Tue Dec 6 17:43:29 UTC 2022 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234 subjid LAB_S01541_standard_20180307_4541_03072018 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 FREESURFER_HOME /usr/local/tools/freesurfer Actual FREESURFER_HOME /usr/local/tools/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 65536 kbytes maxproc unlimited maxlocks unlimited maxsignal 2061951 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 503Gi 5.7Gi 20Gi 4.0Mi 476Gi 495Gi Swap: 2.0Gi 0.0Ki 2.0Gi ######################################## 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: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic 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: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:29-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic 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: 2022/12/06-17:43:30-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/tools/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/tools/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Dec 6 17:43:30 UTC 2022 Found 1 runs /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig/001.mgz /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/rawavg.mgz mri_info /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 146 voxel sizes: 0.937500, 0.937500, 1.200000 type: FLOAT (3) fov: 240.000 dof: 1 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -87.6, zend: 87.6 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 0.0000, y_r = 0.0000, z_r = 1.0000, c_r = 2.4187 : x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = 27.4940 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 41.9060 talairach xfm : Orientation : PIR Primary Slice Direction: sagittal voxel to ras transform: 0.0000 0.0000 1.2000 -85.1813 -0.9375 0.0000 0.0000 147.4940 0.0000 -0.9375 0.0000 161.9060 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1.05469 ras to voxel transform: 0.0000 -1.0667 0.0000 157.3269 0.0000 0.0000 -1.0667 172.6997 0.8333 0.0000 0.0000 70.9844 0.0000 0.0000 0.0000 1.0000 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018 mri_convert /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/rawavg.mgz /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz --conform mri_convert /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/rawavg.mgz /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz --conform reading from /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 5287.03 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz... mri_add_xform_to_header -c /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/transforms/talairach.xfm /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz INFO: extension is mgz mri_info /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz orig.mgz ======================================== Volume information for /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 2.4187 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 27.4940 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 41.9060 talairach xfm : /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 130.4187 0.0000 0.0000 1.0000 -100.5060 0.0000 -1.0000 0.0000 169.9060 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 130.4187 -0.0000 -0.0000 -1.0000 169.9060 -0.0000 1.0000 -0.0000 100.5060 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Tue Dec 6 17:43:37 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri /usr/local/tools/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.3.2 Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Tue Dec 6 17:43:38 UTC 2022 tmpdir is ./tmp.mri_nu_correct.mni.28234 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.28234/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.28234/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.28234/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.28234/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Dec 6 17:47:18 UTC 2022 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Tue Dec 6 17:47:19 UTC 2022 Ended at Tue Dec 6 17:47:42 UTC 2022 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/tools/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.3.2 --src: orig.mgz src image (geometry). --trg: /usr/local/tools/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.16925 -0.01182 0.03532 -2.89507; -0.03304 1.10708 0.20999 -45.59377; 0.00521 -0.35877 1.27174 -22.33403; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Tue Dec 6 17:47:45 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7581, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/tools/freesurfer/bin/extract_talairach_avi_QA.awk /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/transforms/talairach_avi.log tal_QC_AZS /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/transforms/talairach_avi.log TalAviQA: 0.97009 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Tue Dec 6 17:47:45 UTC 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri /usr/local/tools/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.3.2 Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Tue Dec 6 17:47:45 UTC 2022 tmpdir is ./tmp.mri_nu_correct.mni.28472 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.28472/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.28472/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.28472/ones.mgz 7.3.2 cwd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.28472/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.28472/ones.mgz sysname Linux hostname 3c46017221f4 machine x86_64 user sibis input ./tmp.mri_nu_correct.mni.28472/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.28472/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.28472/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28472/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28472/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28472/input.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28472/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28472/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28472/input.mean.dat sysname Linux hostname 3c46017221f4 machine x86_64 user sibis whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28472/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.28472/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28472/ones.mgz --i ./tmp.mri_nu_correct.mni.28472/nu0.mgz --sum ./tmp.mri_nu_correct.mni.28472/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28472/output.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28472/ones.mgz --i ./tmp.mri_nu_correct.mni.28472/nu0.mgz --sum ./tmp.mri_nu_correct.mni.28472/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28472/output.mean.dat sysname Linux hostname 3c46017221f4 machine x86_64 user sibis whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28472/ones.mgz Loading ./tmp.mri_nu_correct.mni.28472/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.28472/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.28472/nu0.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mgz mul .92574756760220037038 Saving result to './tmp.mri_nu_correct.mni.28472/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.28472/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.28472/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.28472/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 21, i2 = 98 #mri_make_uchar# mapping 50 234 to 3 110 : b -26.7545 m 0.585381 : thresh 45.7045 maxsat 481.318 : nzero 15227886 nsat 0 Tue Dec 6 17:52:21 UTC 2022 mri_nu_correct.mni done mri_add_xform_to_header -c /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Dec 6 17:52:21 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.16925 -0.01182 0.03532 -2.89507; -0.03304 1.10708 0.20999 -45.59377; 0.00521 -0.35877 1.27174 -22.33403; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 62 (62), valley at 22 (22) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 65 (65), valley at 22 (22) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 48 seconds. Started at Tue Dec 6 17:43:29 UTC 2022 Ended at Tue Dec 6 17:54:10 UTC 2022 #@#%# recon-all-run-time-hours 0.178 recon-all -s LAB_S01541_standard_20180307_4541_03072018 finished without error at Tue Dec 6 17:54:10 UTC 2022 #New# invocation of recon-all Tue Dec 6 17:54:11 UTC 2022 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon2 -autorecon3 -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -no-fix-with-ga -rng-seed 1234 subjid LAB_S01541_standard_20180307_4541_03072018 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 FREESURFER_HOME /usr/local/tools/freesurfer Actual FREESURFER_HOME /usr/local/tools/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 65536 kbytes maxproc unlimited maxlocks unlimited maxsignal 2061951 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 503Gi 5.7Gi 20Gi 4.0Mi 476Gi 495Gi Swap: 2.0Gi 0.0Ki 2.0Gi ######################################## 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: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic 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: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic 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: 2022/12/06-17:54:11-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/tools/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/tools/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Dec 6 17:54:11 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (63, 83, 38) --> (192, 206, 210) finding center of left hemi white matter using (106, 124, 124) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (90,109,103) --> (121, 139,145) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 111 +- 3.4 after smoothing, mri peak at 111, scaling input intensities by 0.964 scaling channel 0 by 0.963964 initial log_p = -4.400 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.097844 @ (-10.526, -31.579, -10.526) max log p = -3.723460 @ (5.263, 5.263, -5.263) max log p = -3.642858 @ (2.632, 2.632, -2.632) max log p = -3.600203 @ (-1.316, 1.316, 1.316) max log p = -3.584838 @ (0.658, 0.658, 0.658) max log p = -3.584838 @ (0.000, 0.000, 0.000) max log p = -3.584838 @ (0.000, 0.000, 0.000) max log p = -3.584838 @ (0.000, 0.000, 0.000) Found translation: (-3.3, -21.7, -16.4): log p = -3.585 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.392, old_max_log_p =-3.585 (thresh=-3.6) 1.06375 0.00000 0.00000 -11.58282; 0.00000 1.11081 0.22000 -64.14604; 0.00000 -0.31997 0.88261 50.47349; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.392, old_max_log_p =-3.392 (thresh=-3.4) 1.06375 0.00000 0.00000 -11.58282; 0.00000 1.11081 0.22000 -64.14604; 0.00000 -0.31997 0.88261 50.47349; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 28 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.267, old_max_log_p =-3.392 (thresh=-3.4) 1.10061 0.07149 0.03863 -30.84943; -0.06682 1.09856 0.09512 -39.47795; -0.03421 -0.17280 0.92053 25.80363; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.264, old_max_log_p =-3.267 (thresh=-3.3) 1.10061 0.07149 0.03863 -30.84943; -0.06682 1.09856 0.09512 -39.47795; -0.03485 -0.17604 0.93779 24.31081; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.240, old_max_log_p =-3.264 (thresh=-3.3) 1.10079 0.05979 0.00617 -24.44173; -0.04949 1.10076 0.10317 -42.53046; 0.00186 -0.18189 0.93446 21.70440; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.238, old_max_log_p =-3.240 (thresh=-3.2) 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.238 (old=-4.400) transform before final EM align: 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 792928 FSRUNTIME@ mri_em_register 0.0581 hours 4 threads registration took 3 minutes and 29 seconds. #-------------------------------------- #@# CA Normalize Tue Dec 6 17:57:40 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (63, 83, 38) --> (192, 206, 210) finding center of left hemi white matter using (106, 124, 124) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,109,103) --> (121, 139,145) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 111 +- 3.4 after smoothing, mri peak at 111, scaling input intensities by 0.964 scaling channel 0 by 0.963964 using 246437 sample points... INFO: compute sample coordinates transform 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 82, 34) --> (189, 187, 212) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 107.0 5 of 8260 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 82, 34) --> (131, 186, 213) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 107.0 1 of 8182 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 158, 63) --> (171, 201, 121) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 107.0 400 of 644 (62.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 158, 61) --> (127, 198, 123) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 107.0 193 of 510 (37.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 151, 102) --> (143, 214, 134) Brain_Stem: limiting intensities to 103.0 --> 107.0 660 of 889 (74.2%) samples deleted using 18485 total control points for intensity normalization... bias field = 1.009 +- 0.056 122 of 17226 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 82, 34) --> (189, 187, 212) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 4 of 8276 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 82, 34) --> (131, 186, 213) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 111.0 1 of 8184 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 158, 63) --> (171, 201, 121) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 111.0 39 of 661 (5.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 158, 61) --> (127, 198, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 111.0 28 of 544 (5.1%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 151, 102) --> (143, 214, 134) Brain_Stem: limiting intensities to 88.0 --> 111.0 235 of 934 (25.2%) samples deleted using 18599 total control points for intensity normalization... bias field = 1.012 +- 0.047 54 of 18217 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 82, 34) --> (189, 187, 212) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 115.0 8 of 8292 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 82, 34) --> (131, 186, 213) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 115.0 1 of 8219 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 158, 63) --> (171, 201, 121) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 115.0 185 of 675 (27.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 158, 61) --> (127, 198, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 115.0 149 of 530 (28.1%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 151, 102) --> (143, 214, 134) Brain_Stem: limiting intensities to 88.0 --> 115.0 377 of 959 (39.3%) samples deleted using 18675 total control points for intensity normalization... bias field = 1.008 +- 0.040 57 of 17773 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 13 seconds. #-------------------------------------- #@# SubCort Seg Tue Dec 6 17:58:54 UTC 2022 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname 3c46017221f4 machine x86_64 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s LAB_S01541_standard_20180307_4541_03072018 exited with ERRORS at Tue Dec 6 17:59:08 UTC 2022 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Tue Dec 6 17:59:08 UTC 2022 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon2 -autorecon3 -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -no-fix-with-ga -use-new-fixer -rng-seed 1000 subjid LAB_S01541_standard_20180307_4541_03072018 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 FREESURFER_HOME /usr/local/tools/freesurfer Actual FREESURFER_HOME /usr/local/tools/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 65536 kbytes maxproc unlimited maxlocks unlimited maxsignal 2061951 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 503Gi 5.7Gi 20Gi 4.0Mi 476Gi 495Gi Swap: 2.0Gi 0.0Ki 2.0Gi ######################################## 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: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic 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: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic 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: 2022/12/06-17:59:08-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: sibis Machine: 3c46017221f4 Platform: Linux PlatformVersion: 4.15.0-196-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/tools/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/tools/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Dec 6 17:59:09 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (63, 83, 38) --> (192, 206, 210) finding center of left hemi white matter using (106, 124, 124) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (90,109,103) --> (121, 139,145) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 111 +- 3.4 after smoothing, mri peak at 111, scaling input intensities by 0.964 scaling channel 0 by 0.963964 initial log_p = -4.400 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.097844 @ (-10.526, -31.579, -10.526) max log p = -3.723460 @ (5.263, 5.263, -5.263) max log p = -3.642858 @ (2.632, 2.632, -2.632) max log p = -3.600203 @ (-1.316, 1.316, 1.316) max log p = -3.584838 @ (0.658, 0.658, 0.658) max log p = -3.584838 @ (0.000, 0.000, 0.000) max log p = -3.584838 @ (0.000, 0.000, 0.000) max log p = -3.584838 @ (0.000, 0.000, 0.000) Found translation: (-3.3, -21.7, -16.4): log p = -3.585 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.392, old_max_log_p =-3.585 (thresh=-3.6) 1.06375 0.00000 0.00000 -11.58282; 0.00000 1.11081 0.22000 -64.14604; 0.00000 -0.31997 0.88261 50.47349; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 28 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.392, old_max_log_p =-3.392 (thresh=-3.4) 1.06375 0.00000 0.00000 -11.58282; 0.00000 1.11081 0.22000 -64.14604; 0.00000 -0.31997 0.88261 50.47349; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.267, old_max_log_p =-3.392 (thresh=-3.4) 1.10061 0.07149 0.03863 -30.84943; -0.06682 1.09856 0.09512 -39.47795; -0.03421 -0.17280 0.92053 25.80363; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.264, old_max_log_p =-3.267 (thresh=-3.3) 1.10061 0.07149 0.03863 -30.84943; -0.06682 1.09856 0.09512 -39.47795; -0.03485 -0.17604 0.93779 24.31081; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.240, old_max_log_p =-3.264 (thresh=-3.3) 1.10079 0.05979 0.00617 -24.44173; -0.04949 1.10076 0.10317 -42.53046; 0.00186 -0.18189 0.93446 21.70440; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 25 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.238, old_max_log_p =-3.240 (thresh=-3.2) 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.238 (old=-4.400) transform before final EM align: 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 792924 FSRUNTIME@ mri_em_register 0.0563 hours 4 threads registration took 3 minutes and 23 seconds. #-------------------------------------- #@# CA Normalize Tue Dec 6 18:02:31 UTC 2022 /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (63, 83, 38) --> (192, 206, 210) finding center of left hemi white matter using (106, 124, 124) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,109,103) --> (121, 139,145) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 111 +- 3.4 after smoothing, mri peak at 111, scaling input intensities by 0.964 scaling channel 0 by 0.963964 using 246437 sample points... INFO: compute sample coordinates transform 1.09981 0.05221 -0.00232 -21.77925; -0.04043 1.09993 0.10304 -43.56568; 0.01086 -0.18118 0.93338 20.56940; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 82, 34) --> (189, 187, 212) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 107.0 5 of 8260 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 82, 34) --> (131, 186, 213) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 107.0 1 of 8182 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 158, 63) --> (171, 201, 121) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 107.0 400 of 644 (62.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 158, 61) --> (127, 198, 123) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 107.0 193 of 510 (37.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 151, 102) --> (143, 214, 134) Brain_Stem: limiting intensities to 103.0 --> 107.0 660 of 889 (74.2%) samples deleted using 18485 total control points for intensity normalization... bias field = 1.009 +- 0.056 122 of 17226 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 82, 34) --> (189, 187, 212) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 4 of 8276 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 82, 34) --> (131, 186, 213) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 111.0 1 of 8184 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 158, 63) --> (171, 201, 121) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 111.0 39 of 661 (5.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 158, 61) --> (127, 198, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 111.0 28 of 544 (5.1%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 151, 102) --> (143, 214, 134) Brain_Stem: limiting intensities to 88.0 --> 111.0 235 of 934 (25.2%) samples deleted using 18599 total control points for intensity normalization... bias field = 1.012 +- 0.047 54 of 18217 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 82, 34) --> (189, 187, 212) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 115.0 8 of 8292 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 82, 34) --> (131, 186, 213) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 115.0 1 of 8219 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 158, 63) --> (171, 201, 121) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 115.0 185 of 675 (27.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 158, 61) --> (127, 198, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 115.0 149 of 530 (28.1%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 151, 102) --> (143, 214, 134) Brain_Stem: limiting intensities to 88.0 --> 115.0 377 of 959 (39.3%) samples deleted using 18675 total control points for intensity normalization... bias field = 1.008 +- 0.040 57 of 17773 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 19 seconds. #-------------------------------------- #@# SubCort Seg Tue Dec 6 18:03:51 UTC 2022 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname 3c46017221f4 machine x86_64 setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform Linux 3c46017221f4 4.15.0-196-generic #207-Ubuntu SMP Thu Oct 27 21:24:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s LAB_S01541_standard_20180307_4541_03072018 exited with ERRORS at Tue Dec 6 18:04:09 UTC 2022 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting