImageFs N 4 1.28 1.29 1.32 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 MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 357013, nonwhite = 16095196, ambig = 325007, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (101.0): 100.2 +- 6.0 [79.0 --> 125.0] CCS GM (75.0) : 74.5 +- 10.0 [30.0 --> 95.0] white_mean 100.18 white_sigma 6.00685 gray_mean 74.5143 gray_sigma 9.96415 setting bottom of white matter range wm_low to 84.5 setting top of gray matter range gray_hi to 94.4 wm_low 84.4784 wm_hi 125 gray_low 30 gray_hi 94.4426 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=84.4784, wm_hi=125, gray_hi=94.4426 white = 426402, nonwhite = 16211627, ambig = 139187, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 84.4784 wm_hi 125 gray_low 30 gray_hi 94.4426 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 94.4426, wm_low = 84.4784 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=94.4426, wmlow=84.4784 104546 voxels processed (0.62%) 46006 voxels white (0.27%) 58540 voxels non-white (0.35%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=79.4784, gray_hi=94.4426, wsize=13 233748 voxels tested (1.39%) 42899 voxels changed (0.26%) 41942 multi-scale searches (0.25%) Recovering bright white MRIrecoverBrightWhite() wm_low 84.4784 wm_hi 125 slack 6.00685 pct_thresh 0.33 intensity_thresh 131.007 nvox_thresh 8.58 130 voxels tested (0.00%) 52 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=79.4784, hithr=94.4426 smoothing input volume with sigma = 0.250 89199 voxels tested (0.53%) 15001 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 3278 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1527 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4867 filled MRIfindBrightNonWM(): 806 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 0.7 minutes writing output to wm.seg.mgz... @#@FSTIME 2023:08:29:19:47:36 mri_segment N 5 e 43.86 S 0.21 U 43.62 P 99% M 144184 F 0 R 295929 W 0 c 4297 w 1 I 0 O 808 L 1.28 1.29 1.32 @#@FSLOADPOST 2023:08:29:19:48:20 mri_segment N 5 1.32 1.30 1.32 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.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 0.35 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2797 additional wm voxels added 0 additional wm voxels added SEG EDIT: 37473 voxels turned on, 36769 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2023:08:29:19:48:20 mri_edit_wm_with_aseg N 5 e 21.07 S 0.20 U 20.82 P 99% M 462564 F 0 R 317284 W 0 c 2652 w 2 I 0 O 744 L 1.32 1.30 1.32 @#@FSLOADPOST 2023:08:29:19:48:41 mri_edit_wm_with_aseg N 5 1.37 1.31 1.32 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 16 found - 16 modified | TOTAL: 32 pass 2 (xy-): 0 found - 16 modified | TOTAL: 32 pass 1 (yz+): 21 found - 21 modified | TOTAL: 53 pass 2 (yz+): 0 found - 21 modified | TOTAL: 53 pass 1 (yz-): 12 found - 12 modified | TOTAL: 65 pass 2 (yz-): 0 found - 12 modified | TOTAL: 65 pass 1 (xz+): 15 found - 15 modified | TOTAL: 80 pass 2 (xz+): 0 found - 15 modified | TOTAL: 80 pass 1 (xz-): 15 found - 15 modified | TOTAL: 95 pass 2 (xz-): 0 found - 15 modified | TOTAL: 95 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 4 found - 4 modified | TOTAL: 10 pass 2 (+++): 0 found - 4 modified | TOTAL: 10 pass 1 (+++): 8 found - 8 modified | TOTAL: 18 pass 2 (+++): 0 found - 8 modified | TOTAL: 18 pass 1 (+++): 6 found - 6 modified | TOTAL: 24 pass 2 (+++): 0 found - 6 modified | TOTAL: 24 Iteration Number : 1 pass 1 (++): 59 found - 59 modified | TOTAL: 59 pass 2 (++): 0 found - 59 modified | TOTAL: 59 pass 1 (+-): 98 found - 98 modified | TOTAL: 157 pass 2 (+-): 0 found - 98 modified | TOTAL: 157 pass 1 (--): 43 found - 43 modified | TOTAL: 200 pass 2 (--): 0 found - 43 modified | TOTAL: 200 pass 1 (-+): 82 found - 82 modified | TOTAL: 282 pass 2 (-+): 0 found - 82 modified | TOTAL: 282 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 2 found - 2 modified | TOTAL: 8 pass 2 (yz+): 0 found - 2 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 1 found - 1 modified | TOTAL: 10 pass 2 (xz+): 0 found - 1 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 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 = 414 (out of 495261: 0.083592) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:08:29:19:48:41 mri_pretess N 4 e 2.75 S 0.01 U 2.73 P 99% M 56700 F 0 R 12955 W 0 c 267 w 1 I 0 O 744 L 1.37 1.31 1.32 @#@FSLOADPOST 2023:08:29:19:48:44 mri_pretess N 4 1.34 1.30 1.32 #-------------------------------------------- #@# Fill Tue Aug 29 19:48:44 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/7.4.1/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... done. searching for cutting planes...voxel to talairach voxel transform 1.05317 0.12767 0.04677 -31.01361; -0.11329 1.20845 0.14210 -44.94489; -0.03253 -0.08129 1.03404 11.07053; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.05317 0.12767 0.04677 -31.01361; -0.11329 1.20845 0.14210 -44.94489; -0.03253 -0.08129 1.03404 11.07053; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 2481 (min = 350, max = 1400), aspect = 1.29 (min = 0.10, max = 0.75) need search nearby using seed (126, 115, 89), TAL = (2.0, -39.0, 13.0) talairach voxel to voxel transform 0.93777 -0.10100 -0.02854 24.86038; 0.08367 0.81091 -0.11522 40.31705; 0.03608 0.06057 0.95712 -6.75444; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 115, 89) --> (2.0, -39.0, 13.0) done. filling took 0.8 minutes talairach cc position changed to (2.00, -39.00, 13.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -39.00, 13.00) SRC: (111.99, 132.35, 89.29) search lh wm seed point around talairach space (-16.00, -39.00, 13.00), SRC: (145.75, 135.37, 90.59) 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... @#@FSTIME 2023:08:29:19:48:44 mri_fill N 10 e 48.39 S 0.72 U 47.62 P 99% M 972712 F 0 R 513723 W 0 c 4833 w 1 I 0 O 248 L 1.34 1.30 1.32 @#@FSLOADPOST 2023:08:29:19:49:32 mri_fill N 10 1.16 1.26 1.30 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Tue Aug 29 19:49:32 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 9 found - 9 modified | TOTAL: 9 pass 2 (yz+): 0 found - 9 modified | TOTAL: 9 pass 1 (yz-): 10 found - 10 modified | TOTAL: 19 pass 2 (yz-): 0 found - 10 modified | TOTAL: 19 pass 1 (xz+): 0 found - 0 modified | TOTAL: 19 pass 1 (xz-): 1 found - 1 modified | TOTAL: 20 pass 2 (xz-): 0 found - 1 modified | TOTAL: 20 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 20 (out of 239501: 0.008351) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:08:29:19:49:32 mri_pretess N 4 e 1.51 S 0.00 U 1.50 P 99% M 40412 F 0 R 8814 W 0 c 146 w 1 I 0 O 240 L 1.16 1.26 1.30 @#@FSLOADPOST 2023:08:29:19:49:34 mri_pretess N 4 1.15 1.25 1.30 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.4.1 7.4.1 slice 40: 1613 vertices, 1743 faces slice 50: 7718 vertices, 7963 faces slice 60: 15821 vertices, 16139 faces slice 70: 24911 vertices, 25230 faces slice 80: 34047 vertices, 34314 faces slice 90: 43545 vertices, 43865 faces slice 100: 54203 vertices, 54601 faces slice 110: 64652 vertices, 65008 faces slice 120: 74801 vertices, 75161 faces slice 130: 84984 vertices, 85335 faces slice 140: 93719 vertices, 94007 faces slice 150: 101638 vertices, 101921 faces slice 160: 108352 vertices, 108620 faces slice 170: 114619 vertices, 114878 faces slice 180: 119344 vertices, 119507 faces slice 190: 122179 vertices, 122241 faces slice 200: 122302 vertices, 122328 faces slice 210: 122302 vertices, 122328 faces slice 220: 122302 vertices, 122328 faces slice 230: 122302 vertices, 122328 faces slice 240: 122302 vertices, 122328 faces slice 250: 122302 vertices, 122328 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2023:08:29:19:49:34 mri_tessellate N 3 e 1.16 S 0.01 U 1.14 P 99% M 36440 F 0 R 8092 W 0 c 110 w 1 I 0 O 5736 L 1.15 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:35 mri_tessellate N 3 1.15 1.25 1.30 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 122302 voxel in cpt #1: X=-26 [v=122302,e=366984,f=244656] located at (-27.552698, -21.161951, -4.259227) For the whole surface: X=-26 [v=122302,e=366984,f=244656] One single component has been found nothing to do done @#@FSTIME 2023:08:29:19:49:35 mris_extract_main_component N 2 e 0.55 S 0.08 U 0.47 P 99% M 244020 F 0 R 64261 W 0 c 55 w 1 I 0 O 8608 L 1.15 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:35 mris_extract_main_component N 2 1.15 1.25 1.30 #-------------------------------------------- #@# Tessellate rh Tue Aug 29 19:49:35 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 10 found - 10 modified | TOTAL: 11 pass 2 (yz+): 0 found - 10 modified | TOTAL: 11 pass 1 (yz-): 8 found - 8 modified | TOTAL: 19 pass 2 (yz-): 0 found - 8 modified | TOTAL: 19 pass 1 (xz+): 0 found - 0 modified | TOTAL: 19 pass 1 (xz-): 0 found - 0 modified | TOTAL: 19 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 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 = 22 (out of 239414: 0.009189) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:08:29:19:49:35 mri_pretess N 4 e 1.87 S 0.01 U 1.85 P 99% M 40568 F 0 R 8820 W 0 c 178 w 1 I 0 O 240 L 1.15 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:37 mri_pretess N 4 1.15 1.25 1.30 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.4.1 7.4.1 slice 40: 1849 vertices, 1978 faces slice 50: 7288 vertices, 7503 faces slice 60: 15329 vertices, 15651 faces slice 70: 24946 vertices, 25279 faces slice 80: 35214 vertices, 35529 faces slice 90: 44585 vertices, 44923 faces slice 100: 56489 vertices, 56863 faces slice 110: 67206 vertices, 67556 faces slice 120: 77415 vertices, 77764 faces slice 130: 87671 vertices, 87981 faces slice 140: 96266 vertices, 96569 faces slice 150: 103840 vertices, 104102 faces slice 160: 110248 vertices, 110486 faces slice 170: 116113 vertices, 116342 faces slice 180: 120575 vertices, 120728 faces slice 190: 123135 vertices, 123197 faces slice 200: 123380 vertices, 123414 faces slice 210: 123380 vertices, 123414 faces slice 220: 123380 vertices, 123414 faces slice 230: 123380 vertices, 123414 faces slice 240: 123380 vertices, 123414 faces slice 250: 123380 vertices, 123414 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2023:08:29:19:49:37 mri_tessellate N 3 e 1.11 S 0.01 U 1.10 P 99% M 36444 F 0 R 8111 W 0 c 105 w 1 I 0 O 5792 L 1.15 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:38 mri_tessellate N 3 1.13 1.25 1.30 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 123380 voxel in cpt #1: X=-34 [v=123380,e=370242,f=246828] located at (26.678238, -22.193962, 0.476131) For the whole surface: X=-34 [v=123380,e=370242,f=246828] One single component has been found nothing to do done @#@FSTIME 2023:08:29:19:49:38 mris_extract_main_component N 2 e 0.61 S 0.07 U 0.54 P 99% M 246088 F 0 R 64845 W 0 c 58 w 1 I 0 O 8680 L 1.13 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:39 mris_extract_main_component N 2 1.13 1.25 1.30 #-------------------------------------------- #@# Smooth1 lh Tue Aug 29 19:49:39 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:08:29:19:49:39 mris_smooth N 5 e 1.83 S 0.07 U 1.76 P 99% M 194596 F 0 R 58120 W 0 c 181 w 1 I 0 O 8608 L 1.13 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:41 mris_smooth N 5 1.13 1.25 1.30 #-------------------------------------------- #@# Smooth1 rh Tue Aug 29 19:49:41 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:08:29:19:49:41 mris_smooth N 5 e 1.85 S 0.06 U 1.78 P 99% M 196184 F 0 R 58646 W 0 c 179 w 1 I 0 O 8680 L 1.13 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:43 mris_smooth N 5 1.13 1.25 1.30 #-------------------------------------------- #@# Inflation1 lh Tue Aug 29 19:49:43 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.5 mm, total surface area = 65800 mm^2 step 000: RMS=0.148 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.032 (target=0.015) step 060: RMS=0.031 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 11.007459 mris_inflate stimesec 0.659248 mris_inflate ru_maxrss 194876 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 518636 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8608 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1153 @#@FSTIME 2023:08:29:19:49:43 mris_inflate N 3 e 11.68 S 0.66 U 11.00 P 99% M 194876 F 0 R 518641 W 0 c 1153 w 1 I 0 O 8608 L 1.13 1.25 1.30 @#@FSLOADPOST 2023:08:29:19:49:55 mris_inflate N 3 1.10 1.24 1.29 #-------------------------------------------- #@# Inflation1 rh Tue Aug 29 19:49:55 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.2 mm, total surface area = 66398 mm^2 step 000: RMS=0.151 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.035 (target=0.015) step 060: RMS=0.034 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 12.326782 mris_inflate stimesec 0.667068 mris_inflate ru_maxrss 196456 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 523289 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 0 mris_inflate ru_nivcsw 1308 @#@FSTIME 2023:08:29:19:49:55 mris_inflate N 3 e 13.02 S 0.67 U 12.32 P 99% M 196456 F 0 R 523294 W 0 c 1309 w 1 I 0 O 8680 L 1.10 1.24 1.29 @#@FSLOADPOST 2023:08:29:19:50:08 mris_inflate N 3 1.09 1.23 1.29 #-------------------------------------------- #@# QSphere lh Tue Aug 29 19:50:08 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 scaling brain by 0.323... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.05 +- 0.59 (0.00-->7.43) (max @ vno 49403 --> 49415) face area 0.03 +- 0.03 (-0.26-->0.77) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.877, avgs=0 005/300: dt: 0.9000, rms radial error=176.617, avgs=0 010/300: dt: 0.9000, rms radial error=176.059, avgs=0 015/300: dt: 0.9000, rms radial error=175.327, avgs=0 020/300: dt: 0.9000, rms radial error=174.493, avgs=0 025/300: dt: 0.9000, rms radial error=173.600, avgs=0 030/300: dt: 0.9000, rms radial error=172.674, avgs=0 035/300: dt: 0.9000, rms radial error=171.732, avgs=0 040/300: dt: 0.9000, rms radial error=170.781, avgs=0 045/300: dt: 0.9000, rms radial error=169.828, avgs=0 050/300: dt: 0.9000, rms radial error=168.877, avgs=0 055/300: dt: 0.9000, rms radial error=167.930, avgs=0 060/300: dt: 0.9000, rms radial error=166.989, avgs=0 065/300: dt: 0.9000, rms radial error=166.055, avgs=0 070/300: dt: 0.9000, rms radial error=165.126, avgs=0 075/300: dt: 0.9000, rms radial error=164.202, avgs=0 080/300: dt: 0.9000, rms radial error=163.283, avgs=0 085/300: dt: 0.9000, rms radial error=162.369, avgs=0 090/300: dt: 0.9000, rms radial error=161.460, avgs=0 095/300: dt: 0.9000, rms radial error=160.555, avgs=0 100/300: dt: 0.9000, rms radial error=159.655, avgs=0 105/300: dt: 0.9000, rms radial error=158.760, avgs=0 110/300: dt: 0.9000, rms radial error=157.870, avgs=0 115/300: dt: 0.9000, rms radial error=156.985, avgs=0 120/300: dt: 0.9000, rms radial error=156.104, avgs=0 125/300: dt: 0.9000, rms radial error=155.228, avgs=0 130/300: dt: 0.9000, rms radial error=154.357, avgs=0 135/300: dt: 0.9000, rms radial error=153.491, avgs=0 140/300: dt: 0.9000, rms radial error=152.629, avgs=0 145/300: dt: 0.9000, rms radial error=151.771, avgs=0 150/300: dt: 0.9000, rms radial error=150.919, avgs=0 155/300: dt: 0.9000, rms radial error=150.071, avgs=0 160/300: dt: 0.9000, rms radial error=149.227, avgs=0 165/300: dt: 0.9000, rms radial error=148.388, avgs=0 170/300: dt: 0.9000, rms radial error=147.554, avgs=0 175/300: dt: 0.9000, rms radial error=146.724, avgs=0 180/300: dt: 0.9000, rms radial error=145.899, avgs=0 185/300: dt: 0.9000, rms radial error=145.078, avgs=0 190/300: dt: 0.9000, rms radial error=144.262, avgs=0 195/300: dt: 0.9000, rms radial error=143.450, avgs=0 200/300: dt: 0.9000, rms radial error=142.642, avgs=0 205/300: dt: 0.9000, rms radial error=141.839, avgs=0 210/300: dt: 0.9000, rms radial error=141.041, avgs=0 215/300: dt: 0.9000, rms radial error=140.247, avgs=0 220/300: dt: 0.9000, rms radial error=139.457, avgs=0 225/300: dt: 0.9000, rms radial error=138.672, avgs=0 230/300: dt: 0.9000, rms radial error=137.890, avgs=0 235/300: dt: 0.9000, rms radial error=137.114, avgs=0 240/300: dt: 0.9000, rms radial error=136.341, avgs=0 245/300: dt: 0.9000, rms radial error=135.573, avgs=0 250/300: dt: 0.9000, rms radial error=134.809, avgs=0 255/300: dt: 0.9000, rms radial error=134.050, avgs=0 260/300: dt: 0.9000, rms radial error=133.294, avgs=0 265/300: dt: 0.9000, rms radial error=132.543, avgs=0 270/300: dt: 0.9000, rms radial error=131.796, avgs=0 275/300: dt: 0.9000, rms radial error=131.053, avgs=0 280/300: dt: 0.9000, rms radial error=130.314, avgs=0 285/300: dt: 0.9000, rms radial error=129.580, avgs=0 290/300: dt: 0.9000, rms radial error=128.849, avgs=0 295/300: dt: 0.9000, rms radial error=128.123, avgs=0 300/300: dt: 0.9000, rms radial error=127.401, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14063.22 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00033 epoch 2 (K=40.0), pass 1, starting sse = 2217.32 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00063 epoch 3 (K=160.0), pass 1, starting sse = 193.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/17 = 0.00985 epoch 4 (K=640.0), pass 1, starting sse = 6.96 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/21 = 0.00641 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0234 hours FSRUNTIME@ mris_sphere 0.0234 hours 1 threads #VMPC# mris_sphere VmPeak 464176 mris_sphere done @#@FSTIME 2023:08:29:19:50:08 mris_sphere N 9 e 84.08 S 3.68 U 80.24 P 99% M 199232 F 0 R 3185717 W 0 c 8949 w 1 I 0 O 8608 L 1.09 1.23 1.29 @#@FSLOADPOST 2023:08:29:19:51:32 mris_sphere N 9 1.19 1.23 1.28 #-------------------------------------------- #@# QSphere rh Tue Aug 29 19:51:32 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 scaling brain by 0.319... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.04 +- 0.58 (0.00-->6.44) (max @ vno 47710 --> 47711) face area 0.03 +- 0.03 (-0.06-->0.69) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.111, avgs=0 005/300: dt: 0.9000, rms radial error=176.851, avgs=0 010/300: dt: 0.9000, rms radial error=176.292, avgs=0 015/300: dt: 0.9000, rms radial error=175.560, avgs=0 020/300: dt: 0.9000, rms radial error=174.726, avgs=0 025/300: dt: 0.9000, rms radial error=173.835, avgs=0 030/300: dt: 0.9000, rms radial error=172.911, avgs=0 035/300: dt: 0.9000, rms radial error=171.969, avgs=0 040/300: dt: 0.9000, rms radial error=171.020, avgs=0 045/300: dt: 0.9000, rms radial error=170.067, avgs=0 050/300: dt: 0.9000, rms radial error=169.115, avgs=0 055/300: dt: 0.9000, rms radial error=168.165, avgs=0 060/300: dt: 0.9000, rms radial error=167.219, avgs=0 065/300: dt: 0.9000, rms radial error=166.278, avgs=0 070/300: dt: 0.9000, rms radial error=165.342, avgs=0 075/300: dt: 0.9000, rms radial error=164.413, avgs=0 080/300: dt: 0.9000, rms radial error=163.489, avgs=0 085/300: dt: 0.9000, rms radial error=162.570, avgs=0 090/300: dt: 0.9000, rms radial error=161.656, avgs=0 095/300: dt: 0.9000, rms radial error=160.746, avgs=0 100/300: dt: 0.9000, rms radial error=159.842, avgs=0 105/300: dt: 0.9000, rms radial error=158.943, avgs=0 110/300: dt: 0.9000, rms radial error=158.049, avgs=0 115/300: dt: 0.9000, rms radial error=157.159, avgs=0 120/300: dt: 0.9000, rms radial error=156.274, avgs=0 125/300: dt: 0.9000, rms radial error=155.394, avgs=0 130/300: dt: 0.9000, rms radial error=154.519, avgs=0 135/300: dt: 0.9000, rms radial error=153.649, avgs=0 140/300: dt: 0.9000, rms radial error=152.783, avgs=0 145/300: dt: 0.9000, rms radial error=151.923, avgs=0 150/300: dt: 0.9000, rms radial error=151.067, avgs=0 155/300: dt: 0.9000, rms radial error=150.216, avgs=0 160/300: dt: 0.9000, rms radial error=149.369, avgs=0 165/300: dt: 0.9000, rms radial error=148.527, avgs=0 170/300: dt: 0.9000, rms radial error=147.690, avgs=0 175/300: dt: 0.9000, rms radial error=146.858, avgs=0 180/300: dt: 0.9000, rms radial error=146.030, avgs=0 185/300: dt: 0.9000, rms radial error=145.207, avgs=0 190/300: dt: 0.9000, rms radial error=144.388, avgs=0 195/300: dt: 0.9000, rms radial error=143.574, avgs=0 200/300: dt: 0.9000, rms radial error=142.765, avgs=0 205/300: dt: 0.9000, rms radial error=141.961, avgs=0 210/300: dt: 0.9000, rms radial error=141.161, avgs=0 215/300: dt: 0.9000, rms radial error=140.366, avgs=0 220/300: dt: 0.9000, rms radial error=139.575, avgs=0 225/300: dt: 0.9000, rms radial error=138.788, avgs=0 230/300: dt: 0.9000, rms radial error=138.006, avgs=0 235/300: dt: 0.9000, rms radial error=137.229, avgs=0 240/300: dt: 0.9000, rms radial error=136.455, avgs=0 245/300: dt: 0.9000, rms radial error=135.687, avgs=0 250/300: dt: 0.9000, rms radial error=134.923, avgs=0 255/300: dt: 0.9000, rms radial error=134.163, avgs=0 260/300: dt: 0.9000, rms radial error=133.408, avgs=0 265/300: dt: 0.9000, rms radial error=132.656, avgs=0 270/300: dt: 0.9000, rms radial error=131.909, avgs=0 275/300: dt: 0.9000, rms radial error=131.166, avgs=0 280/300: dt: 0.9000, rms radial error=130.428, avgs=0 285/300: dt: 0.9000, rms radial error=129.693, avgs=0 290/300: dt: 0.9000, rms radial error=128.962, avgs=0 295/300: dt: 0.9000, rms radial error=128.236, avgs=0 300/300: dt: 0.9000, rms radial error=127.514, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14243.13 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00033 epoch 2 (K=40.0), pass 1, starting sse = 2246.12 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00061 epoch 3 (K=160.0), pass 1, starting sse = 190.93 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/18 = 0.00934 epoch 4 (K=640.0), pass 1, starting sse = 7.23 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/22 = 0.00571 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0239 hours FSRUNTIME@ mris_sphere 0.0239 hours 1 threads #VMPC# mris_sphere VmPeak 465960 mris_sphere done @#@FSTIME 2023:08:29:19:51:32 mris_sphere N 9 e 86.09 S 3.76 U 82.23 P 99% M 201348 F 0 R 3271192 W 0 c 8593 w 1 I 0 O 8688 L 1.19 1.23 1.28 @#@FSLOADPOST 2023:08:29:19:52:58 mris_sphere N 9 1.25 1.25 1.28 #@# Fix Topology lh Tue Aug 29 19:52:58 PDT 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 EP01 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' 7.4.1 7.4.1 before topology correction, eno=-26 (nv=122302, nf=244656, ne=366984, g=14) 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 7 iterations marking ambiguous vertices... 1423 ambiguous faces found in tessellation segmenting defects... 24 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 24 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.2312 (-4.6156) -vertex loglikelihood: -6.2714 (-3.1357) -normal dot loglikelihood: -3.6520 (-3.6520) -quad curv loglikelihood: -6.1852 (-3.0926) Total Loglikelihood : -25.3398 CORRECTING DEFECT 0 (vertices=45, convex hull=95, v0=1971) After retessellation of defect 0 (v0=1971), euler #=-20 (121368,363590,242202) : difference with theory (-21) = -1 CORRECTING DEFECT 1 (vertices=67, convex hull=116, v0=46178) After retessellation of defect 1 (v0=46178), euler #=-19 (121378,363669,242272) : difference with theory (-20) = -1 CORRECTING DEFECT 2 (vertices=6, convex hull=21, v0=49230) After retessellation of defect 2 (v0=49230), euler #=-18 (121381,363684,242285) : difference with theory (-19) = -1 CORRECTING DEFECT 3 (vertices=11, convex hull=35, v0=50601) After retessellation of defect 3 (v0=50601), euler #=-17 (121383,363699,242299) : difference with theory (-18) = -1 CORRECTING DEFECT 4 (vertices=16, convex hull=56, v0=55282) After retessellation of defect 4 (v0=55282), euler #=-16 (121392,363744,242336) : difference with theory (-17) = -1 CORRECTING DEFECT 5 (vertices=11, convex hull=35, v0=58104) After retessellation of defect 5 (v0=58104), euler #=-15 (121395,363765,242355) : difference with theory (-16) = -1 CORRECTING DEFECT 6 (vertices=7, convex hull=34, v0=65446) After retessellation of defect 6 (v0=65446), euler #=-14 (121397,363778,242367) : difference with theory (-15) = -1 CORRECTING DEFECT 7 (vertices=5, convex hull=20, v0=67484) After retessellation of defect 7 (v0=67484), euler #=-13 (121398,363785,242374) : difference with theory (-14) = -1 CORRECTING DEFECT 8 (vertices=121, convex hull=110, v0=72803) After retessellation of defect 8 (v0=72803), euler #=-13 (121465,364047,242569) : difference with theory (-13) = 0 CORRECTING DEFECT 9 (vertices=23, convex hull=50, v0=75429) After retessellation of defect 9 (v0=75429), euler #=-12 (121473,364088,242603) : difference with theory (-12) = 0 CORRECTING DEFECT 10 (vertices=32, convex hull=72, v0=75595) After retessellation of defect 10 (v0=75595), euler #=-11 (121491,364172,242670) : difference with theory (-11) = 0 CORRECTING DEFECT 11 (vertices=23, convex hull=46, v0=75812) After retessellation of defect 11 (v0=75812), euler #=-10 (121504,364226,242712) : difference with theory (-10) = 0 CORRECTING DEFECT 12 (vertices=36, convex hull=61, v0=76487) After retessellation of defect 12 (v0=76487), euler #=-9 (121524,364310,242777) : difference with theory (-9) = 0 CORRECTING DEFECT 13 (vertices=94, convex hull=42, v0=77693) After retessellation of defect 13 (v0=77693), euler #=-8 (121535,364359,242816) : difference with theory (-8) = 0 CORRECTING DEFECT 14 (vertices=25, convex hull=17, v0=78525) After retessellation of defect 14 (v0=78525), euler #=-7 (121537,364369,242825) : difference with theory (-7) = 0 CORRECTING DEFECT 15 (vertices=120, convex hull=174, v0=81866) After retessellation of defect 15 (v0=81866), euler #=-6 (121591,364610,243013) : difference with theory (-6) = 0 CORRECTING DEFECT 16 (vertices=29, convex hull=29, v0=84695) After retessellation of defect 16 (v0=84695), euler #=-5 (121595,364633,243033) : difference with theory (-5) = 0 CORRECTING DEFECT 17 (vertices=57, convex hull=53, v0=85561) After retessellation of defect 17 (v0=85561), euler #=-4 (121612,364704,243088) : difference with theory (-4) = 0 CORRECTING DEFECT 18 (vertices=177, convex hull=169, v0=85838) After retessellation of defect 18 (v0=85838), euler #=-3 (121673,364965,243289) : difference with theory (-3) = 0 CORRECTING DEFECT 19 (vertices=6, convex hull=24, v0=91343) After retessellation of defect 19 (v0=91343), euler #=-2 (121674,364974,243298) : difference with theory (-2) = 0 CORRECTING DEFECT 20 (vertices=5, convex hull=17, v0=92109) After retessellation of defect 20 (v0=92109), euler #=-1 (121675,364980,243304) : difference with theory (-1) = 0 CORRECTING DEFECT 21 (vertices=25, convex hull=78, v0=106465) After retessellation of defect 21 (v0=106465), euler #=0 (121688,365047,243359) : difference with theory (0) = 0 CORRECTING DEFECT 22 (vertices=15, convex hull=27, v0=111861) After retessellation of defect 22 (v0=111861), euler #=1 (121690,365059,243370) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=8, convex hull=16, v0=121883) After retessellation of defect 23 (v0=121883), euler #=2 (121691,365067,243378) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.05-->7.03) (max @ vno 87886 --> 92144) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.05-->7.03) (max @ vno 87886 --> 92144) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 98 mutations (40.0%), 147 crossovers (60.0%), 56 vertices were eliminated building final representation... 611 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=121691, nf=243378, ne=365067, g=0) writing corrected surface to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 128 intersecting 001: 19 intersecting 002: 6 intersecting terminating search with 0 intersecting topology fixing took 1.4 minutes FSRUNTIME@ mris_fix_topology lh 0.0229 hours 1 threads #VMPC# mris_fix_topology VmPeak 749936 @#@FSTIME 2023:08:29:19:52:58 mris_fix_topology N 14 e 82.54 S 0.23 U 82.26 P 99% M 724080 F 0 R 214162 W 0 c 8267 w 1 I 0 O 11440 L 1.25 1.25 1.28 @#@FSLOADPOST 2023:08:29:19:54:20 mris_fix_topology N 14 1.14 1.20 1.26 #@# Fix Topology rh Tue Aug 29 19:54:20 PDT 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 EP01 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' 7.4.1 7.4.1 before topology correction, eno=-34 (nv=123380, nf=246828, ne=370242, g=18) 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... 2157 ambiguous faces found in tessellation segmenting defects... 29 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 21 into 18 28 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.2798 (-4.6399) -vertex loglikelihood: -6.3295 (-3.1647) -normal dot loglikelihood: -3.6112 (-3.6112) -quad curv loglikelihood: -6.2061 (-3.1031) Total Loglikelihood : -25.4266 CORRECTING DEFECT 0 (vertices=95, convex hull=71, v0=228) After retessellation of defect 0 (v0=228), euler #=-26 (122049,365578,243503) : difference with theory (-25) = 1 CORRECTING DEFECT 1 (vertices=6, convex hull=16, v0=1420) After retessellation of defect 1 (v0=1420), euler #=-25 (122050,365585,243510) : difference with theory (-24) = 1 CORRECTING DEFECT 2 (vertices=46, convex hull=66, v0=5811) After retessellation of defect 2 (v0=5811), euler #=-24 (122066,365655,243565) : difference with theory (-23) = 1 CORRECTING DEFECT 3 (vertices=5, convex hull=30, v0=12292) After retessellation of defect 3 (v0=12292), euler #=-23 (122068,365669,243578) : difference with theory (-22) = 1 CORRECTING DEFECT 4 (vertices=18, convex hull=22, v0=17433) After retessellation of defect 4 (v0=17433), euler #=-22 (122071,365684,243591) : difference with theory (-21) = 1 CORRECTING DEFECT 5 (vertices=16, convex hull=31, v0=35844) After retessellation of defect 5 (v0=35844), euler #=-21 (122076,365708,243611) : difference with theory (-20) = 1 CORRECTING DEFECT 6 (vertices=6, convex hull=23, v0=46361) After retessellation of defect 6 (v0=46361), euler #=-20 (122078,365719,243621) : difference with theory (-19) = 1 CORRECTING DEFECT 7 (vertices=7, convex hull=18, v0=50214) After retessellation of defect 7 (v0=50214), euler #=-19 (122080,365730,243631) : difference with theory (-18) = 1 CORRECTING DEFECT 8 (vertices=26, convex hull=35, v0=75057) After retessellation of defect 8 (v0=75057), euler #=-18 (122086,365761,243657) : difference with theory (-17) = 1 CORRECTING DEFECT 9 (vertices=20, convex hull=38, v0=76168) After retessellation of defect 9 (v0=76168), euler #=-17 (122096,365806,243693) : difference with theory (-16) = 1 CORRECTING DEFECT 10 (vertices=59, convex hull=53, v0=77264) After retessellation of defect 10 (v0=77264), euler #=-16 (122111,365873,243746) : difference with theory (-15) = 1 CORRECTING DEFECT 11 (vertices=28, convex hull=57, v0=77454) After retessellation of defect 11 (v0=77454), euler #=-15 (122122,365927,243790) : difference with theory (-14) = 1 CORRECTING DEFECT 12 (vertices=5, convex hull=24, v0=81600) After retessellation of defect 12 (v0=81600), euler #=-14 (122124,365941,243803) : difference with theory (-13) = 1 CORRECTING DEFECT 13 (vertices=33, convex hull=45, v0=82249) After retessellation of defect 13 (v0=82249), euler #=-13 (122133,365983,243837) : difference with theory (-12) = 1 CORRECTING DEFECT 14 (vertices=6, convex hull=36, v0=83501) After retessellation of defect 14 (v0=83501), euler #=-12 (122136,366005,243857) : difference with theory (-11) = 1 CORRECTING DEFECT 15 (vertices=53, convex hull=103, v0=83719) After retessellation of defect 15 (v0=83719), euler #=-11 (122162,366125,243952) : difference with theory (-10) = 1 CORRECTING DEFECT 16 (vertices=476, convex hull=266, v0=84469) After retessellation of defect 16 (v0=84469), euler #=-10 (122216,366419,244193) : difference with theory (-9) = 1 CORRECTING DEFECT 17 (vertices=24, convex hull=46, v0=84481) After retessellation of defect 17 (v0=84481), euler #=-9 (122226,366463,244228) : difference with theory (-8) = 1 CORRECTING DEFECT 18 (vertices=101, convex hull=80, v0=84574) After retessellation of defect 18 (v0=84574), euler #=-7 (122235,366534,244292) : difference with theory (-7) = 0 CORRECTING DEFECT 19 (vertices=51, convex hull=36, v0=84789) After retessellation of defect 19 (v0=84789), euler #=-6 (122246,366576,244324) : difference with theory (-6) = 0 CORRECTING DEFECT 20 (vertices=29, convex hull=52, v0=87357) After retessellation of defect 20 (v0=87357), euler #=-5 (122258,366632,244369) : difference with theory (-5) = 0 CORRECTING DEFECT 21 (vertices=9, convex hull=21, v0=98503) After retessellation of defect 21 (v0=98503), euler #=-4 (122260,366644,244380) : difference with theory (-4) = 0 CORRECTING DEFECT 22 (vertices=16, convex hull=39, v0=99873) After retessellation of defect 22 (v0=99873), euler #=-3 (122267,366676,244406) : difference with theory (-3) = 0 CORRECTING DEFECT 23 (vertices=33, convex hull=77, v0=115840) After retessellation of defect 23 (v0=115840), euler #=-2 (122286,366765,244477) : difference with theory (-2) = 0 CORRECTING DEFECT 24 (vertices=13, convex hull=20, v0=120208) After retessellation of defect 24 (v0=120208), euler #=-1 (122288,366777,244488) : difference with theory (-1) = 0 CORRECTING DEFECT 25 (vertices=39, convex hull=74, v0=121571) After retessellation of defect 25 (v0=121571), euler #=0 (122309,366872,244563) : difference with theory (0) = 0 CORRECTING DEFECT 26 (vertices=21, convex hull=59, v0=122219) After retessellation of defect 26 (v0=122219), euler #=1 (122318,366920,244603) : difference with theory (1) = 0 CORRECTING DEFECT 27 (vertices=99, convex hull=70, v0=123178) After retessellation of defect 27 (v0=123178), euler #=2 (122327,366975,244650) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.07-->7.65) (max @ vno 648 --> 901) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.07-->7.65) (max @ vno 648 --> 901) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 138 mutations (39.5%), 211 crossovers (60.5%), 144 vertices were eliminated building final representation... 1053 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=122327, nf=244650, ne=366975, g=0) writing corrected surface to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 152 intersecting 001: 12 intersecting terminating search with 0 intersecting topology fixing took 1.9 minutes FSRUNTIME@ mris_fix_topology rh 0.0311 hours 1 threads #VMPC# mris_fix_topology VmPeak 751204 @#@FSTIME 2023:08:29:19:54:20 mris_fix_topology N 14 e 112.09 S 0.21 U 111.82 P 99% M 724752 F 0 R 214456 W 0 c 10967 w 1 I 0 O 11512 L 1.14 1.20 1.26 @#@FSLOADPOST 2023:08:29:19:56:12 mris_fix_topology N 14 1.37 1.25 1.27 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 121691 - 365067 + 243378 = 2 --> 0 holes F =2V-4: 243378 = 243382-4 (0) 2E=3F: 730134 = 730134 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 122327 - 366975 + 244650 = 2 --> 0 holes F =2V-4: 244650 = 244654-4 (0) 2E=3F: 733950 = 733950 (0) total defect index = 0 Tue Aug 29 19:56:13 PDT 2023 setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects cd /usr/local/freesurfer/7.4.1/subjects/EP01/scripts /usr/local/freesurfer/7.4.1/bin/defect2seg --s EP01 --cortex freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 defect2seg 7.4.1 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux pid 886037 mri_label2label --label-cortex /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig.nofix /usr/local/freesurfer/7.4.1/subjects/EP01/mri/aseg.presurf.mgz 0 /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 7528 vertices erasing segment 0 (vno[0] = 31343) erasing segment 1 (vno[0] = 32232) erasing segment 2 (vno[0] = 33083) erasing segment 4 (vno[0] = 72106) erasing segment 5 (vno[0] = 75679) erasing segment 6 (vno[0] = 83667) erasing segment 7 (vno[0] = 84600) erasing segment 8 (vno[0] = 84667) erasing segment 9 (vno[0] = 86465) erasing segment 10 (vno[0] = 87310) mri_label2vol --defects /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig.nofix /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.defect_labels /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz 1000 0 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/surface.defects.mgz /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /usr/local/freesurfer/7.4.1/subjects/EP01/mri/surface.defects.mgz mris_defects_pointset -s /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig.nofix -d /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.defect_labels -o /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.defects.pointset --label /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.nofix.cortex.label Reading in surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig.nofix Reading in defect segmentation /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.defect_labels Reading in label /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 162636 mris_defects_pointset done mri_label2label --label-cortex /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig.nofix /usr/local/freesurfer/7.4.1/subjects/EP01/mri/aseg.presurf.mgz 0 /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 27 non-cortical segments detected only using segment with 7330 vertices erasing segment 1 (vno[0] = 51290) erasing segment 2 (vno[0] = 54781) erasing segment 3 (vno[0] = 55020) erasing segment 4 (vno[0] = 55024) erasing segment 5 (vno[0] = 56291) erasing segment 6 (vno[0] = 62228) erasing segment 7 (vno[0] = 66603) erasing segment 8 (vno[0] = 75239) erasing segment 9 (vno[0] = 79246) erasing segment 10 (vno[0] = 84145) erasing segment 11 (vno[0] = 84443) erasing segment 12 (vno[0] = 86491) erasing segment 13 (vno[0] = 88222) erasing segment 14 (vno[0] = 88244) erasing segment 15 (vno[0] = 88260) erasing segment 16 (vno[0] = 89009) erasing segment 17 (vno[0] = 89022) erasing segment 18 (vno[0] = 89050) erasing segment 19 (vno[0] = 89858) erasing segment 20 (vno[0] = 89914) erasing segment 21 (vno[0] = 90887) erasing segment 22 (vno[0] = 91692) erasing segment 23 (vno[0] = 93140) erasing segment 24 (vno[0] = 95790) erasing segment 25 (vno[0] = 96562) erasing segment 26 (vno[0] = 98940) mri_label2vol --defects /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig.nofix /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.defect_labels /usr/local/freesurfer/7.4.1/subjects/EP01/mri/surface.defects.mgz 2000 1 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/surface.defects.mgz /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /usr/local/freesurfer/7.4.1/subjects/EP01/mri/surface.defects.mgz mris_defects_pointset -s /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig.nofix -d /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.defect_labels -o /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.defects.pointset --label /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.nofix.cortex.label Reading in surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig.nofix Reading in defect segmentation /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.defect_labels Reading in label /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 163972 mris_defects_pointset done Started at Tue Aug 29 19:56:13 PDT 2023 Ended at Tue Aug 29 19:56:36 PDT 2023 Defect2seg-Run-Time-Sec 23 Defect2seg-Run-Time-Min 0.46 Defect2seg-Run-Time-Hours 0.01 tkmeditfv EP01 brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2023:08:29:19:56:13 defect2seg N 3 e 22.57 S 0.54 U 22.04 P 100% M 402852 F 0 R 424547 W 0 c 2213 w 213 I 0 O 20256 L 1.37 1.25 1.27 @#@FSLOADPOST 2023:08:29:19:56:36 defect2seg N 3 1.62 1.31 1.29 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig.premesh --output /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708875 remeshing to edge length 0.708875 with 3 iterations avg qual before : 0.891854 after: 0.971193 Removing intersections Remeshed surface quality stats nv0 = 121691 nv = 127052 1.04405 Area 254100 0.30127 0.03360 0.072324 0.4632 Corner 762300 60.00000 8.79907 16.255433 146.5209 Edge 381150 0.84205 0.08222 0.481560 1.2478 Hinge 381150 9.63977 10.06352 0.000042 122.5740 mris_remesh done @#@FSTIME 2023:08:29:19:56:36 mris_remesh N 7 e 21.17 S 0.26 U 20.89 P 99% M 680684 F 0 R 269725 W 0 c 2072 w 1 I 0 O 8936 L 1.62 1.31 1.29 @#@FSLOADPOST 2023:08:29:19:56:57 mris_remesh N 7 2.07 1.44 1.33 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig.premesh --output /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.71093 remeshing to edge length 0.71093 with 3 iterations avg qual before : 0.889763 after: 0.971256 Removing intersections Remeshed surface quality stats nv0 = 122327 nv = 127453 1.0419 Area 254902 0.30284 0.03371 0.076673 0.5001 Corner 764706 60.00000 8.78855 16.063928 146.5945 Edge 382353 0.84424 0.08233 0.482019 1.2519 Hinge 382353 9.68746 10.27153 0.000011 137.2597 mris_remesh done @#@FSTIME 2023:08:29:19:56:57 mris_remesh N 7 e 21.61 S 0.29 U 21.29 P 99% M 684180 F 0 R 271525 W 0 c 2140 w 1 I 0 O 8968 L 2.07 1.44 1.33 @#@FSLOADPOST 2023:08:29:19:57:19 mris_remesh N 7 1.70 1.40 1.32 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/lh.orig @#@FSTIME 2023:08:29:19:57:19 mris_remove_intersection N 2 e 3.49 S 0.12 U 3.36 P 99% M 319964 F 0 R 92241 W 0 c 333 w 1 I 0 O 8936 L 1.70 1.40 1.32 @#@FSLOADPOST 2023:08:29:19:57:22 mris_remove_intersection N 2 1.70 1.40 1.32 rm -f ../surf/lh.inflated /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/rh.orig @#@FSTIME 2023:08:29:19:57:22 mris_remove_intersection N 2 e 3.36 S 0.12 U 3.23 P 99% M 322708 F 0 R 92992 W 0 c 322 w 1 I 0 O 8968 L 1.70 1.40 1.32 @#@FSLOADPOST 2023:08:29:19:57:26 mris_remove_intersection N 2 1.81 1.43 1.33 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Tue Aug 29 19:57:26 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/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: 226301 voxels (1.35%) border gray 253827 voxels (1.51%) 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=23311, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 99.6 +- 7.6 [70.0 --> 110.0] CCS GM (77.0) : 76.0 +- 10.3 [30.0 --> 110.0] white_mean = 99.6087 +/- 7.58369, gray_mean = 76.018 +/- 10.3172 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=103+-5.2, GM=74+-7.0 white_mode = 103, gray_mode = 74 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 63.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.6 (was 105.000000) setting MIN_BORDER_WHITE to 74.0 (was 85.000000) setting MAX_CSF to 53.4 (was 40.000000) setting MAX_GRAY to 95.4 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 63.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 43.0 (was 40.000000) When placing the white surface white_border_hi = 110.584; white_border_low = 74; white_outside_low = 63.6828; white_inside_hi = 120; white_outside_hi = 110.584; When placing the pial surface pial_border_hi = 63.6828; pial_border_low = 43.0484; pial_outside_low = 10; pial_inside_hi = 95.4163; pial_outside_hi = 58.5242; #VMPC# mris_autodet_gwstats VmPeak 249012 mris_autodet_gwstats done @#@FSTIME 2023:08:29:19:57:26 mris_autodet_gwstats N 8 e 2.88 S 0.08 U 2.80 P 99% M 223028 F 0 R 62944 W 0 c 286 w 1 I 0 O 8 L 1.81 1.43 1.33 @#@FSLOADPOST 2023:08:29:19:57:28 mris_autodet_gwstats N 8 1.81 1.43 1.33 #-------------------------------------------- #@# AutoDetGWStats rh Tue Aug 29 19:57:28 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/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: 226301 voxels (1.35%) border gray 253827 voxels (1.51%) 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=23311, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 99.6 +- 7.6 [70.0 --> 110.0] CCS GM (77.0) : 76.0 +- 10.3 [30.0 --> 110.0] white_mean = 99.6087 +/- 7.58369, gray_mean = 76.018 +/- 10.3172 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=255 nbins=256 intensity peaks found at WM=103+-5.2, GM=74+-7.8 white_mode = 103, gray_mode = 74 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 63.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.6 (was 105.000000) setting MIN_BORDER_WHITE to 74.0 (was 85.000000) setting MAX_CSF to 53.4 (was 40.000000) setting MAX_GRAY to 95.4 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 63.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 43.0 (was 40.000000) When placing the white surface white_border_hi = 110.584; white_border_low = 74; white_outside_low = 63.6828; white_inside_hi = 120; white_outside_hi = 110.584; When placing the pial surface pial_border_hi = 63.6828; pial_border_low = 43.0484; pial_outside_low = 10; pial_inside_hi = 95.4163; pial_outside_hi = 58.5242; #VMPC# mris_autodet_gwstats VmPeak 249924 mris_autodet_gwstats done @#@FSTIME 2023:08:29:19:57:28 mris_autodet_gwstats N 8 e 2.97 S 0.08 U 2.88 P 99% M 223812 F 0 R 66243 W 0 c 289 w 1 I 0 O 8 L 1.81 1.43 1.33 @#@FSLOADPOST 2023:08:29:19:57:31 mris_autodet_gwstats N 8 1.74 1.42 1.33 #-------------------------------------------- #@# WhitePreAparc lh Tue Aug 29 19:57:31 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.4.1 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations Area 254100 0.26643 0.06276 0.001165 0.5761 Corner 762300 60.00000 9.48548 4.346782 158.0841 Edge 381150 0.78814 0.11411 0.049652 1.3563 Hinge 381150 6.40272 6.45348 0.000023 155.4587 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23311, wmmin=5, clip=110 MRIfindBrightNonWM(): 1279 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6246, nmarked2=0, nripped=6246 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 63526: xyz = (-21.9511,-9.94921,41.0214) oxyz = (-21.9511,-9.94921,41.0214) wxzy = (-21.9511,-9.94921,41.0214) pxyz = (0,0,0) CBVO Creating mask 127052 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=6246 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6246, nmarked2=0, nripped=6246 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=2 had to be increased for 77 vertices, nripped=6246 mean border=83.1, 66 (66) missing vertices, mean dist 0.3 [0.7 (%34.6)->0.9 (%65.4))] %54 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1532 min Finding expansion regions mean absolute distance = 0.83 +- 1.01 3436 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=2610435.8, rms=10.118 001: dt: 0.5000, sse=1441079.5, rms=7.356 (27.300%) 002: dt: 0.5000, sse=880512.9, rms=5.560 (24.418%) 003: dt: 0.5000, sse=605155.7, rms=4.411 (20.659%) 004: dt: 0.5000, sse=462964.4, rms=3.679 (16.586%) 005: dt: 0.5000, sse=393081.3, rms=3.259 (11.420%) 006: dt: 0.5000, sse=367306.9, rms=3.041 (6.692%) 007: dt: 0.5000, sse=347595.2, rms=2.944 (3.197%) 008: dt: 0.5000, sse=341467.7, rms=2.886 (1.958%) rms = 2.8654/2.8862, sse=340056.4/341467.6, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=340056.4, rms=2.865 (0.723%) 010: dt: 0.2500, sse=229686.6, rms=1.799 (37.202%) 011: dt: 0.2500, sse=203769.7, rms=1.560 (13.277%) rms = 1.5143/1.5605, sse=201227.0/203769.7, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=201227.0, rms=1.514 (2.959%) rms = 1.4725/1.5143, sse=199991.2/201227.0, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=199991.2, rms=1.472 (2.763%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6246 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 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 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6443, nmarked2=0, nripped=6443 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=1 had to be increased for 137 vertices, nripped=6443 mean border=86.4, 64 (6) missing vertices, mean dist -0.3 [0.4 (%74.6)->0.2 (%25.4))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1026 min Finding expansion regions mean absolute distance = 0.39 +- 0.63 3163 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=699881.8, rms=4.580 014: dt: 0.5000, sse=394297.2, rms=2.846 (37.871%) 015: dt: 0.5000, sse=358406.8, rms=2.630 (7.597%) rms = 2.5857/2.6296, sse=355902.5/358406.8, time step reduction 1 of 3 to 0.250 0 0 1 016: dt: 0.5000, sse=355902.5, rms=2.586 (1.670%) 017: dt: 0.2500, sse=250803.3, rms=1.535 (40.625%) 018: dt: 0.2500, sse=233165.0, rms=1.288 (16.131%) rms = 1.2466/1.2876, sse=230497.4/233165.0, time step reduction 2 of 3 to 0.125 0 0 1 019: dt: 0.2500, sse=230497.4, rms=1.247 (3.183%) rms = 1.2012/1.2466, sse=228948.2/230497.4, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=228948.2, rms=1.201 (3.645%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6443 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 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 #FML# MRISripMidline(): nmarked=6525, nmarked2=1, nripped=6525 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 191 vertices, nripped=6525 mean border=88.7, 67 (5) missing vertices, mean dist -0.1 [0.3 (%71.5)->0.2 (%28.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0562 min Finding expansion regions mean absolute distance = 0.26 +- 0.38 2768 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=413027.0, rms=3.057 021: dt: 0.5000, sse=313190.7, rms=2.236 (26.863%) rms = 2.3703/2.2356, sse=324810.7/313190.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=250336.6, rms=1.568 (29.847%) 023: dt: 0.2500, sse=226446.6, rms=1.208 (22.996%) 024: dt: 0.2500, sse=221375.9, rms=1.121 (7.207%) rms = 1.1133/1.1206, sse=219668.7/221375.9, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=219668.7, rms=1.113 (0.659%) rms = 1.0813/1.1133, sse=218462.2/219668.7, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=218462.2, rms=1.081 (2.874%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6525 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 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6559, nmarked2=1, nripped=6559 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 233 vertices, nripped=6559 mean border=89.3, 107 (4) missing vertices, mean dist -0.0 [0.2 (%54.9)->0.2 (%45.1))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0350 min Finding expansion regions mean absolute distance = 0.21 +- 0.31 2860 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=237418.1, rms=1.430 rms = 1.3507/1.4297, sse=240395.1/237418.1, time step reduction 1 of 3 to 0.250 0 1 0 027: dt: 0.5000, sse=240395.1, rms=1.351 (5.530%) 028: dt: 0.2500, sse=209959.9, rms=1.014 (24.905%) 029: dt: 0.2500, sse=201303.3, rms=0.842 (17.017%) rms = 0.8975/0.8417, sse=226447.6/201303.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.8227/0.8417, sse=200339.4/201303.3, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=200339.4, rms=0.823 (2.259%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.66 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 1954660 mris_place_surface done @#@FSTIME 2023:08:29:19:57:31 mris_place_surface N 18 e 165.13 S 0.43 U 164.57 P 99% M 1689992 F 0 R 445209 W 0 c 16263 w 1 I 0 O 8936 L 1.74 1.42 1.33 @#@FSLOADPOST 2023:08:29:20:00:17 mris_place_surface N 18 1.33 1.33 1.30 #-------------------------------------------- #@# WhitePreAparc rh Tue Aug 29 20:00:17 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.4.1 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations Area 254902 0.26711 0.06347 0.002540 0.5930 Corner 764706 60.00000 9.55067 10.588319 133.2482 Edge 382353 0.78916 0.11526 0.075432 1.3532 Hinge 382353 6.45392 6.56264 0.000126 130.5303 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23311, wmmin=5, clip=110 MRIfindBrightNonWM(): 1279 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5931, nmarked2=0, nripped=5931 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 63727: xyz = (6.27047,-11.461,31.6591) oxyz = (6.27047,-11.461,31.6591) wxzy = (6.27047,-11.461,31.6591) pxyz = (0,0,0) CBVO Creating mask 127453 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=5931 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5931, nmarked2=0, nripped=5931 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=2 had to be increased for 126 vertices, nripped=5931 mean border=83.1, 108 (108) missing vertices, mean dist 0.3 [0.8 (%36.3)->0.8 (%63.7))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1517 min Finding expansion regions mean absolute distance = 0.82 +- 1.03 3303 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=2691250.5, rms=10.249 001: dt: 0.5000, sse=1493715.9, rms=7.478 (27.038%) 002: dt: 0.5000, sse=928497.2, rms=5.717 (23.550%) 003: dt: 0.5000, sse=649666.1, rms=4.603 (19.481%) 004: dt: 0.5000, sse=502870.8, rms=3.886 (15.569%) 005: dt: 0.5000, sse=432982.8, rms=3.480 (10.464%) 006: dt: 0.5000, sse=397341.7, rms=3.264 (6.190%) 007: dt: 0.5000, sse=383150.1, rms=3.169 (2.914%) 008: dt: 0.5000, sse=376701.5, rms=3.119 (1.586%) rms = 3.0920/3.1190, sse=373563.7/376701.5, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=373563.7, rms=3.092 (0.866%) 010: dt: 0.2500, sse=238132.9, rms=1.964 (36.493%) 011: dt: 0.2500, sse=214327.6, rms=1.691 (13.897%) 012: dt: 0.2500, sse=210008.6, rms=1.631 (3.509%) rms = 1.5898/1.6314, sse=206975.4/210008.6, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=206975.4, rms=1.590 (2.553%) rms = 1.5508/1.5898, sse=204158.6/206975.4, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=204158.6, rms=1.551 (2.453%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5931 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6103, nmarked2=0, nripped=6103 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=1 had to be increased for 130 vertices, nripped=6103 mean border=86.3, 58 (26) missing vertices, mean dist -0.3 [0.4 (%72.9)->0.2 (%27.1))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1023 min Finding expansion regions mean absolute distance = 0.39 +- 0.64 3235 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=702691.1, rms=4.587 015: dt: 0.5000, sse=404776.5, rms=2.964 (35.386%) 016: dt: 0.5000, sse=389036.4, rms=2.861 (3.485%) rms = 2.8275/2.8605, sse=384396.3/389036.4, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=384396.3, rms=2.828 (1.152%) 018: dt: 0.2500, sse=257305.8, rms=1.637 (42.115%) 019: dt: 0.2500, sse=236286.9, rms=1.345 (17.829%) 020: dt: 0.2500, sse=233171.6, rms=1.292 (3.970%) rms = 1.2481/1.2915, sse=230739.0/233171.6, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=230739.0, rms=1.248 (3.362%) rms = 1.2150/1.2481, sse=228825.2/230739.0, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=228825.2, rms=1.215 (2.655%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6103 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6177, nmarked2=0, nripped=6177 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 221 vertices, nripped=6177 mean border=88.4, 72 (7) missing vertices, mean dist -0.1 [0.3 (%70.0)->0.2 (%30.0))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0558 min Finding expansion regions mean absolute distance = 0.25 +- 0.40 2785 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=395622.6, rms=2.928 023: dt: 0.5000, sse=327344.9, rms=2.369 (19.114%) rms = 2.5904/2.3686, sse=353305.5/327344.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=253858.2, rms=1.618 (31.675%) 025: dt: 0.2500, sse=228759.5, rms=1.238 (23.507%) 026: dt: 0.2500, sse=223815.2, rms=1.143 (7.643%) rms = 1.1305/1.1433, sse=226268.5/223815.2, time step reduction 2 of 3 to 0.125 0 1 1 027: dt: 0.2500, sse=226268.5, rms=1.131 (1.118%) rms = 1.0915/1.1305, sse=220930.1/226268.5, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=220930.1, rms=1.091 (3.452%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6177 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 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6220, nmarked2=0, nripped=6220 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 289 vertices, nripped=6220 mean border=89.0, 130 (4) missing vertices, mean dist -0.0 [0.2 (%54.2)->0.2 (%45.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0347 min Finding expansion regions mean absolute distance = 0.21 +- 0.33 2521 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=238888.6, rms=1.415 rms = 1.4206/1.4146, sse=242098.2/238888.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=215298.8, rms=1.014 (28.334%) 030: dt: 0.2500, sse=207909.7, rms=0.816 (19.498%) rms = 0.8268/0.8161, sse=210076.0/207909.7, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.8134/0.8161, sse=207249.9/207909.7, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=207249.9, rms=0.813 (0.327%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.77 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2003972 mris_place_surface done @#@FSTIME 2023:08:29:20:00:17 mris_place_surface N 18 e 171.75 S 0.44 U 171.19 P 99% M 1739496 F 0 R 457731 W 0 c 16919 w 1 I 0 O 8968 L 1.33 1.33 1.30 @#@FSLOADPOST 2023:08:29:20:03:08 mris_place_surface N 18 1.17 1.27 1.28 #-------------------------------------------- #@# CortexLabel lh Tue Aug 29 20:03:08 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/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 5 non-cortical segments detected only using segment with 8166 vertices erasing segment 0 (vno[0] = 26822) erasing segment 1 (vno[0] = 28360) erasing segment 3 (vno[0] = 69383) erasing segment 4 (vno[0] = 72490) @#@FSTIME 2023:08:29:20:03:08 mri_label2label N 5 e 10.73 S 0.11 U 10.61 P 99% M 308268 F 0 R 91550 W 0 c 1045 w 1 I 0 O 10392 L 1.17 1.27 1.28 @#@FSLOADPOST 2023:08:29:20:03:19 mri_label2label N 5 1.28 1.29 1.29 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Tue Aug 29 20:03:19 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/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 10 non-cortical segments detected only using segment with 5899 vertices erasing segment 0 (vno[0] = 26822) erasing segment 1 (vno[0] = 28360) erasing segment 3 (vno[0] = 38896) erasing segment 4 (vno[0] = 41490) erasing segment 5 (vno[0] = 46370) erasing segment 6 (vno[0] = 54475) erasing segment 7 (vno[0] = 69164) erasing segment 8 (vno[0] = 72490) erasing segment 9 (vno[0] = 124566) @#@FSTIME 2023:08:29:20:03:19 mri_label2label N 5 e 10.85 S 0.10 U 10.74 P 99% M 330660 F 0 R 97164 W 0 c 1059 w 1 I 0 O 10584 L 1.28 1.29 1.29 @#@FSLOADPOST 2023:08:29:20:03:30 mri_label2label N 5 1.24 1.28 1.28 #-------------------------------------------- #@# CortexLabel rh Tue Aug 29 20:03:30 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/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 9 non-cortical segments detected only using segment with 7821 vertices erasing segment 0 (vno[0] = 27045) erasing segment 1 (vno[0] = 31867) erasing segment 3 (vno[0] = 45719) erasing segment 4 (vno[0] = 47973) erasing segment 5 (vno[0] = 53939) erasing segment 6 (vno[0] = 73666) erasing segment 7 (vno[0] = 77206) erasing segment 8 (vno[0] = 81932) @#@FSTIME 2023:08:29:20:03:30 mri_label2label N 5 e 10.63 S 0.12 U 10.50 P 99% M 326544 F 0 R 96214 W 0 c 1044 w 1 I 0 O 10200 L 1.24 1.28 1.28 @#@FSLOADPOST 2023:08:29:20:03:41 mri_label2label N 5 1.20 1.27 1.28 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Tue Aug 29 20:03:41 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/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 12 non-cortical segments detected only using segment with 5409 vertices erasing segment 0 (vno[0] = 27045) erasing segment 1 (vno[0] = 31867) erasing segment 3 (vno[0] = 37611) erasing segment 4 (vno[0] = 38560) erasing segment 5 (vno[0] = 39466) erasing segment 6 (vno[0] = 45719) erasing segment 7 (vno[0] = 53939) erasing segment 8 (vno[0] = 62521) erasing segment 9 (vno[0] = 73666) erasing segment 10 (vno[0] = 77206) erasing segment 11 (vno[0] = 81932) @#@FSTIME 2023:08:29:20:03:41 mri_label2label N 5 e 10.81 S 0.10 U 10.70 P 99% M 339996 F 0 R 99610 W 0 c 1064 w 1 I 0 O 10416 L 1.20 1.27 1.28 @#@FSLOADPOST 2023:08:29:20:03:52 mri_label2label N 5 1.17 1.26 1.27 #-------------------------------------------- #@# Smooth2 lh Tue Aug 29 20:03:52 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:08:29:20:03:52 mris_smooth N 7 e 2.08 S 0.06 U 2.01 P 99% M 195688 F 0 R 58845 W 0 c 202 w 1 I 0 O 8944 L 1.17 1.26 1.27 @#@FSLOADPOST 2023:08:29:20:03:54 mris_smooth N 7 1.17 1.26 1.27 #-------------------------------------------- #@# Smooth2 rh Tue Aug 29 20:03:54 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:08:29:20:03:54 mris_smooth N 7 e 2.10 S 0.07 U 2.03 P 99% M 196472 F 0 R 59045 W 0 c 204 w 1 I 0 O 8968 L 1.17 1.26 1.27 @#@FSLOADPOST 2023:08:29:20:03:56 mris_smooth N 7 1.16 1.26 1.27 #-------------------------------------------- #@# Inflation2 lh Tue Aug 29 20:03:56 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.4 mm, total surface area = 77513 mm^2 step 000: RMS=0.170 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.019 (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 14.327279 mris_inflate stimesec 0.647064 mris_inflate ru_maxrss 196248 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 492369 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9944 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1537 @#@FSTIME 2023:08:29:20:03:56 mris_inflate N 2 e 15.00 S 0.65 U 14.32 P 99% M 196248 F 0 R 492374 W 0 c 1538 w 1 I 0 O 9944 L 1.16 1.26 1.27 @#@FSLOADPOST 2023:08:29:20:04:11 mris_inflate N 2 1.46 1.33 1.29 #-------------------------------------------- #@# Inflation2 rh Tue Aug 29 20:04:11 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.1 mm, total surface area = 78521 mm^2 step 000: RMS=0.172 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (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 14.426114 mris_inflate stimesec 0.051921 mris_inflate ru_maxrss 197532 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 52733 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9968 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1499 @#@FSTIME 2023:08:29:20:04:11 mris_inflate N 2 e 14.50 S 0.06 U 14.42 P 99% M 197900 F 0 R 52738 W 0 c 1500 w 1 I 0 O 9968 L 1.46 1.33 1.29 @#@FSLOADPOST 2023:08:29:20:04:25 mris_inflate N 2 1.36 1.31 1.29 #-------------------------------------------- #@# Curv .H and .K lh Tue Aug 29 20:04:25 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 11.246*4pi (141.327) --> -10 handles ICI = 160.7, FI = 1379.0, variation=22648.861 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. @#@FSTIME 2023:08:29:20:04:25 mris_curvature N 4 e 1.09 S 0.05 U 1.03 P 99% M 146032 F 0 R 39751 W 0 c 105 w 1 I 0 O 2000 L 1.36 1.31 1.29 @#@FSLOADPOST 2023:08:29:20:04:27 mris_curvature N 4 1.36 1.31 1.29 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 178 vertices thresholded to be in k1 ~ [-0.18 0.39], k2 ~ [-0.11 0.08] total integrated curvature = 0.623*4pi (7.826) --> 0 handles ICI = 1.6, FI = 9.3, variation=161.123 117 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 142 vertices thresholded to be in [-0.13 0.19] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.024 mris_curvature done. @#@FSTIME 2023:08:29:20:04:27 mris_curvature N 12 e 33.84 S 0.18 U 33.64 P 99% M 344520 F 0 R 89524 W 0 c 3314 w 1 I 0 O 2000 L 1.36 1.31 1.29 @#@FSLOADPOST 2023:08:29:20:05:00 mris_curvature N 12 1.27 1.29 1.28 #-------------------------------------------- #@# Curv .H and .K rh Tue Aug 29 20:05:00 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 5.080*4pi (63.840) --> -4 handles ICI = 153.4, FI = 1397.2, variation=22730.978 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. @#@FSTIME 2023:08:29:20:05:00 mris_curvature N 4 e 1.11 S 0.03 U 1.07 P 99% M 146460 F 0 R 39881 W 0 c 109 w 1 I 0 O 2000 L 1.27 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:05:02 mris_curvature N 4 1.27 1.29 1.28 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 211 vertices thresholded to be in k1 ~ [-0.20 0.33], k2 ~ [-0.11 0.05] total integrated curvature = 0.613*4pi (7.706) --> 0 handles ICI = 1.5, FI = 8.9, variation=153.256 127 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 154 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 mris_curvature done. @#@FSTIME 2023:08:29:20:05:02 mris_curvature N 12 e 33.52 S 0.11 U 33.39 P 99% M 345980 F 0 R 89806 W 0 c 3265 w 1 I 0 O 2000 L 1.27 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:05:35 mris_curvature N 12 1.15 1.26 1.27 #-------------------------------------------- #@# Sphere lh Tue Aug 29 20:05:35 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.296... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=rnet-, 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 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.94 pass 1: epoch 2 of 3 starting distance error %19.91 unfolding complete - removing small folds... starting distance error %19.84 removing remaining folds... final distance error %19.87 MRISunfold() return, current seed 1234 -01: dt=0.0000, 11 negative triangles VmPeak 526828 165: dt=0.9900, 11 negative triangles 166: dt=0.9900, 7 negative triangles 167: dt=0.9900, 6 negative triangles 168: dt=0.9900, 4 negative triangles 169: dt=0.9900, 3 negative triangles 170: dt=0.9900, 3 negative triangles 171: dt=0.9900, 4 negative triangles 172: dt=0.9900, 2 negative triangles 173: dt=0.9900, 3 negative triangles 174: dt=0.9900, 1 negative triangles 175: dt=0.9900, 2 negative triangles 176: dt=0.9900, 1 negative triangles 177: dt=0.9900, 1 negative triangles 178: dt=0.9900, 1 negative triangles 179: dt=0.9900, 1 negative triangles 180: dt=0.9900, 1 negative triangles 181: dt=0.9900, 1 negative triangles 182: dt=0.9900, 1 negative triangles 183: dt=0.9900, 1 negative triangles 184: dt=0.9405, 3 negative triangles 185: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0991 hours FSRUNTIME@ mris_sphere 0.0991 hours 1 threads #VMPC# mris_sphere VmPeak 526828 mris_sphere done @#@FSTIME 2023:08:29:20:05:35 mris_sphere N 4 e 356.62 S 13.76 U 342.48 P 99% M 262196 F 0 R 11697492 W 0 c 35550 w 1 I 0 O 8944 L 1.15 1.26 1.27 @#@FSLOADPOST 2023:08:29:20:11:32 mris_sphere N 4 1.18 1.26 1.27 #-------------------------------------------- #@# Sphere rh Tue Aug 29 20:11:32 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.292... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=rnet-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.87 pass 1: epoch 2 of 3 starting distance error %19.87 unfolding complete - removing small folds... starting distance error %19.82 removing remaining folds... final distance error %19.82 MRISunfold() return, current seed 1234 -01: dt=0.0000, 237 negative triangles VmPeak 527660 090: dt=0.9900, 237 negative triangles 091: dt=0.9900, 127 negative triangles 092: dt=0.9900, 99 negative triangles 093: dt=0.9900, 88 negative triangles 094: dt=0.9900, 80 negative triangles 095: dt=0.9900, 78 negative triangles 096: dt=0.9900, 72 negative triangles 097: dt=0.9900, 58 negative triangles 098: dt=0.9900, 59 negative triangles 099: dt=0.9900, 43 negative triangles 100: dt=0.9900, 42 negative triangles 101: dt=0.9900, 39 negative triangles 102: dt=0.9900, 31 negative triangles 103: dt=0.9900, 31 negative triangles 104: dt=0.9900, 32 negative triangles 105: dt=0.9900, 28 negative triangles 106: dt=0.9900, 28 negative triangles 107: dt=0.9900, 26 negative triangles 108: dt=0.9900, 23 negative triangles 109: dt=0.9900, 24 negative triangles 110: dt=0.9900, 26 negative triangles 111: dt=0.9900, 24 negative triangles 112: dt=0.9900, 24 negative triangles 113: dt=0.9900, 22 negative triangles 114: dt=0.9900, 20 negative triangles 115: dt=0.9900, 22 negative triangles 116: dt=0.9900, 21 negative triangles 117: dt=0.9900, 25 negative triangles 118: dt=0.9900, 21 negative triangles 119: dt=0.9900, 19 negative triangles 120: dt=0.9900, 21 negative triangles 121: dt=0.9900, 20 negative triangles 122: dt=0.9900, 19 negative triangles 123: dt=0.9900, 16 negative triangles 124: dt=0.9900, 19 negative triangles 125: dt=0.9900, 17 negative triangles 126: dt=0.9900, 18 negative triangles 127: dt=0.9900, 14 negative triangles 128: dt=0.9900, 9 negative triangles 129: dt=0.9900, 11 negative triangles 130: dt=0.9900, 11 negative triangles 131: dt=0.9900, 7 negative triangles 132: dt=0.9900, 4 negative triangles 133: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0714 hours FSRUNTIME@ mris_sphere 0.0714 hours 1 threads #VMPC# mris_sphere VmPeak 527660 mris_sphere done @#@FSTIME 2023:08:29:20:11:32 mris_sphere N 4 e 256.89 S 7.89 U 248.74 P 99% M 262688 F 0 R 6762800 W 0 c 25514 w 1 I 0 O 8968 L 1.18 1.26 1.27 @#@FSLOADPOST 2023:08:29:20:15:49 mris_sphere N 4 1.17 1.21 1.25 #-------------------------------------------- #@# Surf Reg lh Tue Aug 29 20:15:49 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/7.4.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /usr/local/freesurfer/7.4.1/subjects/EP01/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/7.4.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/7.4.1/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=rnet-, 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=rnet-, 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=rnet-, 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 = 5.465 curvature mean = 0.036, std = 0.817 curvature mean = 0.014, std = 0.872 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (0.50, -12.50, 1.50) sse = 207746.2, elapsed since starting=0.2675 min MRISrigidBodyAlignGlobal() done 0.27 min curvature mean = 0.024, std = 0.833 curvature mean = 0.005, std = 0.953 curvature mean = 0.024, std = 0.845 curvature mean = 0.002, std = 0.982 curvature mean = 0.023, std = 0.848 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.020, std = 0.263 curvature mean = 0.045, std = 0.249 curvature mean = 0.058, std = 0.396 curvature mean = 0.039, std = 0.310 curvature mean = 0.030, std = 0.594 curvature mean = 0.038, std = 0.338 curvature mean = 0.014, std = 0.735 curvature mean = 0.037, std = 0.351 curvature mean = 0.003, std = 0.837 MRISregister() return, current seed 0 -01: dt=0.0000, 6 negative triangles VmPeak 514312 107: dt=0.9900, 6 negative triangles expanding nbhd size to 1 108: dt=0.9900, 9 negative triangles 109: dt=0.9900, 8 negative triangles 110: dt=0.9405, 7 negative triangles 111: dt=0.9405, 7 negative triangles 112: dt=0.9405, 7 negative triangles 113: dt=0.9405, 7 negative triangles 114: dt=0.9405, 7 negative triangles 115: dt=0.9405, 5 negative triangles 116: dt=0.9405, 5 negative triangles 117: dt=0.9405, 5 negative triangles 118: dt=0.9405, 4 negative triangles 119: dt=0.9405, 3 negative triangles 120: dt=0.9405, 2 negative triangles 121: dt=0.9405, 1 negative triangles 122: dt=0.9405, 1 negative triangles 123: dt=0.9405, 1 negative triangles 124: dt=0.9405, 1 negative triangles 125: dt=0.9405, 1 negative triangles 126: dt=0.9405, 1 negative triangles 127: dt=0.9405, 1 negative triangles 128: dt=0.9405, 1 negative triangles 129: dt=0.9405, 1 negative triangles 130: dt=0.9405, 1 negative triangles 131: dt=0.8935, 1 negative triangles 132: dt=0.8935, 1 negative triangles 133: dt=0.8935, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.08 hours #VMPC# mris_register VmPeak 514312 FSRUNTIME@ mris_register 0.0799 hours 1 threads @#@FSTIME 2023:08:29:20:15:49 mris_register N 4 e 287.61 S 8.65 U 278.67 P 99% M 250084 F 0 R 7108877 W 0 c 28800 w 1 I 0 O 8944 L 1.17 1.21 1.25 @#@FSLOADPOST 2023:08:29:20:20:36 mris_register N 4 1.37 1.36 1.30 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Tue Aug 29 20:20:36 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/7.4.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /usr/local/freesurfer/7.4.1/subjects/EP01/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/7.4.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/7.4.1/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=rnet-, 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=rnet-, 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=rnet-, 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 = 5.572 curvature mean = 0.035, std = 0.813 curvature mean = 0.016, std = 0.871 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (7.50, -10.00, 8.50) sse = 209458.0, elapsed since starting=0.2631 min MRISrigidBodyAlignGlobal() done 0.26 min curvature mean = 0.011, std = 0.833 curvature mean = 0.007, std = 0.951 curvature mean = 0.008, std = 0.842 curvature mean = 0.003, std = 0.981 curvature mean = 0.007, std = 0.843 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.020, std = 0.275 curvature mean = 0.037, std = 0.242 curvature mean = 0.064, std = 0.364 curvature mean = 0.033, std = 0.301 curvature mean = 0.033, std = 0.564 curvature mean = 0.032, std = 0.329 curvature mean = 0.017, std = 0.702 curvature mean = 0.032, std = 0.341 curvature mean = 0.005, std = 0.806 MRISregister() return, current seed 0 -01: dt=0.0000, 2 negative triangles VmPeak 513492 104: dt=0.9900, 2 negative triangles 105: dt=0.9900, 1 negative triangles 106: dt=0.9900, 2 negative triangles 107: dt=0.9900, 1 negative triangles 108: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.08 hours #VMPC# mris_register VmPeak 513492 FSRUNTIME@ mris_register 0.0826 hours 1 threads @#@FSTIME 2023:08:29:20:20:36 mris_register N 4 e 297.35 S 8.21 U 288.84 P 99% M 249088 F 0 R 7150510 W 0 c 29987 w 1 I 0 O 8968 L 1.37 1.36 1.30 @#@FSLOADPOST 2023:08:29:20:25:34 mris_register N 4 1.61 1.43 1.33 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Tue Aug 29 20:25:34 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2023:08:29:20:25:34 mris_jacobian N 3 e 0.69 S 0.07 U 0.62 P 99% M 195372 F 0 R 58821 W 0 c 72 w 0 I 0 O 1000 L 1.61 1.43 1.33 @#@FSLOADPOST 2023:08:29:20:25:34 mris_jacobian N 3 1.61 1.43 1.33 #-------------------------------------------- #@# Jacobian white rh Tue Aug 29 20:25:34 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2023:08:29:20:25:34 mris_jacobian N 3 e 0.65 S 0.08 U 0.57 P 99% M 195872 F 0 R 59001 W 0 c 86 w 1 I 0 O 1000 L 1.61 1.43 1.33 @#@FSLOADPOST 2023:08:29:20:25:35 mris_jacobian N 3 1.56 1.42 1.33 #-------------------------------------------- #@# AvgCurv lh Tue Aug 29 20:25:35 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mrisp_paint -a 5 /usr/local/freesurfer/7.4.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/7.4.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2023:08:29:20:25:35 mrisp_paint N 5 e 0.56 S 0.03 U 0.52 P 99% M 150888 F 0 R 41035 W 0 c 57 w 1 I 0 O 1000 L 1.56 1.42 1.33 @#@FSLOADPOST 2023:08:29:20:25:36 mrisp_paint N 5 1.56 1.42 1.33 #-------------------------------------------- #@# AvgCurv rh Tue Aug 29 20:25:36 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mrisp_paint -a 5 /usr/local/freesurfer/7.4.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/7.4.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2023:08:29:20:25:36 mrisp_paint N 5 e 0.53 S 0.04 U 0.48 P 99% M 151424 F 0 R 41154 W 0 c 51 w 1 I 0 O 1000 L 1.56 1.42 1.33 @#@FSLOADPOST 2023:08:29:20:25:36 mrisp_paint N 5 1.56 1.42 1.33 #----------------------------------------- #@# Cortical Parc lh Tue Aug 29 20:25:36 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 EP01 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.4.1/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 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/7.4.1/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 reading surface from /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1362 labels changed using aseg relabeling using gibbs priors... 000: 2890 changed, 127052 examined... 001: 614 changed, 12222 examined... 002: 158 changed, 3496 examined... 003: 56 changed, 968 examined... 004: 17 changed, 351 examined... 005: 4 changed, 117 examined... 006: 0 changed, 25 examined... 198 labels changed using aseg 000: 119 total segments, 73 labels (205 vertices) changed 001: 49 total segments, 3 labels (5 vertices) changed 002: 46 total segments, 1 labels (2 vertices) changed 003: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1752 vertices marked for relabeling... 1752 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 7 seconds. @#@FSTIME 2023:08:29:20:25:36 mris_ca_label N 11 e 7.27 S 0.48 U 6.78 P 99% M 1192268 F 0 R 484818 W 0 c 704 w 1 I 0 O 1992 L 1.56 1.42 1.33 @#@FSLOADPOST 2023:08:29:20:25:44 mris_ca_label N 11 1.60 1.43 1.33 #----------------------------------------- #@# Cortical Parc rh Tue Aug 29 20:25:44 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 EP01 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.4.1/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 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/7.4.1/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 reading surface from /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1176 labels changed using aseg relabeling using gibbs priors... 000: 2633 changed, 127453 examined... 001: 586 changed, 11347 examined... 002: 141 changed, 3414 examined... 003: 45 changed, 892 examined... 004: 12 changed, 280 examined... 005: 6 changed, 78 examined... 006: 1 changed, 36 examined... 007: 1 changed, 6 examined... 008: 0 changed, 8 examined... 186 labels changed using aseg 000: 100 total segments, 61 labels (189 vertices) changed 001: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1453 vertices marked for relabeling... 1453 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 7 seconds. @#@FSTIME 2023:08:29:20:25:44 mris_ca_label N 11 e 7.04 S 0.35 U 6.67 P 99% M 1108092 F 0 R 346141 W 0 c 705 w 1 I 0 O 2000 L 1.60 1.43 1.33 @#@FSLOADPOST 2023:08:29:20:25:51 mris_ca_label N 11 1.50 1.42 1.33 #-------------------------------------------- #@# WhiteSurfs lh Tue Aug 29 20:25:51 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.4.1 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 254100 0.33779 0.11521 0.001844 1.7150 Corner 762300 60.00000 13.92197 0.247817 177.7862 Edge 381150 0.89455 0.19332 0.027007 3.3731 Hinge 381150 11.95807 12.11527 0.000111 179.9576 Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23311, wmmin=5, clip=110 MRIfindBrightNonWM(): 1279 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 8364/127052 vertices (118688 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 387 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 63526: xyz = (-21.9021,-9.63911,41.1997) oxyz = (-21.9021,-9.63911,41.1997) wxzy = (-21.9021,-9.63911,41.1997) pxyz = (0,0,0) CBVO Creating mask 127052 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=2 had to be increased for 149 vertices, nripped=8751 mean border=83.0, 61 (61) missing vertices, mean dist 0.4 [1.7 (%10.3)->0.6 (%89.7))] %50 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1430 min Finding expansion regions mean absolute distance = 0.72 +- 0.97 2480 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=1493832.4, rms=7.453 001: dt: 0.5000, sse=575585.7, rms=4.105 (44.930%) 002: dt: 0.5000, sse=365645.1, rms=2.825 (31.174%) 003: dt: 0.5000, sse=341206.4, rms=2.635 (6.722%) 004: dt: 0.5000, sse=326914.8, rms=2.503 (5.006%) rms = 2.6384/2.5032, sse=352046.2/326914.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=261587.8, rms=1.837 (26.607%) 006: dt: 0.2500, sse=237800.8, rms=1.507 (17.963%) 007: dt: 0.2500, sse=230135.6, rms=1.422 (5.644%) rms = 1.4074/1.4221, sse=232170.4/230135.6, time step reduction 2 of 3 to 0.125 0 1 1 008: dt: 0.2500, sse=232170.4, rms=1.407 (1.036%) rms = 1.3781/1.4074, sse=230920.9/232170.4, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=230920.9, rms=1.378 (2.082%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=1 had to be increased for 108 vertices, nripped=8751 mean border=86.2, 76 (23) missing vertices, mean dist -0.3 [0.4 (%73.0)->0.2 (%27.0))] %69 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1024 min Finding expansion regions mean absolute distance = 0.38 +- 0.64 2575 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=638271.4, rms=4.320 010: dt: 0.5000, sse=369599.2, rms=2.655 (38.555%) 011: dt: 0.5000, sse=338354.9, rms=2.428 (8.551%) rms = 2.4503/2.4277, sse=341126.1/338354.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=273375.8, rms=1.768 (27.164%) 013: dt: 0.2500, sse=246914.1, rms=1.327 (24.938%) 014: dt: 0.2500, sse=236577.4, rms=1.210 (8.827%) rms = 1.1763/1.2101, sse=235914.6/236577.4, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=235914.6, rms=1.176 (2.796%) rms = 1.1469/1.1763, sse=235809.3/235914.6, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=235809.3, rms=1.147 (2.497%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 149 vertices, nripped=8751 mean border=88.6, 80 (10) missing vertices, mean dist -0.2 [0.3 (%72.0)->0.2 (%28.0))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0563 min Finding expansion regions mean absolute distance = 0.26 +- 0.38 2646 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=420039.8, rms=3.063 017: dt: 0.5000, sse=331827.3, rms=2.213 (27.761%) rms = 2.3215/2.2129, sse=315066.8/331827.3, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 018: dt: 0.2500, sse=247909.9, rms=1.540 (30.428%) 019: dt: 0.2500, sse=221596.5, rms=1.166 (24.271%) 020: dt: 0.2500, sse=219999.6, rms=1.073 (7.932%) rms = 1.0733/1.0734, sse=222665.9/219999.6, time step reduction 2 of 3 to 0.125 0 1 1 021: dt: 0.2500, sse=222665.9, rms=1.073 (0.017%) rms = 1.0403/1.0733, sse=219280.0/222665.9, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=219280.0, rms=1.040 (3.070%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 187 vertices, nripped=8751 mean border=89.3, 105 (5) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0350 min Finding expansion regions mean absolute distance = 0.21 +- 0.31 2684 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=237664.5, rms=1.399 rms = 1.3213/1.3985, sse=238837.3/237664.5, time step reduction 1 of 3 to 0.250 0 1 0 023: dt: 0.5000, sse=238837.2, rms=1.321 (5.526%) 024: dt: 0.2500, sse=218452.1, rms=0.990 (25.077%) 025: dt: 0.2500, sse=208030.2, rms=0.814 (17.738%) rms = 0.8703/0.8143, sse=204647.2/208030.2, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.7969/0.8143, sse=207234.9/208030.2, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=207235.0, rms=0.797 (2.136%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.42 minutes Writing output to ../surf/lh.white #VMPC# mris_place_surfaces VmPeak 1913080 mris_place_surface done @#@FSTIME 2023:08:29:20:25:51 mris_place_surface N 25 e 151.61 S 0.44 U 151.06 P 99% M 1648508 F 0 R 449223 W 0 c 14900 w 1 I 0 O 8936 L 1.50 1.42 1.33 @#@FSLOADPOST 2023:08:29:20:28:22 mris_place_surface N 25 1.53 1.41 1.33 #-------------------------------------------- #@# WhiteSurfs rh Tue Aug 29 20:28:22 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.4.1 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 254902 0.34105 0.12183 0.000658 3.3781 Corner 764706 60.00000 14.74974 0.103958 179.2854 Edge 382353 0.89997 0.20337 0.009724 3.5299 Hinge 382353 11.96947 12.55407 0.000029 179.8187 Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23311, wmmin=5, clip=110 MRIfindBrightNonWM(): 1279 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 8025/127453 vertices (119428 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 232 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 63727: xyz = (6.73678,-11.5531,31.4867) oxyz = (6.73678,-11.5531,31.4867) wxzy = (6.73678,-11.5531,31.4867) pxyz = (0,0,0) CBVO Creating mask 127453 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=2 had to be increased for 136 vertices, nripped=8257 mean border=83.1, 54 (54) missing vertices, mean dist 0.3 [1.6 (%12.3)->0.6 (%87.7))] %48 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1397 min Finding expansion regions mean absolute distance = 0.70 +- 1.00 2787 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=1384917.4, rms=7.088 001: dt: 0.5000, sse=544329.4, rms=3.900 (44.981%) 002: dt: 0.5000, sse=375806.0, rms=2.860 (26.654%) rms = 2.8464/2.8605, sse=372796.7/375806.0, time step reduction 1 of 3 to 0.250 0 0 1 003: dt: 0.5000, sse=372796.7, rms=2.846 (0.491%) 004: dt: 0.2500, sse=254410.2, rms=1.739 (38.905%) 005: dt: 0.2500, sse=238108.2, rms=1.527 (12.202%) rms = 1.4769/1.5268, sse=235268.8/238108.2, time step reduction 2 of 3 to 0.125 0 0 1 006: dt: 0.2500, sse=235268.8, rms=1.477 (3.271%) rms = 1.4306/1.4769, sse=232316.3/235268.8, time step reduction 3 of 3 to 0.062 0 0 1 007: dt: 0.1250, sse=232316.2, rms=1.431 (3.137%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=1 had to be increased for 157 vertices, nripped=8257 mean border=86.1, 33 (9) missing vertices, mean dist -0.2 [0.4 (%70.7)->0.2 (%29.3))] %68 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0996 min Finding expansion regions mean absolute distance = 0.37 +- 0.63 2439 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=619150.1, rms=4.232 008: dt: 0.5000, sse=365585.2, rms=2.695 (36.325%) 009: dt: 0.5000, sse=353950.2, rms=2.616 (2.935%) rms = 2.6793/2.6158, sse=362237.3/353950.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 010: dt: 0.2500, sse=269471.0, rms=1.803 (31.068%) 011: dt: 0.2500, sse=233068.7, rms=1.303 (27.736%) 012: dt: 0.2500, sse=227275.0, rms=1.201 (7.824%) rms = 1.1846/1.2011, sse=226790.9/227275.0, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=226790.9, rms=1.185 (1.366%) rms = 1.1537/1.1846, sse=225341.1/226790.9, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=225341.1, rms=1.154 (2.610%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 182 vertices, nripped=8257 mean border=88.3, 88 (5) missing vertices, mean dist -0.1 [0.3 (%70.3)->0.2 (%29.7))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0546 min Finding expansion regions mean absolute distance = 0.25 +- 0.40 2725 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=391772.0, rms=2.922 015: dt: 0.5000, sse=326610.4, rms=2.354 (19.445%) rms = 2.5576/2.3536, sse=345301.4/326610.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 016: dt: 0.2500, sse=253868.5, rms=1.595 (32.225%) 017: dt: 0.2500, sse=225530.5, rms=1.200 (24.792%) 018: dt: 0.2500, sse=220016.2, rms=1.105 (7.887%) rms = 1.0961/1.1051, sse=219615.9/220016.2, time step reduction 2 of 3 to 0.125 0 0 1 019: dt: 0.2500, sse=219616.0, rms=1.096 (0.808%) rms = 1.0582/1.0961, sse=217472.1/219615.9, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=217472.1, rms=1.058 (3.457%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5836870; border_low = 74.0000000; outside_low = 63.6828040; outside_hi = 110.5836870; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 213 vertices, nripped=8257 mean border=88.9, 152 (5) missing vertices, mean dist -0.0 [0.2 (%54.3)->0.2 (%45.7))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0341 min Finding expansion regions mean absolute distance = 0.21 +- 0.33 2321 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface 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=rnet-, 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=235634.9, rms=1.399 rms = 1.4062/1.3994, sse=245601.8/235634.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 021: dt: 0.2500, sse=213187.2, rms=0.995 (28.932%) 022: dt: 0.2500, sse=207149.9, rms=0.792 (20.323%) rms = 0.8156/0.7924, sse=208683.8/207149.9, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.7891/0.7924, sse=206971.6/207149.9, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=206971.6, rms=0.789 (0.422%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.20 minutes Writing output to ../surf/rh.white #VMPC# mris_place_surfaces VmPeak 1894008 mris_place_surface done @#@FSTIME 2023:08:29:20:28:22 mris_place_surface N 25 e 137.69 S 0.47 U 137.12 P 99% M 1629616 F 0 R 444690 W 0 c 13629 w 1 I 0 O 8968 L 1.53 1.41 1.33 @#@FSLOADPOST 2023:08:29:20:30:40 mris_place_surface N 25 1.27 1.33 1.31 #-------------------------------------------- #@# T1PialSurf lh Tue Aug 29 20:30:40 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.4.1 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 254100 0.34034 0.12771 0.000555 2.0757 Corner 762300 60.00000 15.25152 0.162605 179.0368 Edge 381150 0.89955 0.21124 0.014997 3.5402 Hinge 381150 12.08346 12.34967 0.000062 179.9439 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23311, wmmin=5, clip=110 MRIfindBrightNonWM(): 1279 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 69.2324 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 6203/127052 vertices (120849 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 63526: xyz = (-21.9272,-9.63942,41.1958) oxyz = (-21.9272,-9.63942,41.1958) wxzy = (-21.9272,-9.63942,41.1958) pxyz = (-21.9272,-9.63942,41.1958) CBVO Creating mask 127052 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=2 had to be increased for 231 vertices, nripped=6203 mean border=60.7, 109 (109) missing vertices, mean dist 2.0 [0.4 (%0.0)->2.6 (%100.0))] %21 local maxima, %51 large gradients and %22 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1125 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 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=rnet-, 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=20681588.0, rms=29.136 001: dt: 0.5000, sse=14554129.0, rms=24.396 (16.269%) 002: dt: 0.5000, sse=10258722.0, rms=20.426 (16.272%) 003: dt: 0.5000, sse=7579278.0, rms=17.498 (14.335%) 004: dt: 0.5000, sse=5954163.5, rms=15.452 (11.691%) 005: dt: 0.5000, sse=4866611.0, rms=13.915 (9.949%) 006: dt: 0.5000, sse=3989162.0, rms=12.537 (9.903%) 007: dt: 0.5000, sse=3201794.0, rms=11.156 (11.015%) 008: dt: 0.5000, sse=2500609.5, rms=9.763 (12.491%) 009: dt: 0.5000, sse=1915507.2, rms=8.425 (13.705%) 010: dt: 0.5000, sse=1457813.1, rms=7.206 (14.466%) 011: dt: 0.5000, sse=1147084.8, rms=6.243 (13.358%) 012: dt: 0.5000, sse=950116.4, rms=5.546 (11.167%) 013: dt: 0.5000, sse=848591.1, rms=5.148 (7.176%) 014: dt: 0.5000, sse=792583.4, rms=4.913 (4.562%) 015: dt: 0.5000, sse=763424.1, rms=4.785 (2.615%) 016: dt: 0.5000, sse=739470.5, rms=4.676 (2.275%) 017: dt: 0.5000, sse=728097.9, rms=4.622 (1.159%) 018: dt: 0.5000, sse=715106.7, rms=4.560 (1.330%) rms = 4.5327/4.5603, sse=709675.3/715106.7, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=709675.2, rms=4.533 (0.605%) 020: dt: 0.2500, sse=485144.4, rms=3.323 (26.677%) 021: dt: 0.2500, sse=436713.2, rms=3.004 (9.616%) rms = 2.9592/3.0039, sse=430691.5/436713.2, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=430691.5, rms=2.959 (1.488%) 023: dt: 0.1250, sse=391426.9, rms=2.665 (9.928%) 024: dt: 0.1250, sse=384826.5, rms=2.613 (1.962%) rms = 2.6068/2.6131, sse=384099.3/384826.5, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=384099.3, rms=2.607 (0.241%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=1 had to be increased for 4890 vertices, nripped=6203 mean border=58.4, 983 (13) missing vertices, mean dist 0.1 [0.1 (%42.4)->0.4 (%57.6))] %41 local maxima, %36 large gradients and %18 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0336 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 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=rnet-, 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=714033.6, rms=4.320 rms = 4.3042/4.3197, sse=712012.6/714033.6, time step reduction 1 of 3 to 0.250 0 0 1 026: dt: 0.5000, sse=712012.6, rms=4.304 (0.360%) 027: dt: 0.2500, sse=494953.3, rms=3.091 (28.176%) 028: dt: 0.2500, sse=464585.2, rms=2.882 (6.770%) rms = 2.9266/2.8822, sse=470958.3/464585.2, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 029: dt: 0.1250, sse=447824.4, rms=2.757 (4.339%) 030: dt: 0.1250, sse=425759.6, rms=2.582 (6.339%) rms = 2.5400/2.5823, sse=420611.8/425759.6, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=420611.8, rms=2.540 (1.641%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 5516 vertices, nripped=6203 mean border=56.8, 1132 (10) missing vertices, mean dist 0.1 [0.1 (%39.9)->0.3 (%60.1))] %56 local maxima, %20 large gradients and %18 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0198 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 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=rnet-, 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=541827.8, rms=3.370 rms = 4.3459/3.3703, sse=724498.7/541827.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=457377.2, rms=2.800 (16.937%) 033: dt: 0.2500, sse=441071.5, rms=2.675 (4.462%) rms = 2.6862/2.6746, sse=441994.2/441071.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 034: dt: 0.1250, sse=432489.8, rms=2.607 (2.542%) 035: dt: 0.1250, sse=420451.8, rms=2.509 (3.731%) rms = 2.4754/2.5094, sse=416282.2/420451.8, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=416282.2, rms=2.475 (1.355%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127052 Gdiag_no=-1 vno start=0, stop=127052 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 4915 vertices, nripped=6203 mean border=56.1, 2251 (9) missing vertices, mean dist 0.0 [0.2 (%45.5)->0.2 (%54.5))] %60 local maxima, %16 large gradients and %17 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0128 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 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=rnet-, 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=439099.7, rms=2.664 rms = 3.4488/2.6639, sse=553823.7/439099.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=416903.4, rms=2.484 (6.755%) rms = 2.4499/2.4839, sse=412207.6/416903.4, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=412207.6, rms=2.450 (1.371%) 039: dt: 0.1250, sse=402614.7, rms=2.366 (3.409%) rms = 2.3306/2.3664, sse=398340.2/402614.7, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=398340.2, rms=2.331 (1.513%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 28 intersecting 001: 6 intersecting terminating search with 0 intersecting #ET# mris_place_surface 3.08 minutes Writing output to ../surf/lh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1320436 mris_place_surface done @#@FSTIME 2023:08:29:20:30:40 mris_place_surface N 28 e 190.75 S 0.34 U 190.29 P 99% M 1056020 F 0 R 284362 W 0 c 18763 w 1 I 0 O 8936 L 1.27 1.33 1.31 @#@FSLOADPOST 2023:08:29:20:33:51 mris_place_surface N 28 1.20 1.30 1.30 #-------------------------------------------- #@# T1PialSurf rh Tue Aug 29 20:33:51 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.4.1 7.4.1 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 254902 0.34356 0.13232 0.000821 2.2477 Corner 764706 60.00000 15.85425 0.327638 178.5309 Edge 382353 0.90465 0.21839 0.017123 3.5299 Hinge 382353 12.07220 12.66261 0.000033 179.9887 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23311, wmmin=5, clip=110 MRIfindBrightNonWM(): 1279 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 69.2324 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 5613/127453 vertices (121840 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 63727: xyz = (6.68868,-11.5779,31.4579) oxyz = (6.68868,-11.5779,31.4579) wxzy = (6.68868,-11.5779,31.4579) pxyz = (6.68868,-11.5779,31.4579) CBVO Creating mask 127453 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=2 had to be increased for 209 vertices, nripped=5613 mean border=60.8, 157 (157) missing vertices, mean dist 1.9 [1.9 (%0.0)->2.5 (%100.0))] %21 local maxima, %53 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1083 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 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=rnet-, 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=20212556.0, rms=28.686 001: dt: 0.5000, sse=13876232.0, rms=23.717 (17.321%) 002: dt: 0.5000, sse=9532676.0, rms=19.595 (17.379%) 003: dt: 0.5000, sse=6918802.0, rms=16.628 (15.145%) 004: dt: 0.5000, sse=5385730.5, rms=14.607 (12.150%) 005: dt: 0.5000, sse=4402344.0, rms=13.148 (9.993%) 006: dt: 0.5000, sse=3632088.8, rms=11.879 (9.649%) 007: dt: 0.5000, sse=2927477.5, rms=10.586 (10.889%) 008: dt: 0.5000, sse=2302419.8, rms=9.288 (12.261%) 009: dt: 0.5000, sse=1790163.5, rms=8.069 (13.120%) 010: dt: 0.5000, sse=1404914.5, rms=7.013 (13.085%) 011: dt: 0.5000, sse=1136307.4, rms=6.170 (12.019%) 012: dt: 0.5000, sse=974686.1, rms=5.600 (9.238%) 013: dt: 0.5000, sse=875566.0, rms=5.219 (6.809%) 014: dt: 0.5000, sse=818150.7, rms=4.983 (4.525%) 015: dt: 0.5000, sse=783382.5, rms=4.833 (3.003%) 016: dt: 0.5000, sse=761797.4, rms=4.737 (1.995%) 017: dt: 0.5000, sse=744126.2, rms=4.656 (1.702%) rms = 4.6141/4.6562, sse=735301.4/744126.2, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=735301.4, rms=4.614 (0.904%) 019: dt: 0.2500, sse=509931.2, rms=3.440 (25.456%) 020: dt: 0.2500, sse=458007.7, rms=3.111 (9.549%) 021: dt: 0.2500, sse=450571.3, rms=3.059 (1.672%) rms = 3.0097/3.0590, sse=443425.1/450571.3, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=443425.1, rms=3.010 (1.613%) 023: dt: 0.1250, sse=405043.0, rms=2.730 (9.285%) rms = 2.6818/2.7303, sse=398746.5/405043.0, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=398746.5, rms=2.682 (1.774%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=1 had to be increased for 4685 vertices, nripped=5613 mean border=58.2, 837 (28) missing vertices, mean dist 0.1 [0.1 (%41.4)->0.4 (%58.6))] %41 local maxima, %37 large gradients and %17 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0334 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 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=rnet-, 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=763124.6, rms=4.513 rms = 4.4887/4.5127, sse=759347.0/763124.6, time step reduction 1 of 3 to 0.250 0 0 1 025: dt: 0.5000, sse=759347.0, rms=4.489 (0.531%) 026: dt: 0.2500, sse=517384.9, rms=3.199 (28.732%) 027: dt: 0.2500, sse=484873.3, rms=2.984 (6.729%) rms = 3.0279/2.9838, sse=491425.0/484873.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 028: dt: 0.1250, sse=465643.5, rms=2.846 (4.610%) 029: dt: 0.1250, sse=440458.8, rms=2.655 (6.732%) rms = 2.6089/2.6546, sse=434693.0/440458.8, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=434693.1, rms=2.609 (1.724%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 5204 vertices, nripped=5613 mean border=56.4, 1046 (13) missing vertices, mean dist 0.1 [0.2 (%37.6)->0.3 (%62.4))] %57 local maxima, %21 large gradients and %17 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0201 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 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=rnet-, 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=592012.5, rms=3.626 rms = 4.6208/3.6260, sse=793007.8/592012.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=489163.7, rms=2.982 (17.749%) 032: dt: 0.2500, sse=467002.4, rms=2.823 (5.347%) rms = 2.8289/2.8229, sse=467163.2/467002.4, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 033: dt: 0.1250, sse=455954.4, rms=2.741 (2.913%) 034: dt: 0.1250, sse=439689.6, rms=2.616 (4.554%) rms = 2.5803/2.6159, sse=435082.0/439689.5, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=435082.0, rms=2.580 (1.361%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.4163130; border_hi = 63.6828040; border_low = 43.0484160; outside_low = 10.0000000; outside_hi = 58.5242080; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=127453 Gdiag_no=-1 vno start=0, stop=127453 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 4586 vertices, nripped=5613 mean border=55.6, 2141 (11) missing vertices, mean dist 0.0 [0.2 (%44.2)->0.2 (%55.8))] %62 local maxima, %15 large gradients and %17 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0132 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 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=rnet-, 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=462049.6, rms=2.791 rms = 3.6817/2.7914, sse=601281.7/462049.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=437435.0, rms=2.602 (6.780%) rms = 2.5637/2.6022, sse=431950.0/437435.0, time step reduction 2 of 3 to 0.125 0 0 1 037: dt: 0.2500, sse=431950.0, rms=2.564 (1.477%) 038: dt: 0.1250, sse=421611.2, rms=2.478 (3.326%) rms = 2.4411/2.4784, sse=416908.2/421611.2, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=416908.2, rms=2.441 (1.508%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 31 intersecting 001: 12 intersecting 002: 10 intersecting step 1 with no progress (num=13, old_num=10) 003: 13 intersecting terminating search with 0 intersecting #ET# mris_place_surface 3.04 minutes Writing output to ../surf/rh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1326660 mris_place_surface done @#@FSTIME 2023:08:29:20:33:51 mris_place_surface N 28 e 188.47 S 0.33 U 188.01 P 99% M 1062116 F 0 R 285958 W 0 c 18462 w 1 I 0 O 8968 L 1.20 1.30 1.30 @#@FSLOADPOST 2023:08:29:20:36:59 mris_place_surface N 28 1.18 1.21 1.26 #@# white curv lh Tue Aug 29 20:36:59 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2023:08:29:20:36:59 mris_place_surface N 5 e 1.28 S 0.06 U 1.21 P 99% M 175312 F 0 R 47141 W 0 c 125 w 1 I 0 O 1000 L 1.18 1.21 1.26 @#@FSLOADPOST 2023:08:29:20:37:01 mris_place_surface N 5 1.24 1.22 1.27 #@# white area lh Tue Aug 29 20:37:01 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2023:08:29:20:37:01 mris_place_surface N 3 e 0.52 S 0.05 U 0.47 P 100% M 175416 F 0 R 47142 W 0 c 54 w 1 I 0 O 1000 L 1.24 1.22 1.27 @#@FSLOADPOST 2023:08:29:20:37:01 mris_place_surface N 3 1.24 1.22 1.27 #@# pial curv lh Tue Aug 29 20:37:01 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2023:08:29:20:37:01 mris_place_surface N 5 e 1.26 S 0.04 U 1.22 P 99% M 175448 F 0 R 47143 W 0 c 123 w 1 I 0 O 1000 L 1.24 1.22 1.27 @#@FSLOADPOST 2023:08:29:20:37:03 mris_place_surface N 5 1.24 1.22 1.27 #@# pial area lh Tue Aug 29 20:37:03 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2023:08:29:20:37:03 mris_place_surface N 3 e 0.55 S 0.05 U 0.50 P 99% M 175508 F 0 R 47142 W 0 c 54 w 1 I 0 O 1000 L 1.24 1.22 1.27 @#@FSLOADPOST 2023:08:29:20:37:03 mris_place_surface N 3 1.24 1.22 1.27 #@# thickness lh Tue Aug 29 20:37:03 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 127052 vertices processed 25000 of 127052 vertices processed 50000 of 127052 vertices processed 75000 of 127052 vertices processed 100000 of 127052 vertices processed 125000 of 127052 vertices processed 0 of 127052 vertices processed 25000 of 127052 vertices processed 50000 of 127052 vertices processed 75000 of 127052 vertices processed 100000 of 127052 vertices processed 125000 of 127052 vertices processed thickness calculation complete, 123:288 truncations. 59357 vertices at 0 distance 112603 vertices at 1 distance 57096 vertices at 2 distance 17059 vertices at 3 distance 5080 vertices at 4 distance 1744 vertices at 5 distance 648 vertices at 6 distance 221 vertices at 7 distance 106 vertices at 8 distance 50 vertices at 9 distance 18 vertices at 10 distance 19 vertices at 11 distance 16 vertices at 12 distance 13 vertices at 13 distance 16 vertices at 14 distance 10 vertices at 15 distance 10 vertices at 16 distance 12 vertices at 17 distance 11 vertices at 18 distance 7 vertices at 19 distance 8 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2023:08:29:20:37:03 mris_place_surface N 6 e 21.76 S 0.06 U 21.68 P 99% M 175372 F 0 R 53840 W 0 c 2095 w 1 I 0 O 1000 L 1.24 1.22 1.27 @#@FSLOADPOST 2023:08:29:20:37:25 mris_place_surface N 6 1.57 1.29 1.29 #@# area and vertex vol lh Tue Aug 29 20:37:25 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 lh /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.volume masking with /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Total face volume 223313 Total vertex volume 223119 (mask=0) #@# EP01 lh 223119 vertexvol Done @#@FSTIME 2023:08:29:20:37:25 vertexvol N 4 e 1.14 S 0.13 U 1.01 P 99% M 291132 F 0 R 82649 W 0 c 112 w 22 I 0 O 3000 L 1.57 1.29 1.29 @#@FSLOADPOST 2023:08:29:20:37:26 vertexvol N 4 1.53 1.29 1.28 #@# white curv rh Tue Aug 29 20:37:26 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2023:08:29:20:37:26 mris_place_surface N 5 e 1.22 S 0.04 U 1.18 P 99% M 175752 F 0 R 47279 W 0 c 121 w 1 I 0 O 1000 L 1.53 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:37:27 mris_place_surface N 5 1.53 1.29 1.28 #@# white area rh Tue Aug 29 20:37:27 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2023:08:29:20:37:27 mris_place_surface N 3 e 0.52 S 0.05 U 0.46 P 99% M 175856 F 0 R 47283 W 0 c 51 w 1 I 0 O 1000 L 1.53 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:37:28 mris_place_surface N 3 1.53 1.29 1.28 #@# pial curv rh Tue Aug 29 20:37:28 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2023:08:29:20:37:28 mris_place_surface N 5 e 1.21 S 0.03 U 1.17 P 99% M 175804 F 0 R 47282 W 0 c 119 w 1 I 0 O 1000 L 1.53 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:37:29 mris_place_surface N 5 1.53 1.29 1.28 #@# pial area rh Tue Aug 29 20:37:29 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2023:08:29:20:37:29 mris_place_surface N 3 e 0.53 S 0.04 U 0.48 P 99% M 175832 F 0 R 47281 W 0 c 52 w 1 I 0 O 1000 L 1.53 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:37:30 mris_place_surface N 3 1.53 1.29 1.28 #@# thickness rh Tue Aug 29 20:37:30 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 127453 vertices processed 25000 of 127453 vertices processed 50000 of 127453 vertices processed 75000 of 127453 vertices processed 100000 of 127453 vertices processed 125000 of 127453 vertices processed 0 of 127453 vertices processed 25000 of 127453 vertices processed 50000 of 127453 vertices processed 75000 of 127453 vertices processed 100000 of 127453 vertices processed 125000 of 127453 vertices processed thickness calculation complete, 96:350 truncations. 59966 vertices at 0 distance 115907 vertices at 1 distance 56050 vertices at 2 distance 15803 vertices at 3 distance 4550 vertices at 4 distance 1520 vertices at 5 distance 575 vertices at 6 distance 220 vertices at 7 distance 100 vertices at 8 distance 75 vertices at 9 distance 44 vertices at 10 distance 32 vertices at 11 distance 17 vertices at 12 distance 8 vertices at 13 distance 7 vertices at 14 distance 7 vertices at 15 distance 1 vertices at 16 distance 4 vertices at 17 distance 3 vertices at 18 distance 4 vertices at 19 distance 13 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2023:08:29:20:37:30 mris_place_surface N 6 e 22.17 S 0.07 U 22.08 P 99% M 175920 F 0 R 53999 W 0 c 2155 w 1 I 0 O 1000 L 1.53 1.29 1.28 @#@FSLOADPOST 2023:08:29:20:37:52 mris_place_surface N 6 1.60 1.33 1.30 #@# area and vertex vol rh Tue Aug 29 20:37:52 PDT 2023 cd /usr/local/freesurfer/7.4.1/subjects/EP01/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 rh /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.volume masking with /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Total face volume 224290 Total vertex volume 224095 (mask=0) #@# EP01 rh 224095 vertexvol Done @#@FSTIME 2023:08:29:20:37:52 vertexvol N 4 e 1.10 S 0.10 U 0.99 P 99% M 292216 F 0 R 82896 W 0 c 107 w 21 I 0 O 3000 L 1.60 1.33 1.30 @#@FSLOADPOST 2023:08:29:20:37:53 vertexvol N 4 1.60 1.33 1.30 #----------------------------------------- #@# Curvature Stats lh Tue Aug 29 20:37:53 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm EP01 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 [ EP01/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 [ 209 ] Gb_filter = 0 WARN: S lookup min: -0.298350 WARN: S explicit min: 0.000000 vertex = 2690 @#@FSTIME 2023:08:29:20:37:53 mris_curvature_stats N 11 e 1.61 S 0.06 U 1.55 P 99% M 175164 F 0 R 47315 W 0 c 154 w 1 I 0 O 8040 L 1.60 1.33 1.30 @#@FSLOADPOST 2023:08:29:20:37:55 mris_curvature_stats N 11 1.60 1.33 1.30 #----------------------------------------- #@# Curvature Stats rh Tue Aug 29 20:37:55 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm EP01 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 [ EP01/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 [ 218 ] Gb_filter = 0 WARN: S lookup min: -0.058592 WARN: S explicit min: 0.000000 vertex = 49 @#@FSTIME 2023:08:29:20:37:55 mris_curvature_stats N 11 e 1.62 S 0.06 U 1.55 P 99% M 175928 F 0 R 47481 W 0 c 157 w 1 I 0 O 8040 L 1.60 1.33 1.30 @#@FSLOADPOST 2023:08:29:20:37:56 mris_curvature_stats N 11 1.55 1.32 1.29 #-------------------------------------------- #@# Cortical ribbon mask Tue Aug 29 20:37:56 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 SUBJECTS_DIR is /usr/local/freesurfer/7.4.1/subjects loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 52 writing volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/ribbon.mgz mris_volmask took 3.70 minutes writing ribbon files @#@FSTIME 2023:08:29:20:37:56 mris_volmask N 12 e 222.27 S 0.52 U 221.60 P 99% M 946340 F 0 R 509180 W 0 c 21835 w 0 I 0 O 816 L 1.55 1.32 1.29 @#@FSLOADPOST 2023:08:29:20:41:39 mris_volmask N 12 1.57 1.56 1.40 #----------------------------------------- #@# Cortical Parc 2 lh Tue Aug 29 20:41:39 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 EP01 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.4.1/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 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/7.4.1/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 reading surface from /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 31 labels changed using aseg relabeling using gibbs priors... 000: 8502 changed, 127052 examined... 001: 1877 changed, 33133 examined... 002: 558 changed, 10162 examined... 003: 240 changed, 3211 examined... 004: 115 changed, 1364 examined... 005: 50 changed, 666 examined... 006: 29 changed, 292 examined... 007: 18 changed, 175 examined... 008: 12 changed, 98 examined... 009: 8 changed, 71 examined... 010: 7 changed, 41 examined... 011: 4 changed, 33 examined... 012: 4 changed, 25 examined... 013: 3 changed, 21 examined... 014: 1 changed, 14 examined... 015: 0 changed, 7 examined... 6 labels changed using aseg 000: 227 total segments, 140 labels (1607 vertices) changed 001: 93 total segments, 6 labels (37 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1166 vertices marked for relabeling... 1166 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2023:08:29:20:41:39 mris_ca_label N 11 e 9.30 S 0.59 U 8.69 P 99% M 1693508 F 0 R 653889 W 0 c 921 w 1 I 0 O 1992 L 1.57 1.56 1.40 @#@FSLOADPOST 2023:08:29:20:41:48 mris_ca_label N 11 1.88 1.63 1.43 #----------------------------------------- #@# Cortical Parc 2 rh Tue Aug 29 20:41:48 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 EP01 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.4.1/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 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/7.4.1/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 reading surface from /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 44 labels changed using aseg relabeling using gibbs priors... 000: 8549 changed, 127453 examined... 001: 1935 changed, 33354 examined... 002: 572 changed, 10379 examined... 003: 253 changed, 3306 examined... 004: 130 changed, 1493 examined... 005: 75 changed, 783 examined... 006: 42 changed, 415 examined... 007: 32 changed, 252 examined... 008: 15 changed, 172 examined... 009: 5 changed, 88 examined... 010: 4 changed, 33 examined... 011: 5 changed, 24 examined... 012: 4 changed, 23 examined... 013: 1 changed, 17 examined... 014: 0 changed, 7 examined... 17 labels changed using aseg 000: 219 total segments, 135 labels (1921 vertices) changed 001: 94 total segments, 10 labels (58 vertices) changed 002: 85 total segments, 1 labels (1 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 23 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1002 vertices marked for relabeling... 1002 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 10 seconds. @#@FSTIME 2023:08:29:20:41:48 mris_ca_label N 11 e 9.81 S 0.54 U 9.25 P 99% M 1662388 F 0 R 539789 W 0 c 947 w 1 I 0 O 2000 L 1.88 1.63 1.43 @#@FSLOADPOST 2023:08:29:20:41:58 mris_ca_label N 11 1.75 1.61 1.42 #----------------------------------------- #@# Cortical Parc 3 lh Tue Aug 29 20:41:58 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 EP01 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.4.1/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 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/7.4.1/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 reading surface from /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1812 labels changed using aseg relabeling using gibbs priors... 000: 1864 changed, 127052 examined... 001: 443 changed, 8686 examined... 002: 146 changed, 2528 examined... 003: 70 changed, 838 examined... 004: 30 changed, 392 examined... 005: 18 changed, 179 examined... 006: 10 changed, 115 examined... 007: 7 changed, 61 examined... 008: 7 changed, 42 examined... 009: 5 changed, 41 examined... 010: 4 changed, 34 examined... 011: 5 changed, 25 examined... 012: 5 changed, 26 examined... 013: 9 changed, 32 examined... 014: 8 changed, 47 examined... 015: 7 changed, 47 examined... 016: 7 changed, 37 examined... 017: 10 changed, 47 examined... 018: 10 changed, 51 examined... 019: 10 changed, 46 examined... 020: 5 changed, 46 examined... 021: 7 changed, 30 examined... 022: 3 changed, 34 examined... 023: 3 changed, 21 examined... 024: 4 changed, 18 examined... 025: 5 changed, 26 examined... 026: 3 changed, 27 examined... 027: 3 changed, 15 examined... 028: 3 changed, 19 examined... 029: 2 changed, 11 examined... 030: 0 changed, 13 examined... 387 labels changed using aseg 000: 55 total segments, 22 labels (99 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 812 vertices marked for relabeling... 812 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 7 seconds. @#@FSTIME 2023:08:29:20:41:58 mris_ca_label N 11 e 7.49 S 0.31 U 7.16 P 99% M 918628 F 0 R 295223 W 0 c 745 w 1 I 0 O 1992 L 1.75 1.61 1.42 @#@FSLOADPOST 2023:08:29:20:42:05 mris_ca_label N 11 1.69 1.60 1.42 #----------------------------------------- #@# Cortical Parc 3 rh Tue Aug 29 20:42:05 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 EP01 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.4.1/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 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/7.4.1/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 reading surface from /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1909 labels changed using aseg relabeling using gibbs priors... 000: 1899 changed, 127453 examined... 001: 474 changed, 8974 examined... 002: 145 changed, 2646 examined... 003: 61 changed, 853 examined... 004: 35 changed, 359 examined... 005: 15 changed, 176 examined... 006: 12 changed, 88 examined... 007: 13 changed, 70 examined... 008: 11 changed, 71 examined... 009: 5 changed, 50 examined... 010: 7 changed, 29 examined... 011: 3 changed, 38 examined... 012: 1 changed, 16 examined... 013: 2 changed, 8 examined... 014: 2 changed, 10 examined... 015: 4 changed, 14 examined... 016: 3 changed, 19 examined... 017: 6 changed, 21 examined... 018: 3 changed, 21 examined... 019: 3 changed, 16 examined... 020: 2 changed, 15 examined... 021: 2 changed, 12 examined... 022: 1 changed, 10 examined... 023: 2 changed, 7 examined... 024: 2 changed, 13 examined... 025: 2 changed, 12 examined... 026: 3 changed, 12 examined... 027: 1 changed, 13 examined... 028: 2 changed, 8 examined... 029: 2 changed, 12 examined... 030: 4 changed, 11 examined... 031: 5 changed, 17 examined... 032: 4 changed, 25 examined... 033: 1 changed, 23 examined... 034: 0 changed, 6 examined... 411 labels changed using aseg 000: 54 total segments, 21 labels (440 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 515 vertices marked for relabeling... 515 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 7 seconds. @#@FSTIME 2023:08:29:20:42:05 mris_ca_label N 11 e 7.30 S 0.29 U 7.00 P 99% M 916048 F 0 R 291356 W 0 c 715 w 1 I 0 O 2000 L 1.69 1.60 1.42 @#@FSLOADPOST 2023:08:29:20:42:13 mris_ca_label N 11 1.66 1.59 1.42 #----------------------------------------- #@# WM/GM Contrast lh Tue Aug 29 20:42:13 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts pctsurfcon --s EP01 --lh-only Log file is /usr/local/freesurfer/7.4.1/subjects/EP01/scripts/pctsurfcon.log Tue Aug 29 20:42:13 PDT 2023 setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects cd /usr/local/freesurfer/7.4.1/subjects/EP01/scripts /usr/local/freesurfer/7.4.1/bin/pctsurfcon pctsurfcon 7.4.1 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/7.4.1 mri_vol2surf --mov /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.892998/lh.wm.mgh --regheader EP01 --cortex srcvol = /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00003; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Reading surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 107309 Masking with /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Writing to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.892998/lh.wm.mgh Dim: 127052 1 1 mri_vol2surf done mri_vol2surf --mov /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.892998/lh.gm.mgh --projfrac 0.3 --regheader EP01 --cortex srcvol = /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00003; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Reading surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 120810 Masking with /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Writing to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.892998/lh.gm.mgh Dim: 127052 1 1 mri_vol2surf done mri_concat /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.892998/lh.wm.mgh /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.892998/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.w-g.pct.mgh --annot EP01 lh aparc --sum /usr/local/freesurfer/7.4.1/subjects/EP01/stats/lh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.w-g.pct.mgh --annot EP01 lh aparc --sum /usr/local/freesurfer/7.4.1/subjects/EP01/stats/lh.w-g.pct.stats --snr sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.aparc.annot Seg base 1000 MRISannot2seg(): nhits = 118688 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.w-g.pct.mgh Vertex Area is 0.680663 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2023:08:29:20:42:13 pctsurfcon N 3 e 4.33 S 0.43 U 3.90 P 99% M 594584 F 0 R 355983 W 0 c 424 w 64 I 0 O 3104 L 1.66 1.59 1.42 @#@FSLOADPOST 2023:08:29:20:42:17 pctsurfcon N 3 1.60 1.58 1.42 #----------------------------------------- #@# WM/GM Contrast rh Tue Aug 29 20:42:17 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/scripts pctsurfcon --s EP01 --rh-only Log file is /usr/local/freesurfer/7.4.1/subjects/EP01/scripts/pctsurfcon.log Tue Aug 29 20:42:17 PDT 2023 setenv SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects cd /usr/local/freesurfer/7.4.1/subjects/EP01/scripts /usr/local/freesurfer/7.4.1/bin/pctsurfcon pctsurfcon 7.4.1 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/7.4.1 mri_vol2surf --mov /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.893060/rh.wm.mgh --regheader EP01 --cortex srcvol = /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00003; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Reading surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 108080 Masking with /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Writing to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.893060/rh.wm.mgh Dim: 127453 1 1 mri_vol2surf done mri_vol2surf --mov /usr/local/freesurfer/7.4.1/subjects/EP01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.893060/rh.gm.mgh --projfrac 0.3 --regheader EP01 --cortex srcvol = /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00003; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Reading surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 120939 Masking with /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Writing to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.893060/rh.gm.mgh Dim: 127453 1 1 mri_vol2surf done mri_concat /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.893060/rh.wm.mgh /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp.pctsurfcon.893060/rh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/7.4.1/subjects/EP01/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 /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.w-g.pct.mgh --annot EP01 rh aparc --sum /usr/local/freesurfer/7.4.1/subjects/EP01/stats/rh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.w-g.pct.mgh --annot EP01 rh aparc --sum /usr/local/freesurfer/7.4.1/subjects/EP01/stats/rh.w-g.pct.stats --snr sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.annot Seg base 2000 MRISannot2seg(): nhits = 119428 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.w-g.pct.mgh Vertex Area is 0.687115 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2023:08:29:20:42:17 pctsurfcon N 3 e 4.37 S 0.43 U 3.93 P 99% M 594964 F 0 R 356673 W 0 c 420 w 68 I 0 O 3104 L 1.60 1.58 1.42 @#@FSLOADPOST 2023:08:29:20:42:21 pctsurfcon N 3 1.63 1.59 1.42 #----------------------------------------- #@# Relabel Hypointensities Tue Aug 29 20:42:21 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1581 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1360 voxels changed to hypointensity... 2930 hypointense voxels neighboring cortex changed @#@FSTIME 2023:08:29:20:42:21 mri_relabel_hypointensities N 3 e 11.07 S 0.31 U 10.74 P 99% M 462532 F 0 R 330229 W 0 c 1109 w 1 I 0 O 648 L 1.63 1.59 1.42 @#@FSLOADPOST 2023:08:29:20:42:33 mri_relabel_hypointensities N 3 1.61 1.59 1.42 #----------------------------------------- #@# APas-to-ASeg Tue Aug 29 20:42:33 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /usr/local/freesurfer/7.4.1/subjects/EP01/mri/ribbon.mgz --threads 1 --lh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label --lh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white --lh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial --rh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label --rh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white --rh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects outvol aseg.mgz 64 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /usr/local/freesurfer/7.4.1/subjects/EP01/mri/ribbon.mgz Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 0 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 889024 mri_surf2volseg done @#@FSTIME 2023:08:29:20:42:33 mri_surf2volseg N 20 e 7.09 S 0.28 U 6.79 P 99% M 858940 F 0 R 239938 W 0 c 694 w 1 I 0 O 680 L 1.61 1.59 1.42 @#@FSLOADPOST 2023:08:29:20:42:40 mri_surf2volseg N 20 1.56 1.58 1.42 mri_brainvol_stats --subject EP01 ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1530750.0 #CBVS2 BrainSegVol 1068536.0 #CBVS2 BrainSegVolNotVent 1051946.0 #CBVS2 SupraTentVol 933158.0 #CBVS2 SupraTentVolNotVent 916568.0 #CBVS2 lhCtxGM 223380.1 #CBVS2 rhCtxGM 224466.0 #CBVS2 lhCerebralWM 208138.5 #CBVS2 rhCerebralWM 208592.5 #CBVS2 SubCortGMVol 53410.0 #CBVS2 CerebellumVol 135378.0 #CBVS2 CerebellumGMVol 110484.0 #CBVS2 VentChorVol 12836.0 #CBVS2 3rd4th5thCSF 3754.0 #CBVS2 AllCSF 16590.0 #CBVS2 CCVol 4297.0 @#@FSTIME 2023:08:29:20:42:40 mri_brainvol_stats N 2 e 3.77 S 0.14 U 3.62 P 99% M 213764 F 0 R 113016 W 0 c 369 w 1 I 0 O 8 L 1.56 1.58 1.42 @#@FSLOADPOST 2023:08:29:20:42:43 mri_brainvol_stats N 2 1.68 1.60 1.43 #----------------------------------------- #@# AParc-to-ASeg aparc Tue Aug 29 20:42:43 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.aparc.annot 1000 --lh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label --lh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white --lh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial --rh-annot /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.annot 2000 --rh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label --rh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white --rh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects outvol aparc+aseg.mgz 64 avail.processors, using 1 Loading aseg.mgz Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8364 vertices from lh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.aparc.annot Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8025 vertices from rh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 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/usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label --lh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white --lh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial --rh-annot /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label --rh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white --rh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects outvol aparc.a2009s+aseg.mgz 64 avail.processors, using 1 Loading aseg.mgz Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8364 vertices from lh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.aparc.a2009s.annot Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8025 vertices from rh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.a2009s.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 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/usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label --lh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white --lh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial --rh-annot /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label --rh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white --rh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects outvol aparc.DKTatlas+aseg.mgz 64 avail.processors, using 1 Loading aseg.mgz Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8364 vertices from lh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.aparc.DKTatlas.annot Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8025 vertices from rh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.DKTatlas.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 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/usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white --lh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial --rh-annot /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.annot 4000 --rh-cortex-mask /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label --rh-white /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white --rh-pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects outvol wmparc.mgz 64 avail.processors, using 1 Loading aparc+aseg.mgz Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8364 vertices from lh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.aparc.annot Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8025 vertices from rh hemi Loading /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.aparc.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 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--excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject EP01 --surf-wm-vol --ctab /usr/local/freesurfer/7.4.1/WMParcStatsLUT.txt --etiv sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1423268 mm^3 (det: 1.368755 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2023:08:29:20:46:53 mri_segstats N 24 e 370.63 S 0.42 U 369.99 P 99% M 239788 F 0 R 1206331 W 0 c 36573 w 1 I 0 O 24 L 1.21 1.40 1.39 @#@FSLOADPOST 2023:08:29:20:53:04 mri_segstats N 24 1.40 1.35 1.36 #----------------------------------------- #@# Parcellation Stats lh Tue Aug 29 20:53:04 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 223313 Total vertex volume 223119 (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) = 1423268 mm^3 (det: 1.368755 ) 1456 947 2311 2.552 0.428 0.096 0.020 8 1.2 bankssts 834 528 1200 2.516 0.329 0.107 0.021 6 0.7 caudalanteriorcingulate 2863 1867 5094 2.526 0.473 0.110 0.026 25 2.7 caudalmiddlefrontal 1956 1380 3220 2.055 0.448 0.148 0.037 29 2.8 cuneus 541 383 1574 2.977 0.776 0.127 0.044 6 0.7 entorhinal 4362 2970 8351 2.559 0.507 0.123 0.030 49 5.1 fusiform 5843 4063 10432 2.363 0.509 0.121 0.026 63 6.4 inferiorparietal 5149 3681 11732 2.715 0.711 0.140 0.042 67 8.8 inferiortemporal 1388 913 2024 2.121 0.726 0.110 0.029 13 1.5 isthmuscingulate 7295 4944 11372 2.043 0.459 0.135 0.035 94 10.0 lateraloccipital 4295 2910 7968 2.505 0.559 0.130 0.038 55 6.1 lateralorbitofrontal 4479 3005 6454 2.003 0.504 0.130 0.034 61 6.1 lingual 2679 1944 5422 2.578 0.541 0.119 0.031 29 3.4 medialorbitofrontal 4128 3087 10873 2.811 0.652 0.131 0.032 56 5.4 middletemporal 984 648 1834 2.496 0.580 0.098 0.024 8 0.9 parahippocampal 1919 1253 3342 2.442 0.488 0.109 0.026 14 2.0 paracentral 2312 1591 4413 2.458 0.436 0.119 0.027 23 2.5 parsopercularis 1101 778 2760 2.698 0.575 0.135 0.033 16 1.3 parsorbitalis 2192 1513 4085 2.411 0.475 0.122 0.027 24 2.5 parstriangularis 1950 1398 2420 1.858 0.401 0.133 0.035 23 2.5 pericalcarine 5556 3447 8039 2.108 0.500 0.098 0.024 47 4.9 postcentral 1487 1044 2585 2.349 0.561 0.128 0.029 18 2.0 posteriorcingulate 6160 3986 10990 2.568 0.457 0.106 0.027 50 6.7 precentral 4968 3428 8714 2.344 0.430 0.124 0.025 54 5.4 precuneus 1379 964 3105 2.751 0.511 0.124 0.031 18 1.7 rostralanteriorcingulate 7666 5476 15261 2.414 0.534 0.130 0.032 98 9.7 rostralmiddlefrontal 10464 7280 22810 2.711 0.539 0.122 0.030 97 12.6 superiorfrontal 7638 5126 12381 2.143 0.459 0.118 0.025 77 7.8 superiorparietal 5559 3763 11610 2.748 0.573 0.117 0.026 49 6.3 superiortemporal 4566 3123 8588 2.491 0.455 0.123 0.028 52 5.1 supramarginal 369 274 1016 2.907 0.582 0.173 0.048 10 0.7 frontalpole 620 488 2586 3.671 0.705 0.139 0.036 8 0.9 temporalpole 738 485 1433 2.620 0.463 0.133 0.035 9 1.0 transversetemporal 3792 2616 7119 2.795 0.727 0.133 0.043 42 6.2 insula @#@FSTIME 2023:08:29:20:53:04 mris_anatomical_stats N 14 e 6.30 S 0.16 U 6.13 P 99% M 451692 F 0 R 133344 W 0 c 612 w 1 I 0 O 24 L 1.40 1.35 1.36 @#@FSLOADPOST 2023:08:29:20:53:10 mris_anatomical_stats N 14 1.37 1.35 1.36 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 EP01 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 223313 Total vertex volume 223119 (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) = 1423268 mm^3 (det: 1.368755 ) 1456 848 2311 2.552 0.428 0.104 0.032 21 1.6 bankssts 834 500 1200 2.516 0.329 0.140 0.059 35 1.3 caudalanteriorcingulate 2863 2057 5094 2.526 0.473 0.116 0.026 43 3.1 caudalmiddlefrontal 1956 1785 3220 2.055 0.448 0.164 0.038 34 3.0 cuneus 541 695 1574 2.977 0.776 0.251 0.071 11 1.8 entorhinal 4362 3586 8351 2.559 0.507 0.144 0.040 96 6.5 fusiform 5843 4710 10432 2.363 0.509 0.135 0.029 79 7.5 inferiorparietal 5149 4864 11732 2.715 0.711 0.170 0.043 113 9.3 inferiortemporal 1388 1060 2024 2.121 0.726 0.161 0.049 35 2.6 isthmuscingulate 7295 6274 11372 2.043 0.459 0.148 0.032 111 9.4 lateraloccipital 4295 3323 7968 2.505 0.559 0.141 0.038 116 6.1 lateralorbitofrontal 4479 3669 6454 2.003 0.504 0.144 0.037 70 6.7 lingual 2679 2314 5422 2.578 0.541 0.151 0.042 64 4.0 medialorbitofrontal 4128 4423 10873 2.811 0.652 0.166 0.035 51 6.3 middletemporal 984 884 1834 2.496 0.580 0.172 0.045 15 2.0 parahippocampal 1919 1430 3342 2.442 0.488 0.109 0.021 16 1.6 paracentral 2312 1961 4413 2.458 0.436 0.141 0.032 45 2.8 parsopercularis 1101 1225 2760 2.698 0.575 0.171 0.033 16 1.5 parsorbitalis 2192 1821 4085 2.411 0.475 0.138 0.030 27 2.7 parstriangularis 1950 1231 2420 1.858 0.401 0.127 0.028 33 2.2 pericalcarine 5556 4193 8039 2.108 0.500 0.102 0.018 48 3.8 postcentral 1487 1156 2585 2.349 0.561 0.161 0.051 60 3.0 posteriorcingulate 6160 4430 10990 2.568 0.457 0.102 0.020 68 4.7 precentral 4968 3934 8714 2.344 0.430 0.139 0.031 79 6.2 precuneus 1379 1311 3105 2.751 0.511 0.172 0.041 28 2.3 rostralanteriorcingulate 7666 6811 15261 2.414 0.534 0.151 0.034 131 10.5 rostralmiddlefrontal 10464 9004 22810 2.711 0.539 0.135 0.028 156 11.9 superiorfrontal 7638 6186 12381 2.143 0.459 0.129 0.026 86 7.9 superiorparietal 5559 4498 11610 2.748 0.573 0.134 0.033 108 7.2 superiortemporal 4566 3661 8588 2.491 0.455 0.134 0.029 190 5.3 supramarginal 369 412 1016 2.907 0.582 0.195 0.034 7 0.6 frontalpole 620 912 2586 3.671 0.705 0.192 0.035 7 1.0 temporalpole 738 651 1433 2.620 0.463 0.129 0.028 7 0.8 transversetemporal 3792 2398 7119 2.795 0.727 0.155 0.056 131 8.8 insula @#@FSTIME 2023:08:29:20:53:10 mris_anatomical_stats N 14 e 6.23 S 0.14 U 6.08 P 99% M 451704 F 0 R 133344 W 0 c 601 w 1 I 0 O 24 L 1.37 1.35 1.36 @#@FSLOADPOST 2023:08:29:20:53:16 mris_anatomical_stats N 14 1.31 1.33 1.35 #----------------------------------------- #@# Parcellation Stats rh Tue Aug 29 20:53:16 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 224290 Total vertex volume 224095 (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) = 1423268 mm^3 (det: 1.368755 ) 1371 941 2216 2.405 0.371 0.106 0.021 9 1.3 bankssts 974 672 1891 2.434 0.706 0.135 0.031 13 1.1 caudalanteriorcingulate 3227 2204 6223 2.507 0.479 0.111 0.025 24 3.2 caudalmiddlefrontal 2241 1514 3271 1.942 0.403 0.130 0.031 31 2.6 cuneus 574 409 1471 2.659 0.765 0.134 0.049 7 0.8 entorhinal 4170 2834 8633 2.652 0.540 0.118 0.029 42 4.6 fusiform 8240 5798 15306 2.303 0.495 0.122 0.026 97 9.0 inferiorparietal 4715 3280 10592 2.661 0.673 0.118 0.029 48 5.1 inferiortemporal 1093 747 1945 2.328 0.655 0.109 0.028 9 1.1 isthmuscingulate 6427 4416 10380 2.038 0.535 0.134 0.032 84 7.9 lateraloccipital 4697 3267 8255 2.459 0.576 0.136 0.041 59 7.8 lateralorbitofrontal 5002 3450 7241 2.047 0.542 0.144 0.041 68 7.8 lingual 2907 2107 5885 2.486 0.565 0.129 0.036 41 4.0 medialorbitofrontal 4741 3348 11049 2.718 0.612 0.117 0.028 52 4.9 middletemporal 946 592 1480 2.272 0.492 0.093 0.024 6 0.8 parahippocampal 2235 1435 4101 2.554 0.474 0.104 0.025 14 2.2 paracentral 1789 1288 3648 2.512 0.461 0.126 0.030 20 2.1 parsopercularis 1215 851 2852 2.700 0.558 0.131 0.029 16 1.2 parsorbitalis 2203 1564 4216 2.359 0.410 0.120 0.025 26 2.3 parstriangularis 2344 1590 2600 1.732 0.474 0.144 0.042 29 3.9 pericalcarine 4873 3130 7179 2.061 0.471 0.101 0.024 40 4.3 postcentral 1632 1188 3134 2.333 0.666 0.131 0.030 21 2.1 posteriorcingulate 6355 4204 10965 2.466 0.476 0.109 0.027 50 7.2 precentral 4571 3166 7833 2.396 0.461 0.121 0.028 49 4.9 precuneus 792 587 1897 2.986 0.785 0.149 0.037 14 1.2 rostralanteriorcingulate 8373 6169 16665 2.335 0.524 0.135 0.033 115 10.9 rostralmiddlefrontal 9748 6800 21650 2.714 0.561 0.119 0.029 92 10.8 superiorfrontal 7474 5088 12182 2.186 0.425 0.116 0.024 76 7.2 superiorparietal 5159 3462 10855 2.752 0.558 0.109 0.024 42 4.9 superiortemporal 4664 3262 8343 2.367 0.446 0.124 0.026 48 5.0 supramarginal 518 342 968 2.180 0.700 0.145 0.050 9 0.8 frontalpole 680 526 2504 3.359 0.670 0.151 0.046 11 1.1 temporalpole 471 308 836 2.535 0.328 0.127 0.028 5 0.5 transversetemporal 3007 2047 5831 2.928 0.760 0.117 0.033 24 3.8 insula @#@FSTIME 2023:08:29:20:53:16 mris_anatomical_stats N 14 e 6.47 S 0.15 U 6.30 P 99% M 453100 F 0 R 127314 W 0 c 626 w 1 I 0 O 24 L 1.31 1.33 1.35 @#@FSLOADPOST 2023:08:29:20:53:23 mris_anatomical_stats N 14 1.29 1.33 1.35 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 EP01 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 224290 Total vertex volume 224095 (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) = 1423268 mm^3 (det: 1.368755 ) 1371 906 2216 2.405 0.371 0.123 0.035 25 1.9 bankssts 974 850 1891 2.434 0.706 0.190 0.053 86 2.1 caudalanteriorcingulate 3227 2588 6223 2.507 0.479 0.122 0.026 37 3.2 caudalmiddlefrontal 2241 1922 3271 1.942 0.403 0.148 0.031 33 3.0 cuneus 574 714 1471 2.659 0.765 0.259 0.080 15 2.2 entorhinal 4170 3596 8633 2.652 0.540 0.150 0.038 77 6.6 fusiform 8240 7144 15306 2.303 0.495 0.140 0.031 137 10.4 inferiorparietal 4715 4426 10592 2.661 0.673 0.159 0.038 89 7.6 inferiortemporal 1093 935 1945 2.328 0.655 0.165 0.046 21 2.1 isthmuscingulate 6427 5673 10380 2.038 0.535 0.151 0.035 96 9.2 lateraloccipital 4697 3500 8255 2.459 0.576 0.145 0.043 161 7.9 lateralorbitofrontal 5002 3941 7241 2.047 0.542 0.147 0.041 107 8.4 lingual 2907 2668 5885 2.486 0.565 0.169 0.074 223 4.8 medialorbitofrontal 4741 4476 11049 2.718 0.612 0.157 0.036 165 6.6 middletemporal 946 759 1480 2.272 0.492 0.166 0.044 17 2.1 parahippocampal 2235 1719 4101 2.554 0.474 0.106 0.021 20 1.8 paracentral 1789 1558 3648 2.512 0.461 0.143 0.031 24 2.3 parsopercularis 1215 1220 2852 2.700 0.558 0.160 0.032 26 1.5 parsorbitalis 2203 1983 4216 2.359 0.410 0.153 0.031 38 2.8 parstriangularis 2344 1472 2600 1.732 0.474 0.132 0.038 56 3.6 pericalcarine 4873 3794 7179 2.061 0.471 0.110 0.019 36 3.8 postcentral 1632 1476 3134 2.333 0.666 0.160 0.047 39 2.7 posteriorcingulate 6355 4537 10965 2.466 0.476 0.100 0.021 72 5.0 precentral 4571 3377 7833 2.396 0.461 0.128 0.034 77 5.9 precuneus 792 710 1897 2.986 0.785 0.196 0.058 32 1.9 rostralanteriorcingulate 8373 7691 16665 2.335 0.524 0.162 0.037 190 12.5 rostralmiddlefrontal 9748 8594 21650 2.714 0.561 0.140 0.032 162 11.9 superiorfrontal 7474 5954 12182 2.186 0.425 0.130 0.026 100 7.8 superiorparietal 5159 4254 10855 2.752 0.558 0.126 0.028 59 5.6 superiortemporal 4664 3677 8343 2.367 0.446 0.132 0.032 70 6.0 supramarginal 518 508 968 2.180 0.700 0.160 0.038 11 0.7 frontalpole 680 955 2504 3.359 0.670 0.224 0.047 19 1.5 temporalpole 471 363 836 2.535 0.328 0.118 0.027 4 0.4 transversetemporal 3007 1886 5831 2.928 0.760 0.145 0.048 80 6.4 insula @#@FSTIME 2023:08:29:20:53:23 mris_anatomical_stats N 14 e 6.23 S 0.13 U 6.09 P 99% M 453112 F 0 R 124047 W 0 c 607 w 1 I 0 O 24 L 1.29 1.33 1.35 @#@FSLOADPOST 2023:08:29:20:53:29 mris_anatomical_stats N 14 1.27 1.32 1.35 #----------------------------------------- #@# Parcellation Stats 2 lh Tue Aug 29 20:53:29 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 223313 Total vertex volume 223119 (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) = 1423268 mm^3 (det: 1.368755 ) 1116 810 2265 2.430 0.587 0.138 0.037 13 1.6 G_and_S_frontomargin 1270 857 2010 2.129 0.368 0.112 0.027 13 1.2 G_and_S_occipital_inf 1451 930 2763 2.408 0.479 0.115 0.033 15 1.6 G_and_S_paracentral 1240 836 2392 2.518 0.374 0.137 0.032 15 1.6 G_and_S_subcentral 723 570 1949 2.796 0.483 0.171 0.045 15 1.5 G_and_S_transv_frontopol 2431 1726 4808 2.633 0.490 0.126 0.030 27 3.0 G_and_S_cingul-Ant 1468 973 2411 2.518 0.463 0.116 0.027 12 1.5 G_and_S_cingul-Mid-Ant 1432 988 2631 2.517 0.395 0.115 0.026 13 1.5 G_and_S_cingul-Mid-Post 463 339 1151 2.714 0.660 0.142 0.040 7 0.7 G_cingul-Post-dorsal 279 189 545 2.360 0.638 0.109 0.029 3 0.3 G_cingul-Post-ventral 1941 1358 3477 2.081 0.448 0.154 0.044 36 3.0 G_cuneus 1159 802 2664 2.596 0.420 0.134 0.035 17 1.4 G_front_inf-Opercular 424 300 1178 2.779 0.383 0.149 0.037 8 0.5 G_front_inf-Orbital 1336 927 3145 2.622 0.453 0.138 0.033 21 1.7 G_front_inf-Triangul 3851 2719 9846 2.714 0.498 0.135 0.036 62 4.8 G_front_middle 6687 4649 16529 2.851 0.526 0.125 0.033 70 8.7 G_front_sup 631 433 1374 3.037 0.680 0.138 0.044 8 0.9 G_Ins_lg_and_S_cent_ins 716 509 2136 3.301 0.815 0.153 0.055 10 1.5 G_insular_short 2532 1731 5036 2.269 0.494 0.136 0.036 43 3.5 G_occipital_middle 1310 917 2360 2.141 0.460 0.146 0.030 20 1.6 G_occipital_sup 1793 1182 4049 2.761 0.451 0.129 0.034 27 2.1 G_oc-temp_lat-fusifor 3096 2046 4783 1.996 0.533 0.134 0.038 51 4.5 G_oc-temp_med-Lingual 1085 724 2523 2.689 0.716 0.111 0.036 10 1.2 G_oc-temp_med-Parahip 2662 1868 6492 2.633 0.671 0.148 0.047 52 4.4 G_orbital 2250 1530 5088 2.614 0.515 0.135 0.031 36 2.8 G_pariet_inf-Angular 2245 1558 5173 2.612 0.433 0.132 0.034 35 2.8 G_pariet_inf-Supramar 2957 2002 5852 2.298 0.480 0.120 0.025 34 3.2 G_parietal_sup 2196 1250 3451 2.200 0.497 0.097 0.028 23 2.0 G_postcentral 2351 1409 5185 2.799 0.443 0.106 0.034 26 3.0 G_precentral 2218 1571 5085 2.501 0.447 0.143 0.032 38 2.7 G_precuneus 1047 788 2628 2.550 0.533 0.129 0.041 18 1.5 G_rectus 764 510 1258 2.501 0.797 0.128 0.048 10 1.2 G_subcallosal 603 378 1248 2.589 0.450 0.136 0.038 9 0.9 G_temp_sup-G_T_transv 1851 1246 5194 2.987 0.554 0.130 0.032 24 2.4 G_temp_sup-Lateral 679 480 1878 3.325 0.756 0.114 0.027 5 0.8 G_temp_sup-Plan_polar 775 528 1496 2.590 0.391 0.095 0.019 5 0.6 G_temp_sup-Plan_tempo 2601 1907 6783 2.816 0.807 0.153 0.047 42 4.8 G_temporal_inf 2415 1848 7532 2.980 0.669 0.148 0.041 45 3.9 G_temporal_middle 430 288 511 2.166 0.325 0.089 0.016 2 0.3 Lat_Fis-ant-Horizont 265 192 357 2.153 0.454 0.105 0.016 1 0.2 Lat_Fis-ant-Vertical 1044 705 1380 2.521 0.374 0.114 0.023 6 1.1 Lat_Fis-post 1978 1315 2992 1.933 0.511 0.147 0.043 30 3.3 Pole_occipital 1578 1251 5863 3.241 0.739 0.155 0.051 26 3.3 Pole_temporal 2702 1891 3201 1.890 0.415 0.122 0.029 24 3.2 S_calcarine 2718 1840 3378 2.110 0.553 0.096 0.020 12 2.4 S_central 1073 712 1393 2.227 0.372 0.100 0.018 6 0.8 S_cingul-Marginalis 511 350 716 2.528 0.439 0.126 0.034 4 0.9 S_circular_insula_ant 1575 1070 2377 2.724 0.595 0.108 0.025 9 1.9 S_circular_insula_inf 1744 1160 2398 2.492 0.364 0.109 0.023 9 1.9 S_circular_insula_sup 1036 704 1647 2.536 0.480 0.119 0.029 9 1.4 S_collat_transv_ant 479 333 555 1.825 0.390 0.134 0.032 4 0.6 S_collat_transv_post 2413 1604 3199 2.146 0.348 0.105 0.022 17 2.4 S_front_inf 1410 975 2066 2.207 0.485 0.115 0.027 11 1.6 S_front_middle 2651 1807 4196 2.408 0.451 0.101 0.021 15 2.4 S_front_sup 230 159 307 2.477 0.421 0.120 0.023 1 0.2 S_interm_prim-Jensen 2620 1780 3347 2.024 0.402 0.115 0.023 21 2.5 S_intrapariet_and_P_trans 1013 712 1159 1.790 0.322 0.124 0.026 7 1.2 S_oc_middle_and_Lunatus 1213 843 1406 1.837 0.347 0.119 0.022 9 1.2 S_oc_sup_and_transversal 826 568 1381 2.297 0.436 0.124 0.031 8 0.9 S_occipital_ant 959 667 1378 2.374 0.383 0.115 0.023 6 1.0 S_oc-temp_lat 1863 1288 2670 2.360 0.403 0.110 0.022 11 1.7 S_oc-temp_med_and_Lingual 399 286 554 2.037 0.447 0.127 0.024 3 0.4 S_orbital_lateral 874 597 1148 2.286 0.496 0.107 0.023 5 0.9 S_orbital_med-olfact 1602 1074 2643 2.480 0.429 0.121 0.032 15 2.0 S_orbital-H_Shaped 1883 1278 2506 2.198 0.408 0.116 0.023 13 2.0 S_parieto_occipital 1120 715 1106 1.812 0.614 0.115 0.026 13 1.3 S_pericallosal 2634 1725 3246 2.074 0.337 0.093 0.017 13 2.1 S_postcentral 1507 1021 2178 2.415 0.307 0.105 0.020 10 1.4 S_precentral-inf-part 1142 761 1373 2.210 0.335 0.098 0.021 5 1.0 S_precentral-sup-part 705 503 1230 2.739 0.462 0.120 0.025 5 0.8 S_suborbital 960 646 1327 2.267 0.387 0.112 0.021 7 0.9 S_subparietal 1546 1063 2432 2.426 0.536 0.117 0.025 10 1.8 S_temporal_inf 5525 3723 8529 2.455 0.426 0.103 0.020 32 5.0 S_temporal_sup 412 306 602 2.462 0.453 0.125 0.022 3 0.5 S_temporal_transverse @#@FSTIME 2023:08:29:20:53:29 mris_anatomical_stats N 14 e 6.53 S 0.15 U 6.37 P 99% M 451520 F 0 R 130085 W 0 c 633 w 1 I 0 O 40 L 1.27 1.32 1.35 @#@FSLOADPOST 2023:08:29:20:53:36 mris_anatomical_stats N 14 1.32 1.33 1.35 #----------------------------------------- #@# Parcellation Stats 2 rh Tue Aug 29 20:53:36 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 224290 Total vertex volume 224095 (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) = 1423268 mm^3 (det: 1.368755 ) 1058 808 2040 2.172 0.636 0.147 0.035 14 1.6 G_and_S_frontomargin 1224 868 2504 2.247 0.628 0.140 0.031 18 1.5 G_and_S_occipital_inf 1338 846 2584 2.503 0.526 0.109 0.029 13 1.5 G_and_S_paracentral 1022 713 2040 2.500 0.412 0.126 0.027 10 1.1 G_and_S_subcentral 1179 825 2784 2.540 0.631 0.143 0.045 22 1.9 G_and_S_transv_frontopol 2819 2043 5891 2.648 0.651 0.132 0.031 39 3.5 G_and_S_cingul-Ant 1260 858 2310 2.625 0.443 0.109 0.024 8 1.3 G_and_S_cingul-Mid-Ant 1427 1024 2762 2.496 0.476 0.122 0.032 14 1.9 G_and_S_cingul-Mid-Post 516 354 1386 2.906 0.426 0.124 0.030 6 0.6 G_cingul-Post-dorsal 274 182 569 2.458 0.614 0.108 0.037 2 0.3 G_cingul-Post-ventral 2220 1469 3259 1.910 0.444 0.138 0.037 34 3.0 G_cuneus 1147 834 2806 2.592 0.472 0.129 0.034 15 1.3 G_front_inf-Opercular 308 229 840 2.720 0.509 0.143 0.034 6 0.4 G_front_inf-Orbital 943 691 2347 2.578 0.364 0.131 0.031 16 1.2 G_front_inf-Triangul 4529 3338 11270 2.563 0.537 0.140 0.035 73 6.1 G_front_middle 6407 4486 16447 2.871 0.557 0.126 0.033 71 7.7 G_front_sup 487 332 1214 3.449 1.000 0.107 0.035 5 0.5 G_Ins_lg_and_S_cent_ins 752 560 1966 2.973 0.774 0.140 0.045 10 1.1 G_insular_short 2014 1441 4393 2.352 0.464 0.138 0.030 31 2.3 G_occipital_middle 1426 951 2403 2.132 0.460 0.122 0.027 19 1.4 G_occipital_sup 1646 1057 3779 2.773 0.415 0.124 0.029 23 1.9 G_oc-temp_lat-fusifor 3293 2219 5005 2.051 0.544 0.146 0.042 48 5.3 G_oc-temp_med-Lingual 989 653 2302 2.549 0.705 0.120 0.044 10 1.3 G_oc-temp_med-Parahip 2945 2049 7049 2.639 0.622 0.142 0.046 52 4.9 G_orbital 3411 2488 7911 2.491 0.551 0.137 0.032 59 4.5 G_pariet_inf-Angular 2400 1689 5162 2.484 0.465 0.126 0.025 29 2.5 G_pariet_inf-Supramar 2336 1600 4734 2.359 0.472 0.122 0.028 32 2.3 G_parietal_sup 1751 1023 2900 2.169 0.477 0.103 0.029 20 1.6 G_postcentral 2451 1548 5293 2.649 0.492 0.111 0.034 28 3.0 G_precentral 1941 1389 4222 2.496 0.436 0.134 0.033 32 2.3 G_precuneus 860 627 2196 2.546 0.505 0.125 0.045 16 1.3 G_rectus 582 426 1020 2.541 0.786 0.172 0.068 11 1.6 G_subcallosal 337 215 653 2.514 0.302 0.129 0.027 4 0.3 G_temp_sup-G_T_transv 1734 1189 4798 2.996 0.540 0.130 0.033 22 2.0 G_temp_sup-Lateral 1010 689 2163 2.968 0.733 0.113 0.032 8 1.4 G_temp_sup-Plan_polar 823 572 1650 2.531 0.429 0.115 0.028 7 0.8 G_temp_sup-Plan_tempo 2462 1709 6791 2.813 0.677 0.122 0.031 32 2.8 G_temporal_inf 2656 1934 7924 2.944 0.627 0.127 0.033 39 3.0 G_temporal_middle 317 220 416 2.126 0.323 0.101 0.018 2 0.2 Lat_Fis-ant-Horizont 276 195 390 2.241 0.278 0.093 0.014 1 0.2 Lat_Fis-ant-Vertical 1333 906 1851 2.494 0.359 0.115 0.024 9 1.4 Lat_Fis-post 3174 2157 4611 1.903 0.523 0.149 0.045 52 5.3 Pole_occipital 1764 1357 5582 2.912 0.822 0.159 0.053 29 3.2 Pole_temporal 2736 1936 3133 1.845 0.532 0.142 0.038 30 4.2 S_calcarine 2504 1725 3067 2.073 0.505 0.098 0.020 10 2.4 S_central 1111 758 1519 2.251 0.338 0.108 0.022 6 1.1 S_cingul-Marginalis 607 423 953 2.687 0.378 0.109 0.026 3 0.6 S_circular_insula_ant 1197 778 1785 2.790 0.719 0.087 0.016 4 0.9 S_circular_insula_inf 1331 882 1702 2.409 0.341 0.109 0.023 6 1.5 S_circular_insula_sup 1129 782 2316 2.741 0.529 0.110 0.025 9 1.0 S_collat_transv_ant 468 326 503 1.770 0.325 0.131 0.027 4 0.5 S_collat_transv_post 2183 1513 3144 2.223 0.391 0.117 0.026 15 2.3 S_front_inf 1802 1286 2701 2.167 0.406 0.110 0.022 13 1.6 S_front_middle 2399 1618 3352 2.290 0.366 0.100 0.021 12 2.1 S_front_sup 523 370 704 2.162 0.402 0.131 0.027 5 0.6 S_interm_prim-Jensen 3584 2417 4705 2.059 0.340 0.104 0.018 23 3.0 S_intrapariet_and_P_trans 660 456 697 1.787 0.295 0.108 0.016 4 0.5 S_oc_middle_and_Lunatus 1014 688 1224 1.980 0.331 0.118 0.025 7 1.0 S_oc_sup_and_transversal 639 432 914 2.211 0.330 0.093 0.017 3 0.5 S_occipital_ant 1125 761 1654 2.570 0.597 0.109 0.022 7 1.0 S_oc-temp_lat 1963 1341 2773 2.411 0.402 0.099 0.019 8 1.7 S_oc-temp_med_and_Lingual 424 305 545 1.899 0.328 0.126 0.017 3 0.4 S_orbital_lateral 915 621 1093 2.171 0.454 0.113 0.024 6 1.0 S_orbital_med-olfact 1681 1155 2731 2.494 0.452 0.126 0.028 14 2.0 S_orbital-H_Shaped 2053 1393 2887 2.261 0.430 0.109 0.021 13 1.9 S_parieto_occipital 1130 781 1077 1.731 0.534 0.133 0.026 16 1.1 S_pericallosal 2045 1355 2377 1.999 0.353 0.100 0.020 11 1.8 S_postcentral 1546 1037 2183 2.356 0.403 0.106 0.022 10 1.5 S_precentral-inf-part 1140 771 1517 2.279 0.386 0.104 0.019 6 1.1 S_precentral-sup-part 394 310 686 2.464 0.548 0.149 0.026 4 0.5 S_suborbital 673 484 1010 2.326 0.382 0.119 0.027 6 0.7 S_subparietal 1409 939 1792 2.274 0.404 0.102 0.018 8 1.1 S_temporal_inf 5971 4008 8794 2.312 0.390 0.103 0.019 36 5.1 S_temporal_sup 231 171 334 2.297 0.411 0.120 0.029 1 0.3 S_temporal_transverse @#@FSTIME 2023:08:29:20:53:36 mris_anatomical_stats N 14 e 6.48 S 0.14 U 6.33 P 99% M 453096 F 0 R 127316 W 0 c 642 w 1 I 0 O 40 L 1.32 1.33 1.35 @#@FSLOADPOST 2023:08:29:20:53:42 mris_anatomical_stats N 14 1.27 1.32 1.35 #----------------------------------------- #@# Parcellation Stats 3 lh Tue Aug 29 20:53:42 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 223313 Total vertex volume 223119 (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) = 1423268 mm^3 (det: 1.368755 ) 1463 970 2754 2.619 0.443 0.118 0.030 15 1.4 caudalanteriorcingulate 3068 2004 5413 2.509 0.479 0.110 0.026 26 2.9 caudalmiddlefrontal 2632 1835 4307 2.088 0.433 0.139 0.034 35 3.4 cuneus 522 363 1449 2.893 0.782 0.121 0.041 5 0.6 entorhinal 3923 2639 7309 2.550 0.490 0.120 0.029 44 4.3 fusiform 5955 4099 10627 2.365 0.521 0.121 0.026 65 6.5 inferiorparietal 5080 3688 11813 2.708 0.734 0.140 0.041 65 8.7 inferiortemporal 1381 909 2026 2.133 0.720 0.111 0.029 13 1.5 isthmuscingulate 7263 4942 11366 2.044 0.459 0.135 0.035 94 9.9 lateraloccipital 4749 3287 9199 2.487 0.588 0.136 0.043 67 7.6 lateralorbitofrontal 4585 3073 6578 1.993 0.501 0.130 0.035 63 6.2 lingual 2475 1784 5243 2.578 0.583 0.122 0.034 31 3.2 medialorbitofrontal 5695 4126 13482 2.756 0.614 0.129 0.031 66 7.3 middletemporal 1000 664 1870 2.502 0.572 0.096 0.024 7 0.9 parahippocampal 2226 1475 4112 2.522 0.501 0.113 0.028 17 2.4 paracentral 2072 1431 3902 2.474 0.426 0.119 0.028 21 2.2 parsopercularis 1108 769 2451 2.666 0.491 0.126 0.029 12 1.2 parsorbitalis 2709 1853 5029 2.388 0.470 0.120 0.027 30 3.0 parstriangularis 1899 1355 2333 1.866 0.405 0.134 0.035 23 2.5 pericalcarine 6402 3995 9350 2.133 0.498 0.100 0.024 54 5.9 postcentral 1735 1225 3181 2.368 0.557 0.129 0.030 21 2.3 posteriorcingulate 6120 3952 10951 2.576 0.453 0.106 0.027 49 6.7 precentral 4917 3409 8877 2.350 0.430 0.125 0.026 56 5.5 precuneus 1824 1281 3833 2.723 0.529 0.124 0.030 22 2.2 rostralanteriorcingulate 5319 3767 10324 2.383 0.542 0.128 0.030 67 6.4 rostralmiddlefrontal 11481 8048 24680 2.677 0.548 0.124 0.031 117 14.4 superiorfrontal 6110 4110 9696 2.124 0.455 0.119 0.025 61 6.3 superiorparietal 7197 4927 15917 2.790 0.640 0.117 0.027 68 8.4 superiortemporal 4183 2884 7879 2.486 0.447 0.123 0.028 47 4.6 supramarginal 740 486 1437 2.621 0.464 0.135 0.035 9 1.0 transversetemporal 2855 1951 5727 2.943 0.683 0.124 0.037 28 4.2 insula @#@FSTIME 2023:08:29:20:53:42 mris_anatomical_stats N 14 e 6.17 S 0.17 U 6.00 P 99% M 451416 F 0 R 130085 W 0 c 598 w 1 I 0 O 24 L 1.27 1.32 1.35 @#@FSLOADPOST 2023:08:29:20:53:49 mris_anatomical_stats N 14 1.25 1.32 1.35 #----------------------------------------- #@# Parcellation Stats 3 rh Tue Aug 29 20:53:49 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01/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 EP01 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/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 224290 Total vertex volume 224095 (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) = 1423268 mm^3 (det: 1.368755 ) 1072 743 2095 2.438 0.701 0.137 0.032 14 1.3 caudalanteriorcingulate 3368 2301 6397 2.503 0.471 0.112 0.026 25 3.6 caudalmiddlefrontal 2719 1850 3876 1.953 0.396 0.125 0.029 32 3.1 cuneus 540 389 1425 2.658 0.790 0.138 0.050 7 0.8 entorhinal 3890 2603 7606 2.639 0.472 0.114 0.026 37 3.9 fusiform 7967 5623 14762 2.300 0.496 0.122 0.026 93 8.6 inferiorparietal 5033 3540 11920 2.682 0.705 0.121 0.031 54 5.7 inferiortemporal 1095 742 1925 2.317 0.650 0.107 0.027 9 1.0 isthmuscingulate 6604 4531 10615 2.026 0.532 0.135 0.033 91 8.2 lateraloccipital 4951 3492 9015 2.447 0.570 0.141 0.042 67 8.3 lateralorbitofrontal 4972 3434 7124 2.032 0.544 0.145 0.040 66 7.8 lingual 2345 1733 4860 2.457 0.555 0.141 0.042 40 3.9 medialorbitofrontal 5948 4186 13270 2.672 0.587 0.118 0.028 64 6.3 middletemporal 981 619 1542 2.290 0.496 0.093 0.023 6 0.8 parahippocampal 2375 1530 4366 2.557 0.477 0.102 0.024 15 2.3 paracentral 2075 1491 4122 2.486 0.453 0.126 0.030 23 2.4 parsopercularis 1098 753 2408 2.702 0.531 0.122 0.027 13 1.1 parsorbitalis 2179 1540 4073 2.329 0.431 0.117 0.024 24 2.1 parstriangularis 2283 1538 2597 1.769 0.475 0.143 0.042 28 3.8 pericalcarine 5459 3542 7995 2.057 0.468 0.104 0.024 46 5.0 postcentral 1700 1236 3209 2.341 0.652 0.131 0.030 21 2.3 posteriorcingulate 6040 3996 10548 2.477 0.475 0.108 0.027 48 6.8 precentral 4663 3257 8250 2.402 0.467 0.125 0.028 53 5.1 precuneus 1163 848 2611 2.908 0.765 0.148 0.038 21 1.7 rostralanteriorcingulate 5902 4324 11750 2.316 0.530 0.131 0.030 75 7.2 rostralmiddlefrontal 12546 8803 27093 2.630 0.580 0.123 0.031 132 14.9 superiorfrontal 6224 4198 10235 2.212 0.423 0.114 0.023 61 5.7 superiorparietal 6550 4445 14068 2.755 0.603 0.112 0.026 56 6.5 superiortemporal 4509 3148 8046 2.375 0.440 0.122 0.026 45 4.8 supramarginal 477 315 858 2.530 0.330 0.126 0.028 5 0.5 transversetemporal 2700 1832 5432 3.014 0.747 0.111 0.031 20 3.1 insula @#@FSTIME 2023:08:29:20:53:49 mris_anatomical_stats N 14 e 6.28 S 0.14 U 6.13 P 99% M 453140 F 0 R 127314 W 0 c 610 w 1 I 0 O 24 L 1.25 1.32 1.35 @#@FSLOADPOST 2023:08:29:20:53:55 mris_anatomical_stats N 14 1.23 1.31 1.35 #-------------------------------------------- #@# ASeg Stats Tue Aug 29 20:53:55 PDT 2023 /usr/local/freesurfer/7.4.1/subjects/EP01 mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/7.4.1/ASegStatsLUT.txt --subject EP01 setting seed for random number genererator to 1234 7.4.1 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/7.4.1/ASegStatsLUT.txt --subject EP01 sysname Linux hostname rnet-lambda-vector machine x86_64 user bsherma whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1423268 mm^3 (det: 1.368755 ) Computing euler number orig.nofix lheno = -26, rheno = -34 orig.nofix lhholes = 14, rhholes = 18 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2023:08:29:20:53:55 mri_segstats N 32 e 205.29 S 0.30 U 204.88 P 99% M 298324 F 0 R 757076 W 0 c 20243 w 1 I 0 O 24 L 1.23 1.31 1.35 @#@FSLOADPOST 2023:08:29:20:57:20 mri_segstats N 32 1.14 1.24 1.31 /usr/local/freesurfer/7.4.1/subjects/EP01/label #-------------------------------------------- #@# BA_exvivo Labels lh Tue Aug 29 20:57:20 PDT 2023 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject EP01 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4278 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:20 mri_label2label N 12 e 3.28 S 0.19 U 3.08 P 99% M 537472 F 0 R 154304 W 0 c 322 w 1 I 0 O 248 L 1.14 1.24 1.31 @#@FSLOADPOST 2023:08:29:20:57:23 mri_label2label N 12 1.13 1.24 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject EP01 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 169 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8078 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:23 mri_label2label N 12 e 3.57 S 0.16 U 3.40 P 99% M 537460 F 0 R 154370 W 0 c 342 w 1 I 0 O 432 L 1.13 1.24 1.31 @#@FSLOADPOST 2023:08:29:20:57:27 mri_label2label N 12 1.12 1.23 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject EP01 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4084 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:27 mri_label2label N 12 e 3.15 S 0.19 U 2.95 P 99% M 537408 F 0 R 154300 W 0 c 313 w 1 I 0 O 200 L 1.12 1.23 1.31 @#@FSLOADPOST 2023:08:29:20:57:30 mri_label2label N 12 1.12 1.23 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject EP01 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6113 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:30 mri_label2label N 12 e 3.39 S 0.19 U 3.20 P 99% M 537436 F 0 R 154334 W 0 c 326 w 1 I 0 O 312 L 1.12 1.23 1.31 @#@FSLOADPOST 2023:08:29:20:57:34 mri_label2label N 12 1.11 1.23 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject EP01 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5870 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:34 mri_label2label N 12 e 3.54 S 0.25 U 3.28 P 99% M 537416 F 0 R 154327 W 0 c 353 w 1 I 0 O 312 L 1.11 1.23 1.31 @#@FSLOADPOST 2023:08:29:20:57:37 mri_label2label N 12 1.10 1.22 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject EP01 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4138 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:37 mri_label2label N 12 e 3.29 S 0.17 U 3.12 P 99% M 537464 F 0 R 154302 W 0 c 320 w 1 I 0 O 216 L 1.10 1.22 1.30 @#@FSLOADPOST 2023:08:29:20:57:41 mri_label2label N 12 1.10 1.22 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject EP01 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 377 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13966 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:41 mri_label2label N 12 e 4.35 S 0.17 U 4.17 P 99% M 538140 F 0 R 154473 W 0 c 420 w 1 I 0 O 800 L 1.10 1.22 1.30 @#@FSLOADPOST 2023:08:29:20:57:45 mri_label2label N 12 1.09 1.22 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject EP01 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4296 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:45 mri_label2label N 12 e 3.16 S 0.15 U 3.01 P 99% M 537456 F 0 R 154304 W 0 c 308 w 1 I 0 O 248 L 1.09 1.22 1.30 @#@FSLOADPOST 2023:08:29:20:57:48 mri_label2label N 12 1.08 1.22 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject EP01 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 625 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4047 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:48 mri_label2label N 12 e 3.08 S 0.16 U 2.90 P 99% M 537332 F 0 R 154298 W 0 c 304 w 2 I 0 O 312 L 1.08 1.22 1.30 @#@FSLOADPOST 2023:08:29:20:57:51 mri_label2label N 12 1.08 1.22 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject EP01 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 995 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5636 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:51 mri_label2label N 12 e 3.24 S 0.16 U 3.07 P 99% M 537556 F 0 R 154320 W 0 c 313 w 1 I 0 O 448 L 1.08 1.22 1.30 @#@FSLOADPOST 2023:08:29:20:57:54 mri_label2label N 12 1.08 1.21 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject EP01 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 1898 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10012 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:54 mri_label2label N 12 e 3.80 S 0.15 U 3.64 P 99% M 537632 F 0 R 154389 W 0 c 378 w 1 I 0 O 808 L 1.08 1.21 1.30 @#@FSLOADPOST 2023:08:29:20:57:58 mri_label2label N 12 1.07 1.21 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject EP01 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 369 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2387 mri_label2label: Done @#@FSTIME 2023:08:29:20:57:58 mri_label2label N 12 e 3.05 S 0.16 U 2.89 P 99% M 537156 F 0 R 154265 W 0 c 299 w 1 I 0 O 200 L 1.07 1.21 1.30 @#@FSLOADPOST 2023:08:29:20:58:01 mri_label2label N 12 1.07 1.21 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject EP01 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1318 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:01 mri_label2label N 12 e 2.97 S 0.17 U 2.79 P 99% M 537120 F 0 R 157504 W 0 c 293 w 1 I 0 O 80 L 1.07 1.21 1.30 @#@FSLOADPOST 2023:08:29:20:58:04 mri_label2label N 12 1.06 1.21 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject EP01 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1210 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:04 mri_label2label N 12 e 2.86 S 0.15 U 2.70 P 99% M 537084 F 0 R 157505 W 0 c 285 w 1 I 0 O 72 L 1.06 1.21 1.29 @#@FSLOADPOST 2023:08:29:20:58:07 mri_label2label N 12 1.06 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 484 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:07 mri_label2label N 12 e 2.86 S 0.17 U 2.68 P 99% M 537116 F 0 R 154239 W 0 c 281 w 1 I 0 O 40 L 1.06 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:10 mri_label2label N 12 1.06 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 836 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:10 mri_label2label N 12 e 2.89 S 0.19 U 2.69 P 99% M 537300 F 0 R 157504 W 0 c 280 w 1 I 0 O 72 L 1.06 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:13 mri_label2label N 12 1.05 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1954 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:13 mri_label2label N 12 e 3.02 S 0.19 U 2.83 P 99% M 537280 F 0 R 157519 W 0 c 298 w 1 I 0 O 136 L 1.05 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:16 mri_label2label N 12 1.05 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 437 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2538 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:16 mri_label2label N 12 e 2.94 S 0.15 U 2.78 P 99% M 537232 F 0 R 154270 W 0 c 280 w 1 I 0 O 216 L 1.05 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:19 mri_label2label N 12 1.05 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 795 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4672 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:19 mri_label2label N 12 e 3.16 S 0.17 U 2.99 P 99% M 537520 F 0 R 154305 W 0 c 316 w 1 I 0 O 376 L 1.05 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:22 mri_label2label N 12 1.05 1.19 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 764 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3683 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:22 mri_label2label N 12 e 3.05 S 0.15 U 2.88 P 99% M 537220 F 0 R 154287 W 0 c 304 w 1 I 0 O 304 L 1.05 1.19 1.29 @#@FSLOADPOST 2023:08:29:20:58:25 mri_label2label N 12 1.05 1.19 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 324 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1610 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:25 mri_label2label N 12 e 3.04 S 0.17 U 2.86 P 99% M 537276 F 0 R 157511 W 0 c 305 w 1 I 0 O 136 L 1.05 1.19 1.29 @#@FSLOADPOST 2023:08:29:20:58:28 mri_label2label N 12 1.12 1.21 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject EP01 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1195 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:28 mri_label2label N 12 e 2.87 S 0.17 U 2.68 P 99% M 537200 F 0 R 154250 W 0 c 350 w 1 I 0 O 104 L 1.12 1.21 1.29 @#@FSLOADPOST 2023:08:29:20:58:31 mri_label2label N 12 1.12 1.21 1.29 mris_label2annot --s EP01 --ctab /usr/local/freesurfer/7.4.1/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/freesurfer/7.4.1/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/label cmdline mris_label2annot --s EP01 --ctab /usr/local/freesurfer/7.4.1/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 rnet-lambda-vector machine x86_64 user bsherma subject EP01 hemi lh SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects ColorTable /usr/local/freesurfer/7.4.1/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig Index Offset 0 0 reading lh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading lh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading lh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading lh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading lh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading lh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading lh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading lh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 111854 unhit vertices Writing annot to /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.mpm.vpnl.annot @#@FSTIME 2023:08:29:20:58:31 mris_label2annot N 26 e 0.47 S 0.05 U 0.41 P 99% M 148076 F 0 R 40393 W 0 c 47 w 1 I 0 O 1992 L 1.12 1.21 1.29 @#@FSLOADPOST 2023:08:29:20:58:32 mris_label2annot N 26 1.11 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1043 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:32 mri_label2label N 12 e 2.82 S 0.17 U 2.64 P 99% M 537140 F 0 R 157505 W 0 c 275 w 1 I 0 O 72 L 1.11 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:35 mri_label2label N 12 1.11 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2126 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:35 mri_label2label N 12 e 3.05 S 0.19 U 2.85 P 99% M 537024 F 0 R 154265 W 0 c 301 w 1 I 0 O 128 L 1.11 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:38 mri_label2label N 12 1.10 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 1 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1505 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:38 mri_label2label N 12 e 2.84 S 0.16 U 2.67 P 99% M 537292 F 0 R 157513 W 0 c 284 w 1 I 0 O 72 L 1.10 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:41 mri_label2label N 12 1.10 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2018 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:41 mri_label2label N 12 e 2.95 S 0.18 U 2.76 P 99% M 537192 F 0 R 154271 W 0 c 287 w 1 I 0 O 112 L 1.10 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:44 mri_label2label N 12 1.09 1.20 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2336 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:44 mri_label2label N 12 e 3.11 S 0.15 U 2.95 P 99% M 537380 F 0 R 157528 W 0 c 300 w 1 I 0 O 128 L 1.09 1.20 1.29 @#@FSLOADPOST 2023:08:29:20:58:47 mri_label2label N 12 1.09 1.19 1.28 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1553 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:47 mri_label2label N 12 e 2.86 S 0.17 U 2.68 P 99% M 537172 F 0 R 154263 W 0 c 281 w 1 I 0 O 80 L 1.09 1.19 1.28 @#@FSLOADPOST 2023:08:29:20:58:50 mri_label2label N 12 1.09 1.19 1.28 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7176 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:50 mri_label2label N 12 e 3.62 S 0.16 U 3.45 P 99% M 537628 F 0 R 154353 W 0 c 351 w 1 I 0 O 400 L 1.09 1.19 1.28 @#@FSLOADPOST 2023:08:29:20:58:53 mri_label2label N 12 1.08 1.19 1.28 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1951 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:53 mri_label2label N 12 e 2.98 S 0.16 U 2.81 P 99% M 537180 F 0 R 154263 W 0 c 293 w 1 I 0 O 112 L 1.08 1.19 1.28 @#@FSLOADPOST 2023:08:29:20:58:56 mri_label2label N 12 1.08 1.19 1.28 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1463 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:56 mri_label2label N 12 e 2.87 S 0.15 U 2.72 P 99% M 537148 F 0 R 157512 W 0 c 281 w 1 I 0 O 128 L 1.08 1.19 1.28 @#@FSLOADPOST 2023:08:29:20:58:59 mri_label2label N 12 1.07 1.18 1.28 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 664 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4069 mri_label2label: Done @#@FSTIME 2023:08:29:20:58:59 mri_label2label N 12 e 3.18 S 0.17 U 3.01 P 99% M 537364 F 0 R 157549 W 0 c 311 w 1 I 0 O 328 L 1.07 1.18 1.28 @#@FSLOADPOST 2023:08:29:20:59:02 mri_label2label N 12 1.23 1.22 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 893 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4227 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:02 mri_label2label N 12 e 3.24 S 0.18 U 3.05 P 99% M 537384 F 0 R 157551 W 0 c 316 w 2 I 0 O 352 L 1.23 1.22 1.29 @#@FSLOADPOST 2023:08:29:20:59:06 mri_label2label N 12 1.23 1.22 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 644 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:06 mri_label2label N 12 e 2.76 S 0.19 U 2.55 P 99% M 537036 F 0 R 157496 W 0 c 269 w 1 I 0 O 56 L 1.23 1.22 1.29 @#@FSLOADPOST 2023:08:29:20:59:08 mri_label2label N 12 1.29 1.23 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 476 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:08 mri_label2label N 12 e 2.74 S 0.17 U 2.55 P 99% M 537116 F 0 R 154239 W 0 c 270 w 1 I 0 O 32 L 1.29 1.23 1.29 @#@FSLOADPOST 2023:08:29:20:59:11 mri_label2label N 12 1.29 1.23 1.29 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject EP01 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127052 Number of reverse mapping hits = 2 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 452 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:11 mri_label2label N 12 e 2.89 S 0.17 U 2.71 P 99% M 537184 F 0 R 154246 W 0 c 285 w 1 I 0 O 32 L 1.29 1.23 1.29 @#@FSLOADPOST 2023:08:29:20:59:14 mri_label2label N 12 1.35 1.24 1.30 mris_label2annot --s EP01 --hemi lh --ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/label cmdline mris_label2annot --s EP01 --hemi lh --ctab /usr/local/freesurfer/7.4.1/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 rnet-lambda-vector machine x86_64 user bsherma subject EP01 hemi lh SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects ColorTable /usr/local/freesurfer/7.4.1/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89074 unhit vertices Writing annot to /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.BA_exvivo.annot @#@FSTIME 2023:08:29:20:59:14 mris_label2annot N 38 e 0.50 S 0.04 U 0.45 P 99% M 148724 F 0 R 40497 W 0 c 50 w 1 I 0 O 1992 L 1.35 1.24 1.30 @#@FSLOADPOST 2023:08:29:20:59:15 mris_label2annot N 38 1.35 1.24 1.30 mris_label2annot --s EP01 --hemi lh --ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/label cmdline mris_label2annot --s EP01 --hemi lh --ctab /usr/local/freesurfer/7.4.1/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 rnet-lambda-vector machine x86_64 user bsherma subject EP01 hemi lh SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects ColorTable /usr/local/freesurfer/7.4.1/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 104801 unhit vertices Writing annot to /usr/local/freesurfer/7.4.1/subjects/EP01/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2023:08:29:20:59:15 mris_label2annot N 38 e 0.47 S 0.06 U 0.41 P 99% M 148316 F 0 R 40434 W 0 c 48 w 1 I 0 O 1992 L 1.35 1.24 1.30 @#@FSLOADPOST 2023:08:29:20:59:15 mris_label2annot N 38 1.35 1.24 1.30 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab EP01 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 223313 Total vertex volume 223119 (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) = 1423268 mm^3 (det: 1.368755 ) 1119 596 1724 2.193 0.453 0.107 0.036 16 1.0 BA1_exvivo 3390 2175 4888 2.188 0.428 0.094 0.018 20 2.5 BA2_exvivo 885 648 950 1.909 0.321 0.129 0.027 6 1.1 BA3a_exvivo 2055 1303 2873 1.964 0.562 0.102 0.026 18 2.1 BA3b_exvivo 1385 851 2900 2.805 0.406 0.101 0.032 10 1.5 BA4a_exvivo 1096 709 1835 2.675 0.372 0.086 0.019 4 0.9 BA4p_exvivo 8275 5573 17612 2.683 0.531 0.118 0.032 82 10.3 BA6_exvivo 2040 1411 3651 2.429 0.325 0.117 0.029 21 2.2 BA44_exvivo 3260 2238 6148 2.396 0.488 0.121 0.027 35 3.7 BA45_exvivo 3439 2384 4850 1.929 0.467 0.136 0.040 57 5.2 V1_exvivo 7755 5300 11378 1.947 0.459 0.142 0.035 101 10.9 V2_exvivo 2165 1458 3313 2.162 0.430 0.114 0.027 20 2.4 MT_exvivo 575 420 1473 2.853 0.833 0.108 0.025 4 0.6 perirhinal_exvivo 539 386 1425 2.646 1.099 0.150 0.060 11 1.1 entorhinal_exvivo @#@FSTIME 2023:08:29:20:59:15 mris_anatomical_stats N 12 e 2.98 S 0.15 U 2.83 P 99% M 447372 F 0 R 129133 W 0 c 294 w 1 I 0 O 24 L 1.35 1.24 1.30 @#@FSLOADPOST 2023:08:29:20:59:18 mris_anatomical_stats N 12 1.80 1.34 1.33 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab EP01 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 223313 Total vertex volume 223119 (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) = 1423268 mm^3 (det: 1.368755 ) 698 345 1058 2.243 0.445 0.102 0.034 10 0.6 BA1_exvivo 1369 849 2137 2.285 0.404 0.077 0.012 6 0.7 BA2_exvivo 748 557 788 1.912 0.314 0.134 0.028 5 1.0 BA3a_exvivo 1265 816 1466 1.739 0.399 0.082 0.018 6 0.9 BA3b_exvivo 1319 818 2642 2.803 0.426 0.091 0.026 7 1.2 BA4a_exvivo 905 599 1469 2.619 0.376 0.090 0.021 4 0.8 BA4p_exvivo 4491 2943 9172 2.670 0.519 0.116 0.032 43 5.8 BA6_exvivo 1283 884 2423 2.464 0.350 0.123 0.029 15 1.4 BA44_exvivo 1393 965 3155 2.577 0.559 0.135 0.030 19 1.8 BA45_exvivo 3652 2538 5229 1.921 0.478 0.136 0.040 60 5.5 V1_exvivo 3952 2686 5576 1.872 0.429 0.147 0.038 54 5.8 V2_exvivo 614 398 1114 2.303 0.488 0.118 0.035 7 0.9 MT_exvivo 238 162 518 2.776 0.807 0.082 0.016 1 0.2 perirhinal_exvivo 324 231 963 3.015 0.584 0.114 0.042 3 0.4 entorhinal_exvivo @#@FSTIME 2023:08:29:20:59:18 mris_anatomical_stats N 12 e 2.99 S 0.12 U 2.86 P 99% M 447376 F 0 R 129045 W 0 c 291 w 1 I 0 O 32 L 1.80 1.34 1.33 @#@FSLOADPOST 2023:08:29:20:59:21 mris_anatomical_stats N 12 1.80 1.34 1.33 #-------------------------------------------- #@# BA_exvivo Labels rh Tue Aug 29 20:59:21 PDT 2023 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject EP01 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4017 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:21 mri_label2label N 12 e 3.21 S 0.14 U 3.06 P 99% M 538336 F 0 R 154549 W 0 c 311 w 1 I 0 O 208 L 1.80 1.34 1.33 @#@FSLOADPOST 2023:08:29:20:59:24 mri_label2label N 12 1.82 1.35 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject EP01 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6756 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:24 mri_label2label N 12 e 3.57 S 0.15 U 3.41 P 99% M 538536 F 0 R 154600 W 0 c 349 w 1 I 0 O 336 L 1.82 1.35 1.33 @#@FSLOADPOST 2023:08:29:20:59:28 mri_label2label N 12 1.83 1.36 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject EP01 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 3993 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:28 mri_label2label N 12 e 3.34 S 0.13 U 3.20 P 99% M 538256 F 0 R 154547 W 0 c 332 w 1 I 0 O 176 L 1.83 1.36 1.33 @#@FSLOADPOST 2023:08:29:20:59:31 mri_label2label N 12 1.83 1.36 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject EP01 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4559 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:31 mri_label2label N 12 e 3.33 S 0.15 U 3.17 P 99% M 538528 F 0 R 154563 W 0 c 402 w 1 I 0 O 216 L 1.83 1.36 1.33 @#@FSLOADPOST 2023:08:29:20:59:35 mri_label2label N 12 1.76 1.35 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject EP01 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5825 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:35 mri_label2label N 12 e 3.54 S 0.14 U 3.39 P 99% M 538412 F 0 R 154583 W 0 c 347 w 1 I 0 O 312 L 1.76 1.35 1.33 @#@FSLOADPOST 2023:08:29:20:59:38 mri_label2label N 12 1.70 1.35 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject EP01 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4509 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:38 mri_label2label N 12 e 3.25 S 0.16 U 3.08 P 99% M 538448 F 0 R 154561 W 0 c 378 w 1 I 0 O 216 L 1.70 1.35 1.33 @#@FSLOADPOST 2023:08:29:20:59:41 mri_label2label N 12 1.65 1.34 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject EP01 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 279 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12535 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:42 mri_label2label N 12 e 4.19 S 0.15 U 4.02 P 99% M 538876 F 0 R 154699 W 0 c 407 w 1 I 0 O 720 L 1.65 1.34 1.33 @#@FSLOADPOST 2023:08:29:20:59:46 mri_label2label N 12 1.65 1.34 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject EP01 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 268 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7180 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:46 mri_label2label N 12 e 3.62 S 0.15 U 3.45 P 99% M 538604 F 0 R 154608 W 0 c 352 w 1 I 0 O 432 L 1.65 1.34 1.33 @#@FSLOADPOST 2023:08:29:20:59:49 mri_label2label N 12 1.59 1.34 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject EP01 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 537 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5892 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:49 mri_label2label N 12 e 3.45 S 0.15 U 3.28 P 99% M 538380 F 0 R 154577 W 0 c 335 w 1 I 0 O 416 L 1.59 1.34 1.33 @#@FSLOADPOST 2023:08:29:20:59:53 mri_label2label N 12 1.55 1.33 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject EP01 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 1416 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6143 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:53 mri_label2label N 12 e 3.48 S 0.15 U 3.32 P 99% M 538300 F 0 R 154570 W 0 c 338 w 1 I 0 O 496 L 1.55 1.33 1.33 @#@FSLOADPOST 2023:08:29:20:59:56 mri_label2label N 12 1.55 1.33 1.33 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject EP01 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 2179 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10195 mri_label2label: Done @#@FSTIME 2023:08:29:20:59:56 mri_label2label N 12 e 3.71 S 0.19 U 3.51 P 99% M 538848 F 0 R 154641 W 0 c 370 w 1 I 0 O 808 L 1.55 1.33 1.33 @#@FSLOADPOST 2023:08:29:21:00:00 mri_label2label N 12 1.50 1.32 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject EP01 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2120 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:00 mri_label2label N 12 e 3.03 S 0.21 U 2.81 P 99% M 538136 F 0 R 154513 W 0 c 295 w 1 I 0 O 160 L 1.50 1.32 1.32 @#@FSLOADPOST 2023:08:29:21:00:03 mri_label2label N 12 1.46 1.32 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject EP01 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1055 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:03 mri_label2label N 12 e 2.83 S 0.17 U 2.65 P 99% M 537884 F 0 R 154497 W 0 c 273 w 1 I 0 O 72 L 1.46 1.32 1.32 @#@FSLOADPOST 2023:08:29:21:00:06 mri_label2label N 12 1.46 1.32 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject EP01 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 766 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:06 mri_label2label N 12 e 2.98 S 0.26 U 2.72 P 99% M 537964 F 0 R 154489 W 0 c 289 w 1 I 0 O 56 L 1.46 1.32 1.32 @#@FSLOADPOST 2023:08:29:21:00:09 mri_label2label N 12 1.42 1.31 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 721 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:09 mri_label2label N 12 e 2.90 S 0.17 U 2.73 P 99% M 538084 F 0 R 154493 W 0 c 283 w 1 I 0 O 64 L 1.42 1.31 1.32 @#@FSLOADPOST 2023:08:29:21:00:12 mri_label2label N 12 1.39 1.31 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 865 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:12 mri_label2label N 12 e 2.94 S 0.18 U 2.75 P 99% M 538124 F 0 R 157762 W 0 c 287 w 1 I 0 O 72 L 1.39 1.31 1.32 @#@FSLOADPOST 2023:08:29:21:00:15 mri_label2label N 12 1.39 1.31 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1651 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:15 mri_label2label N 12 e 3.02 S 0.19 U 2.83 P 99% M 538192 F 0 R 157778 W 0 c 302 w 1 I 0 O 128 L 1.39 1.31 1.32 @#@FSLOADPOST 2023:08:29:21:00:18 mri_label2label N 12 1.36 1.30 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 257 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1843 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:18 mri_label2label N 12 e 3.00 S 0.15 U 2.84 P 99% M 538064 F 0 R 154506 W 0 c 293 w 1 I 0 O 152 L 1.36 1.30 1.32 @#@FSLOADPOST 2023:08:29:21:00:21 mri_label2label N 12 1.36 1.30 1.32 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 1130 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4797 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:21 mri_label2label N 12 e 3.18 S 0.15 U 3.02 P 99% M 538236 F 0 R 154551 W 0 c 313 w 1 I 0 O 392 L 1.36 1.30 1.32 @#@FSLOADPOST 2023:08:29:21:00:24 mri_label2label N 12 1.33 1.30 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 811 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3530 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:24 mri_label2label N 12 e 3.21 S 0.19 U 3.02 P 99% M 538436 F 0 R 154533 W 0 c 313 w 1 I 0 O 280 L 1.33 1.30 1.31 @#@FSLOADPOST 2023:08:29:21:00:27 mri_label2label N 12 1.30 1.29 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 472 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1700 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:27 mri_label2label N 12 e 3.00 S 0.15 U 2.84 P 99% M 538048 F 0 R 154505 W 0 c 290 w 1 I 0 O 144 L 1.30 1.29 1.31 @#@FSLOADPOST 2023:08:29:21:00:30 mri_label2label N 12 1.30 1.29 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject EP01 --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 315 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1340 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:30 mri_label2label N 12 e 2.96 S 0.19 U 2.77 P 99% M 537948 F 0 R 157768 W 0 c 292 w 1 I 0 O 112 L 1.30 1.29 1.31 @#@FSLOADPOST 2023:08:29:21:00:33 mri_label2label N 12 1.28 1.29 1.31 mris_label2annot --s EP01 --ctab /usr/local/freesurfer/7.4.1/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/freesurfer/7.4.1/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/label cmdline mris_label2annot --s EP01 --ctab /usr/local/freesurfer/7.4.1/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 rnet-lambda-vector machine x86_64 user bsherma subject EP01 hemi rh SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects ColorTable /usr/local/freesurfer/7.4.1/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig Index Offset 0 0 reading rh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading rh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading rh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading rh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading rh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading rh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading rh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading rh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 112289 unhit vertices Writing annot to /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.mpm.vpnl.annot @#@FSTIME 2023:08:29:21:00:33 mris_label2annot N 26 e 0.45 S 0.04 U 0.40 P 99% M 148664 F 0 R 40500 W 0 c 46 w 1 I 0 O 2000 L 1.28 1.29 1.31 @#@FSLOADPOST 2023:08:29:21:00:34 mris_label2annot N 26 1.28 1.29 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 896 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:34 mri_label2label N 12 e 2.94 S 0.15 U 2.78 P 99% M 537928 F 0 R 154494 W 0 c 286 w 1 I 0 O 56 L 1.28 1.29 1.31 @#@FSLOADPOST 2023:08:29:21:00:37 mri_label2label N 12 1.26 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2699 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:37 mri_label2label N 12 e 3.01 S 0.16 U 2.84 P 99% M 538196 F 0 R 154523 W 0 c 294 w 1 I 0 O 128 L 1.26 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:00:40 mri_label2label N 12 1.26 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1702 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:40 mri_label2label N 12 e 2.90 S 0.17 U 2.72 P 99% M 538000 F 0 R 157780 W 0 c 288 w 2 I 0 O 80 L 1.26 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:00:43 mri_label2label N 12 1.24 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2195 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:43 mri_label2label N 12 e 3.07 S 0.15 U 2.91 P 99% M 538184 F 0 R 157786 W 0 c 301 w 1 I 0 O 112 L 1.24 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:00:46 mri_label2label N 12 1.24 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1403 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:46 mri_label2label N 12 e 2.92 S 0.16 U 2.75 P 99% M 538188 F 0 R 157773 W 0 c 379 w 1 I 0 O 80 L 1.24 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:00:49 mri_label2label N 12 1.22 1.27 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1495 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:49 mri_label2label N 12 e 2.95 S 0.18 U 2.76 P 99% M 538204 F 0 R 157774 W 0 c 292 w 1 I 0 O 80 L 1.22 1.27 1.30 @#@FSLOADPOST 2023:08:29:21:00:52 mri_label2label N 12 1.20 1.27 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7092 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:52 mri_label2label N 12 e 3.56 S 0.16 U 3.39 P 99% M 538528 F 0 R 154604 W 0 c 345 w 1 I 0 O 400 L 1.20 1.27 1.30 @#@FSLOADPOST 2023:08:29:21:00:55 mri_label2label N 12 1.20 1.27 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1066 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:55 mri_label2label N 12 e 2.83 S 0.17 U 2.65 P 99% M 537876 F 0 R 154499 W 0 c 273 w 1 I 0 O 72 L 1.20 1.27 1.30 @#@FSLOADPOST 2023:08:29:21:00:58 mri_label2label N 12 1.26 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1259 mri_label2label: Done @#@FSTIME 2023:08:29:21:00:58 mri_label2label N 12 e 2.95 S 0.18 U 2.77 P 99% M 538180 F 0 R 157771 W 0 c 285 w 1 I 0 O 88 L 1.26 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:01:01 mri_label2label N 12 1.26 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 971 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4203 mri_label2label: Done @#@FSTIME 2023:08:29:21:01:01 mri_label2label N 12 e 3.24 S 0.17 U 3.07 P 99% M 538304 F 0 R 154542 W 0 c 316 w 0 I 0 O 344 L 1.26 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:01:05 mri_label2label N 12 1.24 1.27 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 1125 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4562 mri_label2label: Done @#@FSTIME 2023:08:29:21:01:05 mri_label2label N 12 e 3.14 S 0.15 U 2.99 P 99% M 538248 F 0 R 154550 W 0 c 308 w 1 I 0 O 368 L 1.24 1.27 1.30 @#@FSLOADPOST 2023:08:29:21:01:08 mri_label2label N 12 1.22 1.27 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 285 mri_label2label: Done @#@FSTIME 2023:08:29:21:01:08 mri_label2label N 12 e 2.86 S 0.16 U 2.69 P 99% M 538008 F 0 R 154482 W 0 c 277 w 1 I 0 O 24 L 1.22 1.27 1.30 @#@FSLOADPOST 2023:08:29:21:01:11 mri_label2label N 12 1.22 1.27 1.30 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 705 mri_label2label: Done @#@FSTIME 2023:08:29:21:01:11 mri_label2label N 12 e 2.91 S 0.18 U 2.72 P 99% M 538088 F 0 R 157763 W 0 c 283 w 2 I 0 O 48 L 1.22 1.27 1.30 @#@FSLOADPOST 2023:08:29:21:01:14 mri_label2label N 12 1.28 1.28 1.31 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject EP01 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/7.4.1/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = EP01 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 /usr/local/freesurfer/7.4.1/subjects FREESURFER_HOME /usr/local/freesurfer/7.4.1 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white Reading target registration /usr/local/freesurfer/7.4.1/subjects/EP01/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 127453 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 297 mri_label2label: Done @#@FSTIME 2023:08:29:21:01:14 mri_label2label N 12 e 2.92 S 0.15 U 2.76 P 99% M 537832 F 0 R 154488 W 0 c 295 w 1 I 0 O 24 L 1.28 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:01:16 mri_label2label N 12 1.28 1.28 1.31 mris_label2annot --s EP01 --hemi rh --ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/label cmdline mris_label2annot --s EP01 --hemi rh --ctab /usr/local/freesurfer/7.4.1/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 rnet-lambda-vector machine x86_64 user bsherma subject EP01 hemi rh SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects ColorTable /usr/local/freesurfer/7.4.1/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89819 unhit vertices Writing annot to /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.BA_exvivo.annot @#@FSTIME 2023:08:29:21:01:16 mris_label2annot N 38 e 0.50 S 0.05 U 0.44 P 100% M 148992 F 0 R 40682 W 0 c 48 w 1 I 0 O 2000 L 1.28 1.28 1.31 @#@FSLOADPOST 2023:08:29:21:01:17 mris_label2annot N 38 1.26 1.28 1.30 mris_label2annot --s EP01 --hemi rh --ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /usr/local/freesurfer/7.4.1/subjects/EP01/label cmdline mris_label2annot --s EP01 --hemi rh --ctab /usr/local/freesurfer/7.4.1/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 rnet-lambda-vector machine x86_64 user bsherma subject EP01 hemi rh SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects ColorTable /usr/local/freesurfer/7.4.1/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 106257 unhit vertices Writing annot to /usr/local/freesurfer/7.4.1/subjects/EP01/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2023:08:29:21:01:17 mris_label2annot N 38 e 0.45 S 0.05 U 0.40 P 99% M 148696 F 0 R 40533 W 0 c 43 w 1 I 0 O 2000 L 1.26 1.28 1.30 @#@FSLOADPOST 2023:08:29:21:01:17 mris_label2annot N 38 1.26 1.28 1.30 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab EP01 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 224290 Total vertex volume 224095 (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) = 1423268 mm^3 (det: 1.368755 ) 815 446 1313 2.144 0.472 0.109 0.038 12 1.0 BA1_exvivo 2644 1722 3682 2.113 0.420 0.096 0.019 16 2.1 BA2_exvivo 867 641 915 1.848 0.335 0.126 0.029 6 1.2 BA3a_exvivo 1572 1045 2179 1.878 0.431 0.100 0.023 12 1.3 BA3b_exvivo 1408 879 2620 2.646 0.474 0.095 0.022 8 1.3 BA4a_exvivo 1057 686 1731 2.598 0.375 0.089 0.020 4 1.0 BA4p_exvivo 7445 5010 15795 2.646 0.544 0.117 0.032 71 9.2 BA6_exvivo 3162 2238 5790 2.448 0.429 0.121 0.027 31 3.5 BA44_exvivo 4074 2892 8447 2.455 0.507 0.127 0.029 50 4.5 BA45_exvivo 4115 2764 5337 1.813 0.526 0.146 0.048 59 7.4 V1_exvivo 7849 5390 11068 1.958 0.482 0.141 0.036 109 10.5 V2_exvivo 1780 1255 3203 2.267 0.476 0.128 0.025 19 1.8 MT_exvivo 341 240 652 2.546 0.664 0.097 0.022 1 0.3 perirhinal_exvivo 505 368 1422 2.743 0.738 0.128 0.045 5 0.7 entorhinal_exvivo @#@FSTIME 2023:08:29:21:01:17 mris_anatomical_stats N 12 e 3.00 S 0.11 U 2.87 P 99% M 448824 F 0 R 126266 W 0 c 298 w 1 I 0 O 24 L 1.26 1.28 1.30 @#@FSLOADPOST 2023:08:29:21:01:20 mris_anatomical_stats N 12 1.26 1.28 1.30 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab EP01 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/7.4.1/subjects/EP01/mri/wm.mgz... reading input surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... reading input pial surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.pial... reading input white surface /usr/local/freesurfer/7.4.1/subjects/EP01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 224290 Total vertex volume 224095 (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) = 1423268 mm^3 (det: 1.368755 ) 545 284 757 2.003 0.424 0.110 0.044 8 0.7 BA1_exvivo 1424 893 2152 2.167 0.427 0.088 0.016 8 0.9 BA2_exvivo 767 568 763 1.851 0.331 0.125 0.029 5 1.0 BA3a_exvivo 1233 831 1471 1.762 0.335 0.095 0.018 6 1.0 BA3b_exvivo 871 539 1915 2.781 0.468 0.108 0.031 6 1.0 BA4a_exvivo 868 569 1434 2.658 0.394 0.088 0.019 3 0.8 BA4p_exvivo 4701 3132 9620 2.615 0.553 0.117 0.032 44 5.7 BA6_exvivo 804 607 1925 2.530 0.453 0.138 0.035 13 1.1 BA44_exvivo 990 733 2421 2.571 0.427 0.126 0.029 13 1.0 BA45_exvivo 3949 2647 5065 1.809 0.520 0.146 0.047 56 7.0 V1_exvivo 4279 2931 5615 1.882 0.507 0.150 0.042 66 6.6 V2_exvivo 239 170 436 2.306 0.334 0.130 0.023 2 0.2 MT_exvivo 29 21 40 2.271 0.460 0.108 0.019 0 0.0 perirhinal_exvivo 497 359 1175 2.581 0.640 0.124 0.043 5 0.7 entorhinal_exvivo @#@FSTIME 2023:08:29:21:01:21 mris_anatomical_stats N 12 e 3.00 S 0.12 U 2.87 P 99% M 448776 F 0 R 126261 W 0 c 295 w 1 I 0 O 24 L 1.26 1.28 1.30 @#@FSLOADPOST 2023:08:29:21:01:24 mris_anatomical_stats N 12 1.56 1.34 1.32 /usr/local/freesurfer/7.4.1/subjects/EP01/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Aug 29 21:01:24 PDT 2023 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2022 The MathWorks, Inc. R2022b (9.13.0.2049777) 64-bit (glnxa64) August 24, 2022 [Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function isrow has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function narginchk has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function isequaln has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function istable has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function isfile has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function isfolder has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] [Warning: Function isstring has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.] For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com. >> {Unrecognized function or variable 'make_outer_surface'. } >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Command exited with non-zero status 1 @#@FSTIME 2023:08:29:21:01:24 mris_compute_lgi N 2 e 10.14 S 2.58 U 18.37 P 206% M 1373192 F 0 R 412101 W 0 c 5705 w 117257 I 0 O 17200 L 1.56 1.34 1.32 @#@FSLOADPOST 2023:08:29:21:01:34 mris_compute_lgi N 2 1.63 1.36 1.33 Linux rnet-lambda-vector 5.15.0-78-generic #85~20.04.1-Ubuntu SMP Mon Jul 17 09:42:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s EP01 exited with ERRORS at Tue Aug 29 21:01:34 PDT 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting