Fri Sep 22 16:45:39 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001 setenv SUBJECTS_DIR /out/sourcedata/freesurfer /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 16 -subjid sub-3001 -sd /out/sourcedata/freesurfer subjid sub-3001 setenv SUBJECTS_DIR /out/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 Linux b1acb5b95ebd 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 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 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 514130 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 11Gi 38Gi 2.0Mi 75Gi 112Gi Swap: 32Gi 0B 32Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:39-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/22-16:45:40-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: b1acb5b95ebd Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 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 /opt/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Tessellate rh Fri Sep 22 16:45:40 UTC 2023 /out/sourcedata/freesurfer/sub-3001/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 18 found - 18 modified | TOTAL: 19 pass 2 (yz+): 0 found - 18 modified | TOTAL: 19 pass 1 (yz-): 20 found - 20 modified | TOTAL: 39 pass 2 (yz-): 0 found - 20 modified | TOTAL: 39 pass 1 (xz+): 5 found - 5 modified | TOTAL: 44 pass 2 (xz+): 0 found - 5 modified | TOTAL: 44 pass 1 (xz-): 0 found - 0 modified | TOTAL: 44 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 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 50 (out of 623758: 0.008016) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 60: 2743 vertices, 2941 faces slice 70: 12135 vertices, 12520 faces slice 80: 24038 vertices, 24469 faces slice 90: 37155 vertices, 37647 faces slice 100: 52778 vertices, 53361 faces slice 110: 68647 vertices, 69124 faces slice 120: 83754 vertices, 84251 faces slice 130: 100093 vertices, 100621 faces slice 140: 115754 vertices, 116306 faces slice 150: 132169 vertices, 132703 faces slice 160: 146487 vertices, 147033 faces slice 170: 161852 vertices, 162384 faces slice 180: 176363 vertices, 176845 faces slice 190: 188821 vertices, 189236 faces slice 200: 199413 vertices, 199836 faces slice 210: 209846 vertices, 210251 faces slice 220: 219013 vertices, 219349 faces slice 230: 227616 vertices, 227970 faces slice 240: 236207 vertices, 236531 faces slice 250: 242929 vertices, 243132 faces slice 260: 244498 vertices, 244542 faces slice 270: 244498 vertices, 244542 faces slice 280: 244498 vertices, 244542 faces slice 290: 244498 vertices, 244542 faces slice 300: 244498 vertices, 244542 faces slice 310: 244498 vertices, 244542 faces slice 320: 244498 vertices, 244542 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 244498 voxel in cpt #1: X=-44 [v=244498,e=733626,f=489084] located at (26.940832, -11.125500, 46.113605) For the whole surface: X=-44 [v=244498,e=733626,f=489084] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri Sep 22 16:45:51 UTC 2023 /out/sourcedata/freesurfer/sub-3001/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... #-------------------------------------------- #@# Inflation1 rh Fri Sep 22 16:45:58 UTC 2023 /out/sourcedata/freesurfer/sub-3001/scripts mris_inflate -no-save-sulc -n 50 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix niterations = 50 Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.6 mm, total surface area = 88808 mm^2 resetting # of iterations to 63 for highres volume step 000: RMS=0.132 (target=0.015) step 005: RMS=0.104 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.034 (target=0.015) step 050: RMS=0.033 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.030 (target=0.015) step 065: RMS=0.029 (target=0.015) step 070: RMS=0.028 (target=0.015) step 075: RMS=0.028 (target=0.015) step 080: RMS=0.027 (target=0.015) step 085: RMS=0.027 (target=0.015) step 090: RMS=0.027 (target=0.015) step 095: RMS=0.027 (target=0.015) step 100: RMS=0.026 (target=0.015) step 105: RMS=0.027 (target=0.015) step 110: RMS=0.026 (target=0.015) step 115: RMS=0.026 (target=0.015) step 120: RMS=0.026 (target=0.015) step 125: RMS=0.026 (target=0.015) step 130: RMS=0.026 (target=0.015) step 135: RMS=0.026 (target=0.015) step 140: RMS=0.026 (target=0.015) step 145: RMS=0.026 (target=0.015) step 150: RMS=0.026 (target=0.015) step 155: RMS=0.026 (target=0.015) step 160: RMS=0.026 (target=0.015) step 165: RMS=0.026 (target=0.015) step 170: RMS=0.026 (target=0.015) step 175: RMS=0.025 (target=0.015) step 180: RMS=0.025 (target=0.015) step 185: RMS=0.025 (target=0.015) step 190: RMS=0.025 (target=0.015) step 195: RMS=0.025 (target=0.015) step 200: RMS=0.025 (target=0.015) step 205: RMS=0.025 (target=0.015) step 210: RMS=0.025 (target=0.015) step 215: RMS=0.025 (target=0.015) step 220: RMS=0.025 (target=0.015) step 225: RMS=0.025 (target=0.015) step 230: RMS=0.025 (target=0.015) step 235: RMS=0.025 (target=0.015) step 240: RMS=0.025 (target=0.015) step 245: RMS=0.025 (target=0.015) step 250: RMS=0.025 (target=0.015) step 255: RMS=0.025 (target=0.015) step 260: RMS=0.025 (target=0.015) step 265: RMS=0.025 (target=0.015) step 270: RMS=0.025 (target=0.015) step 275: RMS=0.025 (target=0.015) step 280: RMS=0.025 (target=0.015) step 285: RMS=0.025 (target=0.015) step 290: RMS=0.025 (target=0.015) step 295: RMS=0.025 (target=0.015) step 300: RMS=0.025 (target=0.015) step 305: RMS=0.025 (target=0.015) step 310: RMS=0.025 (target=0.015) step 315: RMS=0.025 (target=0.015) step 320: RMS=0.026 (target=0.015) step 325: RMS=0.028 (target=0.015) step 330: RMS=0.027 (target=0.015) step 335: RMS=0.027 (target=0.015) step 340: RMS=0.027 (target=0.015) step 345: RMS=0.027 (target=0.015) step 350: RMS=0.027 (target=0.015) step 355: RMS=0.027 (target=0.015) step 360: RMS=0.027 (target=0.015) step 365: RMS=0.027 (target=0.015) step 370: RMS=0.027 (target=0.015) step 375: RMS=0.027 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.9 minutes inflation complete. Not saving sulc mris_inflate utimesec 1676.703855 mris_inflate stimesec 38.038481 mris_inflate ru_maxrss 385920 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 3749848 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 41443 mris_inflate ru_nivcsw 110224 #-------------------------------------------- #@# QSphere rh Fri Sep 22 16:47:49 UTC 2023 /out/sourcedata/freesurfer/sub-3001/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: 7.3.2 available threads: 16 scaling brain by 0.297... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.73 +- 0.39 (0.00-->7.77) (max @ vno 140528 --> 141990) face area 0.02 +- 0.02 (-0.14-->0.65) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.157, avgs=0 005/300: dt: 0.9000, rms radial error=173.901, avgs=0 010/300: dt: 0.9000, rms radial error=173.350, avgs=0 015/300: dt: 0.9000, rms radial error=172.627, avgs=0 020/300: dt: 0.9000, rms radial error=171.803, avgs=0 025/300: dt: 0.9000, rms radial error=170.922, avgs=0 030/300: dt: 0.9000, rms radial error=170.008, avgs=0 035/300: dt: 0.9000, rms radial error=169.077, avgs=0 040/300: dt: 0.9000, rms radial error=168.138, avgs=0 045/300: dt: 0.9000, rms radial error=167.197, avgs=0 050/300: dt: 0.9000, rms radial error=166.257, avgs=0 055/300: dt: 0.9000, rms radial error=165.319, avgs=0 060/300: dt: 0.9000, rms radial error=164.385, avgs=0 065/300: dt: 0.9000, rms radial error=163.455, avgs=0 070/300: dt: 0.9000, rms radial error=162.531, avgs=0 075/300: dt: 0.9000, rms radial error=161.611, avgs=0 080/300: dt: 0.9000, rms radial error=160.696, avgs=0 085/300: dt: 0.9000, rms radial error=159.786, avgs=0 090/300: dt: 0.9000, rms radial error=158.881, avgs=0 095/300: dt: 0.9000, rms radial error=157.982, avgs=0 100/300: dt: 0.9000, rms radial error=157.088, avgs=0 105/300: dt: 0.9000, rms radial error=156.198, avgs=0 110/300: dt: 0.9000, rms radial error=155.314, avgs=0 115/300: dt: 0.9000, rms radial error=154.435, avgs=0 120/300: dt: 0.9000, rms radial error=153.561, avgs=0 125/300: dt: 0.9000, rms radial error=152.692, avgs=0 130/300: dt: 0.9000, rms radial error=151.828, avgs=0 135/300: dt: 0.9000, rms radial error=150.968, avgs=0 140/300: dt: 0.9000, rms radial error=150.114, avgs=0 145/300: dt: 0.9000, rms radial error=149.265, avgs=0 150/300: dt: 0.9000, rms radial error=148.420, avgs=0 155/300: dt: 0.9000, rms radial error=147.580, avgs=0 160/300: dt: 0.9000, rms radial error=146.745, avgs=0 165/300: dt: 0.9000, rms radial error=145.914, avgs=0 170/300: dt: 0.9000, rms radial error=145.089, avgs=0 175/300: dt: 0.9000, rms radial error=144.268, avgs=0 180/300: dt: 0.9000, rms radial error=143.451, avgs=0 185/300: dt: 0.9000, rms radial error=142.639, avgs=0 190/300: dt: 0.9000, rms radial error=141.832, avgs=0 195/300: dt: 0.9000, rms radial error=141.030, avgs=0 200/300: dt: 0.9000, rms radial error=140.232, avgs=0 205/300: dt: 0.9000, rms radial error=139.438, avgs=0 210/300: dt: 0.9000, rms radial error=138.649, avgs=0 215/300: dt: 0.9000, rms radial error=137.865, avgs=0 220/300: dt: 0.9000, rms radial error=137.085, avgs=0 225/300: dt: 0.9000, rms radial error=136.309, avgs=0 230/300: dt: 0.9000, rms radial error=135.538, avgs=0 235/300: dt: 0.9000, rms radial error=134.771, avgs=0 240/300: dt: 0.9000, rms radial error=134.009, avgs=0 245/300: dt: 0.9000, rms radial error=133.251, avgs=0 250/300: dt: 0.9000, rms radial error=132.497, avgs=0 255/300: dt: 0.9000, rms radial error=131.747, avgs=0 260/300: dt: 0.9000, rms radial error=131.002, avgs=0 265/300: dt: 0.9000, rms radial error=130.261, avgs=0 270/300: dt: 0.9000, rms radial error=129.524, avgs=0 275/300: dt: 0.9000, rms radial error=128.791, avgs=0 280/300: dt: 0.9000, rms radial error=128.063, avgs=0 285/300: dt: 0.9000, rms radial error=127.339, avgs=0 290/300: dt: 0.9000, rms radial error=126.618, avgs=0 295/300: dt: 0.9000, rms radial error=125.902, avgs=0 300/300: dt: 0.9000, rms radial error=125.190, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 30334.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 5631.91 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 648.89 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/14 = 0.00444 epoch 4 (K=640.0), pass 1, starting sse = 34.31 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/15 = 0.00847 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0275 hours FSRUNTIME@ mris_sphere 0.0275 hours 16 threads #VMPC# mris_sphere VmPeak 1708308 mris_sphere done #@# Fix Topology rh Fri Sep 22 16:49:29 UTC 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-3001 rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-44 (nv=244498, nf=489084, ne=733626, g=23) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 5382 ambiguous faces found in tessellation segmenting defects... 33 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 33 defects to be corrected 0 vertices coincident reading input surface /out/sourcedata/freesurfer/sub-3001/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: -9.1609 (-4.5804) -vertex loglikelihood: -5.5328 (-2.7664) -normal dot loglikelihood: -3.5147 (-3.5147) -quad curv loglikelihood: -6.0900 (-3.0450) Total Loglikelihood : -24.2984 CORRECTING DEFECT 0 (vertices=1206, convex hull=359, v0=496) After retessellation of defect 0 (v0=496), euler #=-30 (241411,723514,482073) : difference with theory (-30) = 0 CORRECTING DEFECT 1 (vertices=18, convex hull=34, v0=1493) After retessellation of defect 1 (v0=1493), euler #=-29 (241413,723529,482087) : difference with theory (-29) = 0 CORRECTING DEFECT 2 (vertices=373, convex hull=57, v0=5910) After retessellation of defect 2 (v0=5910), euler #=-28 (241424,723589,482137) : difference with theory (-28) = 0 CORRECTING DEFECT 3 (vertices=38, convex hull=24, v0=61345) After retessellation of defect 3 (v0=61345), euler #=-27 (241428,723608,482153) : difference with theory (-27) = 0 CORRECTING DEFECT 4 (vertices=26, convex hull=25, v0=72793) After retessellation of defect 4 (v0=72793), euler #=-26 (241430,723621,482165) : difference with theory (-26) = 0 CORRECTING DEFECT 5 (vertices=126, convex hull=146, v0=85234) After retessellation of defect 5 (v0=85234), euler #=-25 (241456,723760,482279) : difference with theory (-25) = 0 CORRECTING DEFECT 6 (vertices=30, convex hull=55, v0=96341) After retessellation of defect 6 (v0=96341), euler #=-24 (241462,723796,482310) : difference with theory (-24) = 0 CORRECTING DEFECT 7 (vertices=11, convex hull=22, v0=99517) After retessellation of defect 7 (v0=99517), euler #=-23 (241464,723806,482319) : difference with theory (-23) = 0 CORRECTING DEFECT 8 (vertices=14, convex hull=18, v0=113706) After retessellation of defect 8 (v0=113706), euler #=-22 (241464,723809,482323) : difference with theory (-22) = 0 CORRECTING DEFECT 9 (vertices=391, convex hull=410, v0=132107) After retessellation of defect 9 (v0=132107), euler #=-21 (241553,724275,482701) : difference with theory (-21) = 0 CORRECTING DEFECT 10 (vertices=6, convex hull=15, v0=136069) After retessellation of defect 10 (v0=136069), euler #=-20 (241555,724285,482710) : difference with theory (-20) = 0 CORRECTING DEFECT 11 (vertices=29, convex hull=17, v0=144608) After retessellation of defect 11 (v0=144608), euler #=-19 (241558,724296,482719) : difference with theory (-19) = 0 CORRECTING DEFECT 12 (vertices=58, convex hull=76, v0=144652) After retessellation of defect 12 (v0=144652), euler #=-18 (241573,724370,482779) : difference with theory (-18) = 0 CORRECTING DEFECT 13 (vertices=107, convex hull=66, v0=152351) After retessellation of defect 13 (v0=152351), euler #=-17 (241582,724426,482827) : difference with theory (-17) = 0 CORRECTING DEFECT 14 (vertices=42, convex hull=70, v0=154866) After retessellation of defect 14 (v0=154866), euler #=-16 (241592,724486,482878) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=91, convex hull=39, v0=155166) After retessellation of defect 15 (v0=155166), euler #=-15 (241598,724519,482906) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=15, convex hull=24, v0=161378) After retessellation of defect 16 (v0=161378), euler #=-14 (241601,724534,482919) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=35, convex hull=67, v0=162891) After retessellation of defect 17 (v0=162891), euler #=-13 (241610,724586,482963) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=134, convex hull=46, v0=164197) After retessellation of defect 18 (v0=164197), euler #=-12 (241616,724618,482990) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=26, convex hull=32, v0=165855) After retessellation of defect 19 (v0=165855), euler #=-11 (241618,724638,483009) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=52, convex hull=59, v0=165929) After retessellation of defect 20 (v0=165929), euler #=-10 (241627,724688,483051) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=74, convex hull=43, v0=169011) After retessellation of defect 21 (v0=169011), euler #=-9 (241631,724720,483080) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=14, convex hull=22, v0=174800) After retessellation of defect 22 (v0=174800), euler #=-8 (241633,724731,483090) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=12, convex hull=23, v0=175828) After retessellation of defect 23 (v0=175828), euler #=-7 (241635,724744,483102) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=6, convex hull=26, v0=186250) After retessellation of defect 24 (v0=186250), euler #=-6 (241636,724756,483114) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=10, convex hull=23, v0=188787) After retessellation of defect 25 (v0=188787), euler #=-5 (241637,724765,483123) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=24, convex hull=57, v0=191785) After retessellation of defect 26 (v0=191785), euler #=-4 (241646,724813,483163) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=47, convex hull=36, v0=193148) After retessellation of defect 27 (v0=193148), euler #=-3 (241648,724832,483181) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=57, convex hull=58, v0=209409) After retessellation of defect 28 (v0=209409), euler #=-2 (241656,724880,483222) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=24, convex hull=66, v0=218880) After retessellation of defect 29 (v0=218880), euler #=-1 (241662,724927,483264) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=21, convex hull=58, v0=219009) After retessellation of defect 30 (v0=219009), euler #=0 (241669,724969,483300) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=7, convex hull=25, v0=225914) After retessellation of defect 31 (v0=225914), euler #=1 (241670,724981,483312) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=26, convex hull=60, v0=240184) After retessellation of defect 32 (v0=240184), euler #=2 (241676,725022,483348) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.72 +- 0.17 (0.10-->13.80) (max @ vno 1411 --> 9364) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.72 +- 0.17 (0.10-->13.80) (max @ vno 1411 --> 9364) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 116 mutations (41.0%), 167 crossovers (59.0%), 31 vertices were eliminated building final representation... 2822 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=241676, nf=483348, ne=725022, g=0) writing corrected surface to /out/sourcedata/freesurfer/sub-3001/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 141 intersecting 001: 33 intersecting 002: 10 intersecting terminating search with 0 intersecting topology fixing took 1.8 minutes FSRUNTIME@ mris_fix_topology rh 0.0296 hours 16 threads #VMPC# mris_fix_topology VmPeak 2611740 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 241676 - 725022 + 483348 = 2 --> 0 holes F =2V-4: 483348 = 483352-4 (0) 2E=3F: 1450044 = 1450044 (0) total defect index = 0 Fri Sep 22 16:51:17 UTC 2023 setenv SUBJECTS_DIR /out/sourcedata/freesurfer cd /out/sourcedata/freesurfer/sub-3001/scripts /opt/freesurfer/bin/defect2seg --s sub-3001 --rh-only --cortex freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 defect2seg 7.3.2 Linux b1acb5b95ebd 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux pid 1671 mri_label2label --label-cortex /out/sourcedata/freesurfer/sub-3001/surf/rh.orig.nofix /out/sourcedata/freesurfer/sub-3001/mri/aseg.presurf.mgz 0 /out/sourcedata/freesurfer/sub-3001/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 55 non-cortical segments detected only using segment with 12221 vertices erasing segment 0 (vno[0] = 2444) erasing segment 1 (vno[0] = 4601) erasing segment 2 (vno[0] = 6537) erasing segment 3 (vno[0] = 6599) erasing segment 4 (vno[0] = 8385) erasing segment 5 (vno[0] = 9647) erasing segment 6 (vno[0] = 10376) erasing segment 7 (vno[0] = 12351) erasing segment 8 (vno[0] = 16679) erasing segment 9 (vno[0] = 30856) erasing segment 10 (vno[0] = 32062) erasing segment 11 (vno[0] = 43418) erasing segment 12 (vno[0] = 45096) erasing segment 13 (vno[0] = 46792) erasing segment 14 (vno[0] = 50045) erasing segment 15 (vno[0] = 58515) erasing segment 16 (vno[0] = 59183) erasing segment 17 (vno[0] = 60867) erasing segment 18 (vno[0] = 64163) erasing segment 19 (vno[0] = 65550) erasing segment 20 (vno[0] = 66995) erasing segment 21 (vno[0] = 68314) erasing segment 23 (vno[0] = 77447) erasing segment 24 (vno[0] = 77716) erasing segment 25 (vno[0] = 85209) erasing segment 26 (vno[0] = 90936) erasing segment 27 (vno[0] = 94216) erasing segment 28 (vno[0] = 96360) erasing segment 29 (vno[0] = 97969) erasing segment 30 (vno[0] = 101298) erasing segment 31 (vno[0] = 101382) erasing segment 32 (vno[0] = 109367) erasing segment 33 (vno[0] = 114264) erasing segment 34 (vno[0] = 114289) erasing segment 35 (vno[0] = 117082) erasing segment 36 (vno[0] = 123763) erasing segment 37 (vno[0] = 123824) erasing segment 38 (vno[0] = 142070) erasing segment 39 (vno[0] = 147684) erasing segment 40 (vno[0] = 155168) erasing segment 41 (vno[0] = 161380) erasing segment 42 (vno[0] = 162859) erasing segment 43 (vno[0] = 164197) erasing segment 44 (vno[0] = 165841) erasing segment 45 (vno[0] = 167214) erasing segment 46 (vno[0] = 167562) erasing segment 47 (vno[0] = 168932) erasing segment 48 (vno[0] = 172007) erasing segment 49 (vno[0] = 174519) erasing segment 50 (vno[0] = 174709) erasing segment 51 (vno[0] = 174743) erasing segment 52 (vno[0] = 175804) erasing segment 53 (vno[0] = 196050) erasing segment 54 (vno[0] = 209421) mri_label2vol --defects /out/sourcedata/freesurfer/sub-3001/surf/rh.orig.nofix /out/sourcedata/freesurfer/sub-3001/surf/rh.defect_labels /out/sourcedata/freesurfer/sub-3001/mri/orig.mgz 2000 0 /out/sourcedata/freesurfer/sub-3001/mri/rh.surface.defects.mgz /out/sourcedata/freesurfer/sub-3001/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /out/sourcedata/freesurfer/sub-3001/label/rh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=2000, merge=0 Writing to /out/sourcedata/freesurfer/sub-3001/mri/rh.surface.defects.mgz mris_defects_pointset -s /out/sourcedata/freesurfer/sub-3001/surf/rh.orig.nofix -d /out/sourcedata/freesurfer/sub-3001/surf/rh.defect_labels -o /out/sourcedata/freesurfer/sub-3001/surf/rh.defects.pointset --label /out/sourcedata/freesurfer/sub-3001/label/rh.nofix.cortex.label Reading in surface /out/sourcedata/freesurfer/sub-3001/surf/rh.orig.nofix Reading in defect segmentation /out/sourcedata/freesurfer/sub-3001/surf/rh.defect_labels Reading in label /out/sourcedata/freesurfer/sub-3001/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 1380608 mris_defects_pointset done Started at Fri Sep 22 16:51:17 UTC 2023 Ended at Fri Sep 22 16:51:49 UTC 2023 Defect2seg-Run-Time-Sec 32 Defect2seg-Run-Time-Min 0.64 Defect2seg-Run-Time-Hours 0.01 tkmeditfv sub-3001 brain.finalsurfs.mgz -defect defect2seg Done mris_remesh --remesh --iters 3 --input /out/sourcedata/freesurfer/sub-3001/surf/rh.orig.premesh --output /out/sourcedata/freesurfer/sub-3001/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.57334 remeshing to edge length 0.57334 with 3 iterations avg qual before : 0.888938 after: 0.97161 Removing intersections Remeshed surface quality stats nv0 = 241676 nv = 252437 1.04453 Area 504870 0.19693 0.02175 0.043036 0.3095 Corner 1514610 60.00000 8.74139 15.175693 148.5474 Edge 757305 0.68072 0.06595 0.354467 1.0044 Hinge 757305 8.13048 8.59888 0.000000 128.0165 mris_remesh done /out/sourcedata/freesurfer/sub-3001/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats rh Fri Sep 22 16:52:50 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.2 cd /out/sourcedata/freesurfer/sub-3001/mri setenv SUBJECTS_DIR /out/sourcedata/freesurfer mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 477889 voxels (1.46%) border gray 499061 voxels (1.52%) 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=23898, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (104.0): 103.7 +- 5.5 [70.0 --> 110.0] CCS GM (86.0) : 85.8 +- 8.8 [30.0 --> 110.0] white_mean = 103.683 +/- 5.49771, gray_mean = 85.8245 +/- 8.79055 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=203 nbins=204 intensity peaks found at WM=109+-2.6, GM=80+-7.0 white_mode = 109, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 71.2 (was 70.000000) setting MAX_BORDER_WHITE to 114.5 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 62.4 (was 40.000000) setting MAX_GRAY to 103.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 71.2 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 53.6 (was 40.000000) When placing the white surface white_border_hi = 114.498; white_border_low = 80; white_outside_low = 71.2094; white_inside_hi = 120; white_outside_hi = 114.498; When placing the pial surface pial_border_hi = 71.2094; pial_border_low = 53.6284; pial_outside_low = 10; pial_inside_hi = 103.502; pial_outside_hi = 66.8142; #VMPC# mris_autodet_gwstats VmPeak 1512624 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc rh Fri Sep 22 16:52:56 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 16 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /out/sourcedata/freesurfer/sub-3001/mri setenv SUBJECTS_DIR /out/sourcedata/freesurfer mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 16 --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 504870 0.17954 0.03903 0.000411 0.4149 Corner 1514610 60.00000 8.81784 6.359133 153.4047 Edge 757305 0.64670 0.08667 0.034055 1.0994 Hinge 757305 5.56045 5.67042 0.000017 159.2582 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23898, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=10543, nmarked2=105, nripped=10543 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 126219: xyz = (47.3951,-0.34019,35.6753) oxyz = (47.3951,-0.34019,35.6753) wxzy = (47.3951,-0.34019,35.6753) pxyz = (0,0,0) CBVO Creating mask 252437 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=10543 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=10543, nmarked2=105, nripped=10543 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 = 114.4977110; border_low = 80.0000000; outside_low = 71.2094500; outside_hi = 114.4977110; sigma = 2; max_thickness = 10; step_size=0.4; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=252437 Gdiag_no=-1 vno start=0, stop=252437 Replacing 255s with 0s #SI# sigma=2 had to be increased for 183 vertices, nripped=10543 mean border=91.0, 80 (80) missing vertices, mean dist 0.3 [0.4 (%31.5)->0.6 (%68.5))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0403 min Finding expansion regions mean absolute distance = 0.56 +- 0.72 10386 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=b1acb, 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=2817581.0, rms=7.366 001: dt: 0.5000, sse=1422327.0, rms=5.058 (31.324%) 002: dt: 0.5000, sse=843046.3, rms=3.687 (27.106%) 003: dt: 0.5000, sse=575195.6, rms=2.832 (23.194%) 004: dt: 0.5000, sse=447556.1, rms=2.324 (17.950%) 005: dt: 0.5000, sse=393781.6, rms=2.061 (11.291%) 006: dt: 0.5000, sse=381105.7, rms=1.968 (4.541%) rms = 1.9246/1.9678, sse=372009.3/381105.7, time step reduction 1 of 3 to 0.250 0 0 1 007: dt: 0.5000, sse=372009.3, rms=1.925 (2.194%) 008: dt: 0.2500, sse=235529.0, rms=0.921 (52.135%) 009: dt: 0.2500, sse=226989.7, rms=0.778 (15.565%) rms = 0.7455/0.7778, sse=223709.2/226989.7, time step reduction 2 of 3 to 0.125 0 0 1 010: dt: 0.2500, sse=223709.2, rms=0.746 (4.148%) rms = 0.7139/0.7455, sse=228173.4/223709.2, time step reduction 3 of 3 to 0.062 0 1 1 011: dt: 0.1250, sse=228173.4, rms=0.714 (4.239%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=10543 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 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 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=10999, nmarked2=230, nripped=10999 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 = 114.4977110; border_low = 80.0000000; outside_low = 71.2094500; outside_hi = 114.4977110; sigma = 1; max_thickness = 10; step_size=0.4; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=252437 Gdiag_no=-1 vno start=0, stop=252437 Replacing 255s with 0s #SI# sigma=1 had to be increased for 79 vertices, nripped=10999 mean border=93.5, 104 (17) missing vertices, mean dist -0.2 [0.4 (%77.2)->0.2 (%22.8))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0279 min Finding expansion regions mean absolute distance = 0.32 +- 0.49 11471 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=b1acb, 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=989061.2, rms=3.944 012: dt: 0.5000, sse=529285.4, rms=2.455 (37.757%) 013: dt: 0.5000, sse=434162.3, rms=1.999 (18.547%) 014: dt: 0.5000, sse=389980.1, rms=1.753 (12.324%) rms = 1.7100/1.7530, sse=377729.2/389980.1, time step reduction 1 of 3 to 0.250 0 0 1 015: dt: 0.5000, sse=377729.2, rms=1.710 (2.452%) 016: dt: 0.2500, sse=272608.9, rms=0.803 (53.031%) 017: dt: 0.2500, sse=260896.7, rms=0.651 (18.968%) rms = 0.6073/0.6508, sse=260265.4/260896.7, time step reduction 2 of 3 to 0.125 0 0 1 018: dt: 0.2500, sse=260265.4, rms=0.607 (6.693%) rms = 0.5761/0.6073, sse=258957.7/260265.4, time step reduction 3 of 3 to 0.062 0 0 1 019: dt: 0.1250, sse=258957.7, rms=0.576 (5.127%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=10999 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=11090, nmarked2=230, nripped=11090 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 = 114.4977110; border_low = 80.0000000; outside_low = 71.2094500; outside_hi = 114.4977110; sigma = 0.5; max_thickness = 10; step_size=0.4; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=252437 Gdiag_no=-1 vno start=0, stop=252437 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 81 vertices, nripped=11090 mean border=94.8, 105 (8) missing vertices, mean dist -0.1 [0.3 (%61.0)->0.1 (%39.0))] %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0163 min Finding expansion regions mean absolute distance = 0.20 +- 0.34 8764 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=b1acb, 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=429753.7, rms=2.010 020: dt: 0.5000, sse=328836.4, rms=1.349 (32.868%) rms = 1.3122/1.3495, sse=342729.1/328836.4, time step reduction 1 of 3 to 0.250 0 1 1 021: dt: 0.5000, sse=342729.1, rms=1.312 (2.762%) 022: dt: 0.2500, sse=275447.2, rms=0.660 (49.682%) 023: dt: 0.2500, sse=263265.9, rms=0.570 (13.601%) rms = 0.5568/0.5705, sse=265945.3/263265.9, time step reduction 2 of 3 to 0.125 0 1 1 024: dt: 0.2500, sse=265945.3, rms=0.557 (2.403%) rms = 0.5334/0.5568, sse=269221.2/265945.3, time step reduction 3 of 3 to 0.062 0 1 1 025: dt: 0.1250, sse=269221.2, rms=0.533 (4.205%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=11090 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=11135, nmarked2=231, nripped=11135 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 = 114.4977110; border_low = 80.0000000; outside_low = 71.2094500; outside_hi = 114.4977110; sigma = 0.25; max_thickness = 10; step_size=0.4; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=252437 Gdiag_no=-1 vno start=0, stop=252437 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 88 vertices, nripped=11135 mean border=95.3, 116 (6) missing vertices, mean dist -0.0 [0.2 (%42.8)->0.1 (%57.2))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0111 min Finding expansion regions mean absolute distance = 0.17 +- 0.29 7246 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=b1acb, 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=299682.8, rms=0.991 026: dt: 0.5000, sse=283646.9, rms=0.740 (25.307%) rms = 0.8613/0.7404, sse=278928.0/283646.9, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 027: dt: 0.2500, sse=260399.5, rms=0.543 (26.621%) 028: dt: 0.2500, sse=256470.0, rms=0.476 (12.433%) rms = 0.4667/0.4758, sse=252768.9/256470.0, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=252768.9, rms=0.467 (1.897%) rms = 0.4373/0.4667, sse=252666.8/252768.9, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=252666.8, rms=0.437 (6.312%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 3.79 minutes #VMPC# mris_place_surfaces VmPeak 4215072 mris_place_surface done #-------------------------------------------- #@# CortexLabel rh Fri Sep 22 16:56:53 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/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 42 non-cortical segments detected only using segment with 12899 vertices erasing segment 0 (vno[0] = 3500) erasing segment 1 (vno[0] = 4825) erasing segment 2 (vno[0] = 5453) erasing segment 3 (vno[0] = 5637) erasing segment 4 (vno[0] = 7212) erasing segment 5 (vno[0] = 7320) erasing segment 6 (vno[0] = 9083) erasing segment 7 (vno[0] = 9327) erasing segment 8 (vno[0] = 12931) erasing segment 9 (vno[0] = 13048) erasing segment 10 (vno[0] = 26215) erasing segment 11 (vno[0] = 26274) erasing segment 12 (vno[0] = 37443) erasing segment 13 (vno[0] = 41793) erasing segment 14 (vno[0] = 49204) erasing segment 15 (vno[0] = 53865) erasing segment 16 (vno[0] = 54034) erasing segment 17 (vno[0] = 55924) erasing segment 18 (vno[0] = 57685) erasing segment 20 (vno[0] = 65693) erasing segment 21 (vno[0] = 67350) erasing segment 22 (vno[0] = 73916) erasing segment 23 (vno[0] = 80319) erasing segment 24 (vno[0] = 83660) erasing segment 25 (vno[0] = 85198) erasing segment 26 (vno[0] = 87822) erasing segment 27 (vno[0] = 97833) erasing segment 28 (vno[0] = 100264) erasing segment 29 (vno[0] = 103466) erasing segment 30 (vno[0] = 106105) erasing segment 31 (vno[0] = 107650) erasing segment 32 (vno[0] = 107696) erasing segment 33 (vno[0] = 115606) erasing segment 34 (vno[0] = 140554) erasing segment 35 (vno[0] = 145449) erasing segment 36 (vno[0] = 150294) erasing segment 37 (vno[0] = 152625) erasing segment 38 (vno[0] = 209769) erasing segment 39 (vno[0] = 209807) erasing segment 40 (vno[0] = 218900) erasing segment 41 (vno[0] = 237246) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Fri Sep 22 16:57:17 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/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 47 non-cortical segments detected only using segment with 9866 vertices erasing segment 0 (vno[0] = 3500) erasing segment 1 (vno[0] = 4825) erasing segment 2 (vno[0] = 5453) erasing segment 3 (vno[0] = 5637) erasing segment 4 (vno[0] = 7212) erasing segment 5 (vno[0] = 7320) erasing segment 6 (vno[0] = 9083) erasing segment 7 (vno[0] = 9327) erasing segment 8 (vno[0] = 12931) erasing segment 9 (vno[0] = 13048) erasing segment 10 (vno[0] = 26215) erasing segment 11 (vno[0] = 26274) erasing segment 12 (vno[0] = 37443) erasing segment 13 (vno[0] = 41793) erasing segment 14 (vno[0] = 49204) erasing segment 15 (vno[0] = 53865) erasing segment 16 (vno[0] = 54034) erasing segment 17 (vno[0] = 55924) erasing segment 18 (vno[0] = 57685) erasing segment 20 (vno[0] = 65693) erasing segment 21 (vno[0] = 67350) erasing segment 22 (vno[0] = 73916) erasing segment 23 (vno[0] = 77782) erasing segment 24 (vno[0] = 80319) erasing segment 25 (vno[0] = 80755) erasing segment 26 (vno[0] = 83660) erasing segment 27 (vno[0] = 85198) erasing segment 28 (vno[0] = 87822) erasing segment 29 (vno[0] = 90768) erasing segment 30 (vno[0] = 97833) erasing segment 31 (vno[0] = 100264) erasing segment 32 (vno[0] = 103466) erasing segment 33 (vno[0] = 106105) erasing segment 34 (vno[0] = 107650) erasing segment 35 (vno[0] = 107696) erasing segment 36 (vno[0] = 124248) erasing segment 37 (vno[0] = 130545) erasing segment 38 (vno[0] = 136859) erasing segment 39 (vno[0] = 139377) erasing segment 40 (vno[0] = 140554) erasing segment 41 (vno[0] = 145449) erasing segment 42 (vno[0] = 150294) erasing segment 43 (vno[0] = 152625) erasing segment 44 (vno[0] = 210413) erasing segment 45 (vno[0] = 218900) erasing segment 46 (vno[0] = 237246) #-------------------------------------------- #@# Smooth2 rh Fri Sep 22 16:57:41 UTC 2023 /out/sourcedata/freesurfer/sub-3001/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... #-------------------------------------------- #@# Inflation2 rh Fri Sep 22 16:57:48 UTC 2023 /out/sourcedata/freesurfer/sub-3001/scripts mris_inflate -n 50 ../surf/rh.smoothwm ../surf/rh.inflated niterations = 50 Reading ../surf/rh.smoothwm avg radius = 48.6 mm, total surface area = 99145 mm^2 resetting # of iterations to 63 for highres volume step 000: RMS=0.145 (target=0.015) step 005: RMS=0.103 (target=0.015) step 010: RMS=0.077 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.029 (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=0.018 (target=0.015) step 065: RMS=0.017 (target=0.015) step 070: RMS=0.016 (target=0.015) step 075: RMS=0.015 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 353.684350 mris_inflate stimesec 5.936619 mris_inflate ru_maxrss 386816 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 55831 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 44470 mris_inflate ru_nivcsw 54984 #-------------------------------------------- #@# Curv .H and .K rh Fri Sep 22 16:58:14 UTC 2023 /out/sourcedata/freesurfer/sub-3001/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 38.371*4pi (482.187) --> -37 handles ICI = 203.7, FI = 1836.3, variation=29326.807 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H Linux b1acb5b95ebd 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-3001 exited with ERRORS at Fri Sep 22 16:58:18 UTC 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Mon Sep 25 02:10:16 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001 setenv SUBJECTS_DIR /out/sourcedata/freesurfer /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 16 -subjid sub-3001 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nosmooth2 -noinflate2 subjid sub-3001 setenv SUBJECTS_DIR /out/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 Linux 7d3c530edba1 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 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 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 514130 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 2.7Gi 47Gi 11Mi 75Gi 121Gi Swap: 32Gi 0B 32Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:16-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2023/09/25-02:10:17-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: root Machine: 7d3c530edba1 Platform: Linux PlatformVersion: 5.10.16.3-microsoft-standard-WSL2 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 /opt/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# AutoDetGWStats rh Mon Sep 25 02:10:17 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh Update not needed #-------------------------------------------- #@# WhitePreAparc rh Mon Sep 25 02:10:17 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 16 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Update not needed #-------------------------------------------- #@# CortexLabel rh Mon Sep 25 02:10:17 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Update not needed #-------------------------------------------- #@# CortexLabel+HipAmyg rh Mon Sep 25 02:10:17 UTC 2023 cd /out/sourcedata/freesurfer/sub-3001/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Update not needed #-------------------------------------------- #@# Curv .H and .K rh Mon Sep 25 02:10:17 UTC 2023 /out/sourcedata/freesurfer/sub-3001/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 38.371*4pi (482.187) --> -37 handles ICI = 203.7, FI = 1836.3, variation=29326.807 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H Linux 7d3c530edba1 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-3001 exited with ERRORS at Mon Sep 25 02:10:22 UTC 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting