Fri Apr 10 06:43:52 PM JST 2026 cd /mnt/data4/test/sub-01 setenv SUBJECTS_DIR /mnt/data4/test /usr/local/freesurfer/8.1.0/bin/recon-all -all -subjid sub-01 -i /mnt/data4/Subjects/T1_MPR.nii -T2 /mnt/data4/Subjects/T2_SPC.nii -T2pial -hires -expert /home/kami/expert.opts -xopts-overwrite -openmp 8 subjid sub-01 setenv SUBJECTS_DIR /mnt/data4/test FREESURFER_HOME /usr/local/freesurfer/8.1.0 Actual FREESURFER_HOME /usr/local/freesurfer/8.1.0 build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 8188644 kbytes maxproc 255557 maxlocks unlimited maxsignal 255557 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 62Gi 1.5Gi 57Gi 7.0Mi 3.5Gi 60Gi Swap: 2.0Gi 0B 2.0Gi ######################################## program versions used 8.1.0 (freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed) 8.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 8.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 8.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 mris_convert -all-info ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:52-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 8.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2026/04/10-09:43:53-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: kami Machine: kami-image3 Platform: Linux PlatformVersion: 6.8.0-107-generic CompilerName: GCC CompilerVersion: 8.4.0 ####################################### GCADIR /usr/local/freesurfer/8.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/8.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /mnt/data4/test/sub-01 mri_convert /mnt/data4/Subjects/T1_MPR.nii /mnt/data4/test/sub-01/mri/orig/001.mgz mri_convert /mnt/data4/Subjects/T1_MPR.nii /mnt/data4/test/sub-01/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=1) reading from /mnt/data4/Subjects/T1_MPR.nii... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99956, 0, -0.0296663) j_ras = (0.00156295, 0.998611, 0.0526614) k_ras = (0.029625, -0.0526846, 0.998172) writing to /mnt/data4/test/sub-01/mri/orig/001.mgz... @#@FSTIME 2026:04:10:18:43:53 mri_convert N 2 e 3.58 S 0.11 U 3.99 P 114% M 49280 F 3 R 11053 W 0 c 24 w 339 I 84800 O 50272 L 0.43 0.43 0.19 @#@FSLOADPOST 2026:04:10:18:43:56 mri_convert N 2 0.43 0.43 0.19 #-------------------------------------------- #@# T2/FLAIR Input Fri Apr 10 06:43:57 PM JST 2026 /mnt/data4/test/sub-01 mri_convert --no_scale 1 /mnt/data4/Subjects/T2_SPC.nii /mnt/data4/test/sub-01/mri/orig/T2raw.mgz mri_convert --no_scale 1 /mnt/data4/Subjects/T2_SPC.nii /mnt/data4/test/sub-01/mri/orig/T2raw.mgz INFO: using NIfTI-1 sform (sform_code=1) reading from /mnt/data4/Subjects/T2_SPC.nii... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99956, 0, -0.0296663) j_ras = (0.00156295, 0.998611, 0.0526614) k_ras = (0.029625, -0.0526846, 0.998172) writing to /mnt/data4/test/sub-01/mri/orig/T2raw.mgz... @#@FSTIME 2026:04:10:18:43:57 mri_convert N 4 e 3.68 S 0.11 U 4.16 P 116% M 49280 F 0 R 11048 W 0 c 28 w 328 I 84008 O 42768 L 0.43 0.43 0.19 @#@FSLOADPOST 2026:04:10:18:44:01 mri_convert N 4 0.48 0.44 0.20 #-------------------------------------------- #@# MotionCor Fri Apr 10 06:44:01 PM JST 2026 Found 1 runs /mnt/data4/test/sub-01/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /mnt/data4/test/sub-01/mri/orig/001.mgz /mnt/data4/test/sub-01/mri/rawavg.mgz mri_info /mnt/data4/test/sub-01/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /mnt/data4/test/sub-01/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 224 x 300 x 320 voxel sizes: 0.800000, 0.800000, 0.800000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -89.6, xend: 89.6 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2500.00 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 = 0.9996, y_r = 0.0016, z_r = 0.0296, c_r = 4.6781 : x_a = 0.0000, y_a = 0.9986, z_a = -0.0527, c_a = -8.4963 : x_s = -0.0297, y_s = 0.0527, z_s = 0.9982, c_s = 2.6792 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.7996 0.0013 0.0237 -88.8620 0.0000 0.7989 -0.0421 -121.5860 -0.0237 0.0421 0.7985 -128.7480 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.512 ras to voxel transform: 1.2494 0.0000 -0.0371 106.2543 0.0020 1.2483 0.0658 160.4201 0.0370 -0.0659 1.2477 155.9243 0.0000 0.0000 0.0000 1.0000 /mnt/data4/test/sub-01 mri_convert /mnt/data4/test/sub-01/mri/rawavg.mgz /mnt/data4/test/sub-01/mri/orig.mgz --conform_min mri_convert /mnt/data4/test/sub-01/mri/rawavg.mgz /mnt/data4/test/sub-01/mri/orig.mgz --conform_min reading from /mnt/data4/test/sub-01/mri/rawavg.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99956, 0, -0.0296663) j_ras = (0.00156295, 0.998611, 0.0526614) k_ras = (0.029625, -0.0526846, 0.998172) volume geometry: valid : 1021424672 extent : (320, 320, 320) voxel : ( 0.8000, 0.8000, 0.8000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 4.6781, -8.4963, 2.6792) shears : ( 0.0000, 0.0000, 0.0000) file : /mnt/data4/test/sub-01/mri/rawavg.mgz changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4095 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /mnt/data4/test/sub-01/mri/orig.mgz... @#@FSTIME 2026:04:10:18:44:05 mri_convert N 3 e 5.10 S 0.05 U 5.59 P 110% M 71008 F 0 R 32485 W 0 c 40 w 10 I 0 O 26192 L 0.44 0.43 0.20 @#@FSLOADPOST 2026:04:10:18:44:10 mri_convert N 3 0.49 0.44 0.20 mri_add_xform_to_header -c /mnt/data4/test/sub-01/mri/transforms/talairach.xfm /mnt/data4/test/sub-01/mri/orig.mgz /mnt/data4/test/sub-01/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2026:04:10:18:44:10 mri_add_xform_to_header N 4 e 1.49 S 0.04 U 2.00 P 137% M 38528 F 13 R 8548 W 0 c 20 w 26 I 3640 O 26192 L 0.49 0.44 0.20 @#@FSLOADPOST 2026:04:10:18:44:11 mri_add_xform_to_header N 4 0.49 0.44 0.20 mri_info /mnt/data4/test/sub-01/mri/orig.mgz orig.mgz ======================================== Volume information for /mnt/data4/test/sub-01/mri/orig.mgz type: MGH intent: MRI (0) dimensions: 320 x 320 x 320 voxel sizes: 0.800000, 0.800000, 0.800000 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: 2500.00 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 = 4.6781 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -8.4963 : x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 2.6792 talairach xfm : /mnt/data4/test/sub-01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -0.8000 -0.0000 -0.0000 132.6781 0.0000 0.0000 0.8000 -136.4962 0.0000 -0.8000 -0.0000 130.6792 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.512 ras to voxel transform: -1.2500 -0.0000 0.0000 165.8476 -0.0000 -0.0000 -1.2500 163.3490 0.0000 1.2500 -0.0000 170.6203 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /mnt/data4/test/sub-01/mri/rawavg.mgz --trg /mnt/data4/test/sub-01/mri/orig.mgz --outlta /mnt/data4/test/sub-01/mri/rawavg2orig.lta --subject sub-01 8.1.0 --inlta: identity.nofile input LTA transform. --src: /mnt/data4/test/sub-01/mri/rawavg.mgz src image (geometry). --trg: /mnt/data4/test/sub-01/mri/orig.mgz trg image (geometry). --outlta: /mnt/data4/test/sub-01/mri/rawavg2orig.lta output LTA. --s: sub-01 subject name LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; setting subject to sub-01 Writing LTA to file /mnt/data4/test/sub-01/mri/rawavg2orig.lta... lta_convert successful. @#@FSTIME 2026:04:10:18:44:12 lta_convert N 10 e 0.37 S 0.00 U 0.37 P 99% M 6048 F 5 R 250 W 0 c 4 w 6 I 952 O 8 L 0.49 0.44 0.20 @#@FSLOADPOST 2026:04:10:18:44:12 lta_convert N 10 0.49 0.44 0.20 mri_synthstrip --threads 8 -i /mnt/data4/test/sub-01/mri/orig.mgz -o /mnt/data4/test/sub-01/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /mnt/data4/test/sub-01/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /mnt/data4/test/sub-01/mri/synthstrip.mgz If you use SynthStrip in your analysis, please cite: ---------------------------------------------------- SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://doi.org/10.1016/j.neuroimage.2022.119474 Website: https://synthstrip.io @#@FSTIME 2026:04:10:18:44:12 mri_synthstrip N 6 e 14.58 S 13.48 U 33.09 P 319% M 5977460 F 999 R 6349179 W 0 c 301 w 3844 I 407432 O 6360 L 0.49 0.44 0.20 @#@FSLOADPOST 2026:04:10:18:44:27 mri_synthstrip N 6 1.20 0.60 0.26 mri_synthseg --i /mnt/data4/test/sub-01/mri/orig.mgz --o /mnt/data4/test/sub-01/mri/synthseg.rca.mgz --threads 8 --vol /mnt/data4/test/sub-01/stats/synthseg.vol.csv --keepgeom --addctab --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 8 threads addctab True predicting 1/1 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 80s 80s/step Reslicing to have same geom as the input [0.80000001 0.80000001 0.80000001] segmentation saved in: /mnt/data4/test/sub-01/mri/synthseg.rca.mgz volumes saved in: /mnt/data4/test/sub-01/stats/synthseg.vol.csv #@# mri_synthseg vmpeak 119248512 If you use this tool in a publication, please cite: SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl, A.V. Dalca, J.E. Iglesias Medical Image Analysis, 2023. @#@FSTIME 2026:04:10:18:44:27 mri_synthseg N 11 e 111.64 S 51.81 U 607.51 P 590% M 25002976 F 2229 R 25787942 W 0 c 2377 w 15403 I 825432 O 3496 L 1.20 0.60 0.26 @#@FSLOADPOST 2026:04:10:18:46:18 mri_synthseg N 11 4.40 2.18 0.88 Fri Apr 10 06:46:19 PM JST 2026 setenv SUBJECTS_DIR /mnt/data4/test cd /mnt/data4/test/sub-01 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg --i /mnt/data4/test/sub-01/mri/synthstrip.mgz --t /usr/local/freesurfer/8.1.0/average/mni305.cor.stripped.mgz --affine-only --o /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305 --threads 8 -rwxr-xr-x 1 root root 30890 Jul 19 2025 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux pid 10844 Fri Apr 10 06:46:19 PM JST 2026 mri_synthmorph -m affine -t /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/aff.lta /mnt/data4/test/sub-01/mri/synthstrip.mgz /usr/local/freesurfer/8.1.0/average/mni305.cor.stripped.mgz -j 8 #@# mri_synthmorph: affine, threads: 8, VmPeak: 8271324 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io @#@FSTIME 2026:04:10:18:46:19 mri_synthmorph N 8 e 15.86 S 21.36 U 40.85 P 392% M 5354608 F 188 R 9407675 W 0 c 374 w 8817 I 178384 O 432 L 4.40 2.18 0.88 @#@FSLOADPOST 2026:04:10:18:46:35 mri_synthmorph N 8 4.68 2.35 0.96 /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305 /mnt/data4/test/sub-01 /mnt/data4/test/sub-01 lta_convert --invert --inlta /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/aff.lta --outlta /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta 8.1.0 --invert: will invert transform. --inlta: /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/aff.lta input LTA transform. --outlta: /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta output LTA. LTA read, type : 1 1.10236 -0.04518 -0.01931 -6.72919; 0.01709 0.98443 0.13562 -8.59800; 0.03511 -0.06584 1.04939 -22.58477; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta... lta_convert successful. @#@FSTIME 2026:04:10:18:46:35 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 100% M 5824 F 0 R 221 W 0 c 1 w 1 I 0 O 8 L 4.68 2.35 0.96 @#@FSLOADPOST 2026:04:10:18:46:35 lta_convert N 5 4.68 2.35 0.96 To check affine registration tkregisterfv --mov /mnt/data4/test/sub-01/mri/synthstrip.mgz --targ /usr/local/freesurfer/8.1.0/average/mni305.cor.stripped.mgz --reg /mnt/data4/test/sub-01/mri/transforms/synthmorph.mni305/aff.lta AffineOnly specified, so exiting now Started at Fri Apr 10 06:46:19 PM JST 2026 Ended at Fri Apr 10 06:46:35 PM JST 2026 Fs-Synthmorph-Reg-Run-Time-Sec 16 Fs-Synthmorph-Reg-Run-Time-Min 0.27 Fs-Synthmorph-Reg-Run-Time-Hours 0.00 fs-synthmorph-reg Done @#@FSTIME 2026:04:10:18:46:19 fs-synthmorph-reg N 9 e 16.26 S 21.62 U 41.04 P 385% M 5354608 F 188 R 9425946 W 0 c 404 w 9134 I 178448 O 456 L 4.40 2.18 0.88 @#@FSLOADPOST 2026:04:10:18:46:35 fs-synthmorph-reg N 9 4.68 2.35 0.96 8.1.0 --ltavox2vox: output LTA as VOX_TO_VOX transform. --inlta: synthmorph.mni305/aff.lta input LTA transform. --outlta: talairach.xfm.lta output LTA. LTA read, type : 1 1.10236 -0.04518 -0.01931 -6.72919; 0.01709 0.98443 0.13562 -8.59800; 0.03511 -0.06584 1.04939 -22.58477; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file talairach.xfm.lta... lta_convert successful. 8.1.0 --inlta: talairach.xfm.lta input LTA transform. --outmni: talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.10236 -0.04518 -0.01931 -6.72919; 0.01709 0.98443 0.13562 -8.59801; 0.03511 -0.06584 1.04939 -22.58476; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. fs-synthmorph-reg --s sub-01 --threads 8 --i /mnt/data4/test/sub-01/mri/orig.mgz --test Fri Apr 10 06:46:35 PM JST 2026 setenv SUBJECTS_DIR /mnt/data4/test cd /mnt/data4/test/sub-01 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg --s sub-01 --threads 8 --i /mnt/data4/test/sub-01/mri/orig.mgz --test -rwxr-xr-x 1 root root 30890 Jul 19 2025 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux pid 11167 mri_mask -bb 3 /mnt/data4/test/sub-01/mri/orig.mgz /mnt/data4/test/sub-01/mri/orig.mgz /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz cropping npad = 3 DoAbs = 0 Computing bounding box, npad = 3, 3, 3, 3, 3, 3 41 0 0 239 320 320 maskval=0, outval=0 Writing masked volume to /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done. lta_convert --inlta identity.nofile --src /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --trg /mnt/data4/test/sub-01/mri/orig.mgz --outlta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta 8.1.0 --inlta: identity.nofile input LTA transform. --src: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz src image (geometry). --trg: /mnt/data4/test/sub-01/mri/orig.mgz trg image (geometry). --outlta: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta... lta_convert successful. Fri Apr 10 06:46:38 PM JST 2026 mri_synthmorph -m affine -t /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 8 #@# mri_synthmorph: affine, threads: 8, VmPeak: 8361540 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io @#@FSTIME 2026:04:10:18:46:38 mri_synthmorph N 8 e 15.15 S 20.58 U 40.37 P 402% M 5454772 F 0 R 9381829 W 0 c 314 w 7229 I 15192 O 432 L 4.39 2.33 0.96 @#@FSLOADPOST 2026:04:10:18:46:53 mri_synthmorph N 8 4.35 2.43 1.02 Fri Apr 10 06:46:53 PM JST 2026 mri_concatenate_lta -invert1 -invertout /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta invert the first LTA before applying it invert the output LTA Read individual LTAs Warning: dst volume of lta1 doesn't match src volume of lta2 Volume geometry for lta1-dst: volume geometry: extent : (239, 320, 320) voxel : ( 0.8000, 0.8000, 0.8000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 4.2781, -8.4963, 2.6792) shears : ( 0.0000, 0.0000, 0.0000) file : none Volume geometry for lta2-src: volume geometry: extent : (239, 320, 320) voxel : ( 0.8000, 0.8000, 0.8000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : (-0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, -0.0000) c_(ras) : ( 4.2781, -8.4963, 2.6792) shears : ( 0.0000, 0.0000, 0.0000) file : /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Inverting output LTA Writing combined LTA to file /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta... mri_concatenate_lta successful. @#@FSTIME 2026:04:10:18:46:53 mri_concatenate_lta N 5 e 0.00 S 0.00 U 0.00 P 100% M 5152 F 0 R 216 W 0 c 0 w 1 I 0 O 8 L 4.35 2.43 1.02 @#@FSLOADPOST 2026:04:10:18:46:53 mri_concatenate_lta N 5 4.35 2.43 1.02 mri_concatenate_lta -invert2 /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert the second LTA before applying it Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta... mri_concatenate_lta successful. @#@FSTIME 2026:04:10:18:46:53 mri_concatenate_lta N 4 e 0.02 S 0.00 U 0.00 P 33% M 5152 F 0 R 216 W 0 c 1 w 2 I 8 O 8 L 4.35 2.43 1.02 @#@FSLOADPOST 2026:04:10:18:46:53 mri_concatenate_lta N 4 4.35 2.43 1.02 lta_convert --invert --inlta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --outlta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta 8.1.0 --invert: will invert transform. --inlta: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta input LTA transform. --outlta: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta output LTA. LTA read, type : 1 0.86668 0.04890 0.01088 7.18063; -0.02332 0.97868 -0.08806 4.68120; -0.03189 0.07027 0.89649 22.17511; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta... lta_convert successful. @#@FSTIME 2026:04:10:18:46:53 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 85% M 5824 F 0 R 220 W 0 c 2 w 0 I 0 O 8 L 4.35 2.43 1.02 @#@FSLOADPOST 2026:04:10:18:46:53 lta_convert N 5 4.35 2.43 1.02 lta_convert --inlta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta --outmni /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm 8.1.0 --inlta: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta input LTA transform. --outmni: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm output MNI/XFM matrix. LTA read, type : 1 1.15159 -0.05614 -0.01948 -7.57432; 0.03091 1.01313 0.09914 -7.16294; 0.03855 -0.08141 1.10699 -24.44342; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. To check affine registration tkregisterfv --mov /mnt/data4/test/sub-01/mri/orig.mgz --targ /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --reg /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta mri_synthmorph -m deform -t /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz -i /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 8 -o /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz #@# mri_synthmorph: deform, threads: 8, VmPeak: 20183864 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io @#@FSTIME 2026:04:10:18:46:53 mri_synthmorph N 12 e 121.56 S 89.95 U 621.62 P 585% M 14149240 F 11 R 43737861 W 0 c 2594 w 35514 I 6854992 O 120104 L 4.35 2.43 1.02 @#@FSLOADPOST 2026:04:10:18:48:55 mri_synthmorph N 12 6.54 3.78 1.67 mri_warp_convert --inras /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz --insrcgeom /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --outm3z /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz --vg-thresh 1e-5 --lta1-inv /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta --lta2 /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta 8.1.0 --inras: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz input RAS warp. --insrcgeom: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz atlas/source image (used for geometry). --outm3z: /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz output M3Z. Setting vg_isEqual_Threshold to 0.000010 Applying LTAs to the GCAM GCAMwrite(/mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [193 x 229 x 193] [INFO] Warpfield::convert(): gcam image [320 x 320 x 320] [INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193] [INFO] Warpfield::convert(): total out of range voxel count: 0 [INFO] niiWrite(): MGZ_INTENT_WARPMAP => NIFTI_INTENT_DISPVECT, intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [INFO] niiWrite(): convert displacement from 0 to 3 mri_warp_convert successful. @#@FSTIME 2026:04:10:18:48:55 mri_warp_convert N 12 e 17.02 S 1.43 U 16.48 P 105% M 3406268 F 16 R 869974 W 0 c 71 w 40 I 4216 O 90552 L 6.54 3.78 1.67 @#@FSLOADPOST 2026:04:10:18:49:12 mri_warp_convert N 12 5.31 3.65 1.66 mri_ca_register -invert-and-save /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading gcam [INFO] niiRead(): intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 Computing inverse of GCAM Filling inverse of GCAM Allocating inv_gcam...(320, 320, 320) Saving inverse to /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz GCAMwrite(/mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [320 x 320 x 320] [INFO] Warpfield::convert(): gcam image [193 x 229 x 193] [INFO] Warpfield::convert(): gcam atlas [320 x 320 x 320] [INFO] Warpfield::convert(): total out of range voxel count: 0 [INFO] niiWrite(): MGZ_INTENT_WARPMAP => NIFTI_INTENT_DISPVECT, intent_code = 1006, dimensions = {5, 320, 320, 320, 1, 3, 1, 1} [INFO] niiWrite(): convert displacement from 0 to 3 @#@FSTIME 2026:04:10:18:49:12 mri_ca_register N 3 e 155.08 S 4.83 U 259.90 P 170% M 11695824 F 11 R 3127569 W 0 c 2039 w 1996 I 1856 O 472920 L 5.31 3.65 1.66 @#@FSLOADPOST 2026:04:10:18:51:47 mri_ca_register N 3 2.17 2.97 1.71 mri_vol2vol --regheader --mov /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz --targ /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --o /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz movvol /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz targvol /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz outvol /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776273238 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 13.50000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -20.00000; 0.00000 1.00000 0.00000 -20.00000; 0.00000 0.00000 1.00000 -2.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done @#@FSTIME 2026:04:10:18:51:47 mri_vol2vol N 7 e 1.01 S 0.06 U 1.60 P 164% M 48160 F 5 R 19710 W 0 c 9 w 18 I 1296 O 32704 L 2.17 2.97 1.71 @#@FSLOADPOST 2026:04:10:18:51:48 mri_vol2vol N 7 2.08 2.94 1.71 mri_convert -rt nearest /mnt/data4/test/sub-01/mri/orig.mgz -at /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz mri_convert -rt nearest /mnt/data4/test/sub-01/mri/orig.mgz -at /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /mnt/data4/test/sub-01/mri/orig.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.45519e-10, 0) j_ras = (-2.32831e-09, 0, -1) k_ras = (-1.45519e-10, 1, -4.65661e-09) INFO: Reading transformation from file /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... INFO: Applying transformation from file /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... Applying morph_3d ... [INFO] niiRead(): intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 morphing to atlas with resample type 0 writing to /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz... @#@FSTIME 2026:04:10:18:51:48 mri_convert N 6 e 6.18 S 1.00 U 18.29 P 311% M 2382016 F 1 R 596288 W 0 c 332 w 65 I 256 O 7824 L 2.08 2.94 1.71 @#@FSLOADPOST 2026:04:10:18:51:54 mri_convert N 6 2.55 3.02 1.74 mri_diff --po /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz mri_diff --po /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz diffcount 4622901 Volumes differ in pixel data maxdiff 128.55043030 at 92 144 24 0 tkmeditfv -f /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -aux /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz Started at Fri Apr 10 06:46:35 PM JST 2026 Ended at Fri Apr 10 06:51:55 PM JST 2026 Fs-Synthmorph-Reg-Run-Time-Sec 320 Fs-Synthmorph-Reg-Run-Time-Min 5.33 Fs-Synthmorph-Reg-Run-Time-Hours 0.09 fs-synthmorph-reg Done @#@FSTIME 2026:04:10:18:46:35 fs-synthmorph-reg N 7 e 319.91 S 118.57 U 963.26 P 338% M 14149240 F 53 R 57826296 W 0 c 5454 w 45585 I 6880504 O 750544 L 4.68 2.35 0.96 @#@FSLOADPOST 2026:04:10:18:51:55 fs-synthmorph-reg N 7 2.55 3.02 1.74 #-------------------------------------------- #@# Nu Intensity Correction Fri Apr 10 06:51:55 PM JST 2026 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 /usr/bin/bc /mnt/data4/test/sub-01/mri /usr/local/freesurfer/8.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 8.1.0 Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux Fri Apr 10 06:51:55 PM JST 2026 tmpdir is ./tmp.mri_nu_correct.mni.13856 cd /mnt/data4/test/sub-01/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.13856/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.13856/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.13856/ones.mgz 8.1.0 cwd /mnt/data4/test/sub-01/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.13856/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.13856/ones.mgz sysname Linux hostname kami-image3 machine x86_64 user kami input ./tmp.mri_nu_correct.mni.13856/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.13856/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 32768000 values in range Counting number of voxels in first frame Found 32768000 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.13856/ones.mgz Count: 32768000 16777216.796875 32768000 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13856/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13856/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13856/input.mean.dat 8.1.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13856/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13856/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13856/input.mean.dat sysname Linux hostname kami-image3 machine x86_64 user kami whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13856/ones.mgz Loading orig.mgz Voxel Volume is 0.512 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.13856/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13856/ones.mgz --i ./tmp.mri_nu_correct.mni.13856/nu0.mgz --sum ./tmp.mri_nu_correct.mni.13856/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13856/output.mean.dat 8.1.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13856/ones.mgz --i ./tmp.mri_nu_correct.mni.13856/nu0.mgz --sum ./tmp.mri_nu_correct.mni.13856/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13856/output.mean.dat sysname Linux hostname kami-image3 machine x86_64 user kami whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13856/ones.mgz Loading ./tmp.mri_nu_correct.mni.13856/nu0.mgz Voxel Volume is 0.512 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.13856/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.13856/nu0.mgz ./tmp.mri_nu_correct.mni.13856/nu0.mgz mul 1.15177197904595387670 Packing Done packing Unpacking Saving result to './tmp.mri_nu_correct.mni.13856/nu0.mgz' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 459896 mri_convert ./tmp.mri_nu_correct.mni.13856/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.13856/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.13856/nu0.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.45519e-10, 0) j_ras = (-2.32831e-09, 0, -1) k_ras = (-1.45519e-10, 1, -4.65661e-09) 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 = 4, i2 = 68 #mri_make_uchar# mapping 10 175 to 3 110 : b -4.16563 m 0.651811 : thresh 6.39085 maxsat 397.609 : nzero 22024299 nsat 0 Fri Apr 10 06:57:33 PM JST 2026 mri_nu_correct.mni done @#@FSTIME 2026:04:10:18:51:55 mri_nu_correct.mni N 10 e 337.88 S 2.44 U 344.96 P 102% M 1192088 F 52 R 1222174 W 0 c 1509 w 321 I 13144 O 161208 L 2.55 3.02 1.74 @#@FSLOADPOST 2026:04:10:18:57:33 mri_nu_correct.mni N 10 1.62 1.86 1.59 mri_add_xform_to_header -c /mnt/data4/test/sub-01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2026:04:10:18:57:33 mri_add_xform_to_header N 4 e 0.80 S 0.02 U 1.48 P 188% M 39200 F 1 R 8551 W 0 c 18 w 10 I 512 O 16984 L 1.62 1.86 1.59 @#@FSLOADPOST 2026:04:10:18:57:34 mri_add_xform_to_header N 4 1.62 1.86 1.59 #-------------------------------------------- #@# Intensity Normalization Fri Apr 10 06:57:34 PM JST 2026 /mnt/data4/test/sub-01/mri mri_normalize -g 1 -seed 1234 -mprage -noconform 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 not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.10236 -0.04518 -0.01931 -6.72919; 0.01709 0.98443 0.13562 -8.59801; 0.03511 -0.06584 1.04939 -22.58476; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 74 (74), valley at 24 (24) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 75 (75), valley at 23 (23) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 5 seconds. @#@FSTIME 2026:04:10:18:57:34 mri_normalize N 8 e 185.08 S 0.83 U 204.68 P 111% M 1131092 F 14 R 521772 W 0 c 853 w 77 I 1752 O 16416 L 1.62 1.86 1.59 @#@FSLOADPOST 2026:04:10:19:00:39 mri_normalize N 8 1.13 1.52 1.50 #-------------------------------------- #@# MCADura Segmentation Fri Apr 10 07:00:39 PM JST 2026 mri_mcadura_seg --i /mnt/data4/test/sub-01/mri/nu.mgz --o /mnt/data4/test/sub-01/mri/mca-dura.mgz --threads 8 --synthmorphdir /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm Fri Apr 10 07:00:39 PM JST 2026 setenv SUBJECTS_DIR /mnt/data4/test cd /mnt/data4/test/sub-01/mri /usr/local/freesurfer/8.1.0/bin/mri_mcadura_seg --i /mnt/data4/test/sub-01/mri/nu.mgz --o /mnt/data4/test/sub-01/mri/mca-dura.mgz --threads 8 --synthmorphdir /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root root 13384 Jul 19 2025 /usr/local/freesurfer/8.1.0/bin/mri_mcadura_seg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux pid 17685 /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685 /mnt/data4/test/sub-01/mri /mnt/data4/test/sub-01/mri mri_vol2vol --reg /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/mcadura.prior.lh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.15159 0.05614 0.01948 2.26230; 0.03855 -0.08141 1.10699 -39.10555; -0.03091 -1.01313 -0.09914 -2.13947; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz outvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/mcadura.prior.lh.nii.gz regfile /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776345737 Final tkRAS-to-tkRAS Matrix is: -1.15159 0.05614 0.01948 2.26230; 0.03855 -0.08141 1.10699 -39.10555; -0.03091 -1.01313 -0.09914 -2.13947; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.92128 0.01559 -0.04491 246.33331; -0.02473 -0.07931 0.81050 3.60501; -0.03084 -0.88560 -0.06513 214.44420; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /mnt/data4/test/sub-01/mri/nu.mgz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/mcadura.prior.lh.nii.gz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/lh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 13279 voxels in mask (pct= 0.04) MRIcropToFoV(): thresh=0.001 FoV = (100,100,100) nhits=13279 centroid = (199.3,156.509,208.038) min = (166,125,185) max = (222,181,230) delta = (57,57,46) Region 149 107 158 100 100 100 149 107 158 100 100 100 maskval=0, outval=0 Writing masked volume to /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/lh.crop.nii.gz...done. mri_vol2vol --regheader --mov /mnt/data4/test/sub-01/mri/nu.mgz --targ /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/lh.crop.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.lh.crop.nii.gz movvol /mnt/data4/test/sub-01/mri/nu.mgz targvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/lh.crop.nii.gz outvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.lh.crop.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776394512 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -31.20000; 0.00000 1.00000 0.00000 38.39999; 0.00000 -0.00000 1.00000 2.39999; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 149.00000; 0.00000 1.00000 0.00000 107.00002; 0.00000 0.00000 1.00000 158.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 8 --fov 72 --i /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.lh.crop.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.mgz /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 8 --fov 72 --i /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.lh.crop.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 8 thread(s) Loaded lookup table /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 Loaded input image from /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.lh.crop.nii.gz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 1s 506ms/step Wrote segmentation to /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.mgz vmpcma: 6767632 done mri_vol2vol --regheader --interp nearest --mov /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.mgz --targ /mnt/data4/test/sub-01/mri/nu.mgz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.uncropped.mgz movvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.mgz targvol /mnt/data4/test/sub-01/mri/nu.mgz outvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.uncropped.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1775980867 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 -0.00000 0.00000 31.20001; 0.00000 1.00000 0.00000 -38.39999; 0.00000 -0.00000 1.00000 -2.40001; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -149.00003; 0.00000 1.00000 0.00000 -106.99998; 0.00000 -0.00000 1.00000 -157.99998; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --reg /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/mcadura.prior.rh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.15159 0.05614 0.01948 2.26230; 0.03855 -0.08141 1.10699 -39.10555; -0.03091 -1.01313 -0.09914 -2.13947; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz outvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/mcadura.prior.rh.nii.gz regfile /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776302439 Final tkRAS-to-tkRAS Matrix is: -1.15159 0.05614 0.01948 2.26230; 0.03855 -0.08141 1.10699 -39.10555; -0.03091 -1.01313 -0.09914 -2.13947; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.92128 0.01559 -0.04491 246.33331; -0.02473 -0.07931 0.81050 3.60501; -0.03084 -0.88560 -0.06513 214.44420; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /mnt/data4/test/sub-01/mri/nu.mgz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/mcadura.prior.rh.nii.gz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/rh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 13976 voxels in mask (pct= 0.04) MRIcropToFoV(): thresh=0.001 FoV = (100,100,100) nhits=13976 centroid = (113.846,159.72,207.359) min = (89,130,185) max = (144,183,232) delta = (56,54,48) Region 64 110 157 100 100 100 64 110 157 100 100 100 maskval=0, outval=0 Writing masked volume to /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/rh.crop.nii.gz...done. mri_vol2vol --regheader --mov /mnt/data4/test/sub-01/mri/nu.mgz --targ /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/rh.crop.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.nii.gz movvol /mnt/data4/test/sub-01/mri/nu.mgz targvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/rh.crop.nii.gz outvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776374723 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 36.80000; 0.00000 1.00000 0.00000 37.59999; 0.00000 -0.00000 1.00000 -0.00002; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 64.00000; 0.00000 1.00000 0.00000 110.00002; 0.00000 0.00000 1.00000 156.99998; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.nii.gz --left-right-reverse-pix /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.lrrev.nii.gz mri_convert /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.nii.gz --left-right-reverse-pix /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.lrrev.nii.gz reading from /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.nii.gz... WARNING: applying left-right reversal to the input pixels without changing geometry. This will likely make the volume geometry WRONG, so make sure you know what you are doing. Reversing pixels for the columns TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.45519e-10, 0) j_ras = (-2.32831e-09, 0, -1) k_ras = (-1.45519e-10, 1, -4.65661e-09) writing to /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.lrrev.nii.gz... mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 8 --fov 72 --i /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.lrrev.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.lrrev.mgz /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 8 --fov 72 --i /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.lrrev.nii.gz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.lrrev.mgz Keeping anterior commissure in vols and stats Using CPU Using 8 thread(s) Loaded lookup table /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 Loaded input image from /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/invol.rh.crop.lrrev.nii.gz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 491ms/step Wrote segmentation to /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.lrrev.mgz vmpcma: 6732752 done mri_convert /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.lrrev.mgz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.mgz --left-right-swap-label-table /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.index /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.rh.index --left-right-reverse-pix mri_convert /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.lrrev.mgz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.mgz --left-right-swap-label-table /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.lh.index /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/dumca.rh.index --left-right-reverse-pix reading from /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.lrrev.mgz... Performing left-right swap of labels MRIlrswapSeg(): nswaps 1274 WARNING: applying left-right reversal to the input pixels without changing geometry. This will likely make the volume geometry WRONG, so make sure you know what you are doing. Reversing pixels for the columns TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.45519e-10, 0) j_ras = (0, 0, -1) k_ras = (1.45519e-10, 1, 0) writing to /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.mgz... mri_vol2vol --regheader --interp nearest --mov /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.mgz --targ /mnt/data4/test/sub-01/mri/nu.mgz --o /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.uncropped.mgz movvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.mgz targvol /mnt/data4/test/sub-01/mri/nu.mgz outvol /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.uncropped.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776411862 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 -0.00000 0.00000 -36.80000; 0.00000 1.00000 0.00000 -37.59999; 0.00000 -0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -64.00003; 0.00000 1.00000 0.00000 -110.00000; 0.00000 -0.00000 1.00000 -156.99997; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_concat /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.lh.uncropped.mgz /mnt/data4/test/sub-01/mri/tmp.mri_mcadura_seg.17685/seg.rh.uncropped.mgz --sum --ctab /usr/local/freesurfer/8.1.0/models/mca-dura.ctab --o /mnt/data4/test/sub-01/mri/mca-dura.mgz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing sum across frames Writing to /mnt/data4/test/sub-01/mri/mca-dura.mgz fsvglrun freeview -neuro-view --hide-3d-slices --view coronal /mnt/data4/test/sub-01/mri/nu.mgz /mnt/data4/test/sub-01/mri/mca-dura.mgz:isosurface=1:outline=1 Started at Fri Apr 10 07:00:39 PM JST 2026 Ended at Fri Apr 10 07:01:02 PM JST 2026 mri_mcadura_seg-Run-Time-Sec 23 mri_mcadura_seg Done #-------------------------------------- #@# VSinus Segmentation Fri Apr 10 07:01:02 PM JST 2026 mri_vsinus_seg --s sub-01 --rca-synthseg --threads 8 --synthmorphdir /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm Fri Apr 10 07:01:02 PM JST 2026 setenv SUBJECTS_DIR /mnt/data4/test cd /mnt/data4/test/sub-01/mri /usr/local/freesurfer/8.1.0/bin/mri_vsinus_seg --s sub-01 --rca-synthseg --threads 8 --synthmorphdir /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root root 20960 Jul 19 2025 /usr/local/freesurfer/8.1.0/bin/mri_vsinus_seg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux pid 18241 mri_vol2vol --mov /usr/local/freesurfer/8.1.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz --lta /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --targ /mnt/data4/test/sub-01/mri/nu.mgz --o /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz Matrix from LTA: -1.15159 0.05614 0.01948 2.26227; 0.03855 -0.08141 1.10699 -39.10551; -0.03091 -1.01313 -0.09914 -2.13946; 0.00000 0.00000 0.00000 1.00000; /usr/local/freesurfer/8.1.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz /mnt/data4/test/sub-01/mri/nu.mgz movvol /usr/local/freesurfer/8.1.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz targvol /mnt/data4/test/sub-01/mri/nu.mgz outvol /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz regfile /mnt/data4/test/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1776011305 Final tkRAS-to-tkRAS Matrix is: -1.15159 0.05614 0.01948 2.26228; 0.03855 -0.08141 1.10699 -39.10550; -0.03091 -1.01313 -0.09914 -2.13944; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.92128 0.01559 -0.04491 246.33331; -0.02473 -0.07931 0.81050 3.60497; -0.03084 -0.88560 -0.06513 214.44423; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop 0 /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mgz /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz threshold mask volume at 0.001 cropping npad = 0 DoAbs = 0 Found 180720 voxels in mask (pct= 0.55) Computing bounding box, npad = 0, 0, 0, 0, 0, 0 85 28 39 150 159 121 maskval=0, outval=0 Writing masked volume to /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz...done. mri_binarize --crop-around-ras /mnt/data4/test/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz /mnt/data4/test/sub-01/mri/nu.mgz nolta cras /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz 0 144 144 144 Getting cras from /mnt/data4/test/sub-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz final ras2vox matrix -1.25000 -0.00000 0.00000 165.84764; -0.00000 -0.00000 -1.25000 163.34904; 0.00000 1.25000 -0.00000 170.62033; -0.00000 -0.00000 -0.00000 1.00000; -------------------------- ostr LIA (144 144 144) (144 144 144) rasCenter 4.67812 -56.8963 44.6792 crsCenter 160 107.5 99.5 MRIcropAroundCRS() vol size 320 320 320 center 160 107.5 99.5 fov 144 144 144 limits 89 232 37 180 29 172 using MRIextractRegion() mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.no-sp.ctab --keep_ac --conform --percentile 99.9 --vmp --output-base vsinus --logfile mri_vsinus_seg.log --fov 144 --threads 8 --no-cite-sclimbic --i /mnt/data4/test/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.no-sp.ctab --keep_ac --conform --percentile 99.9 --vmp --output-base vsinus --logfile mri_vsinus_seg.log --fov 144 --threads 8 --no-cite-sclimbic --i /mnt/data4/test/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz Keeping anterior commissure in vols and stats Using CPU Using 8 thread(s) Loaded lookup table /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.no-sp.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 6 inshape (144, 144, 144) features 24 (None, 144, 144, 144, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 Segmenting image 1/1 Loaded input image from /mnt/data4/test/sub-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 2s 2s/step Wrote segmentation to /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz vmpcma: 13673156 done mri_binarize --i /mnt/data4/test/sub-01/mri/synthseg.rca.mgz --match 3 42 --inv --o /mnt/data4/test/sub-01/mri/tmp.vsinus/ctxsegmask.mgz 8.1.0 cwd /mnt/data4/test/sub-01/mri cmdline mri_binarize --i /mnt/data4/test/sub-01/mri/synthseg.rca.mgz --match 3 42 --inv --o /mnt/data4/test/sub-01/mri/tmp.vsinus/ctxsegmask.mgz sysname Linux hostname kami-image3 machine x86_64 user kami input /mnt/data4/test/sub-01/mri/synthseg.rca.mgz frame 0 nErode3d 0 nErode2d 0 output /mnt/data4/test/sub-01/mri/tmp.vsinus/ctxsegmask.mgz Binarizing based on matching values nMatch 2 0 3 1 42 binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 1105461 values in range Counting number of voxels in first frame Found 1105461 voxels in final mask Writing output to /mnt/data4/test/sub-01/mri/tmp.vsinus/ctxsegmask.mgz Count: 1105461 565996.058883 32768000 3.373599 mri_binarize done mri_vol2vol --mov /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz --targ /mnt/data4/test/sub-01/mri/nu.mgz --interp nearest --o /mnt/data4/test/sub-01/mri/vsinus.mgz --regheader movvol /mnt/data4/test/sub-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz targvol /mnt/data4/test/sub-01/mri/nu.mgz outvol /mnt/data4/test/sub-01/mri/vsinus.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1775832753 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.79999; 0.00000 1.00000 0.00000 47.20000; 0.00000 -0.00000 1.00000 -40.79999; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 -88.99998; 0.00000 1.00000 0.00000 -37.00002; 0.00000 0.00000 1.00000 -29.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask /mnt/data4/test/sub-01/mri/vsinus.mgz /mnt/data4/test/sub-01/mri/tmp.vsinus/ctxsegmask.mgz /mnt/data4/test/sub-01/mri/vsinus.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /mnt/data4/test/sub-01/mri/vsinus.mgz...done. mri_segstats --i /mnt/data4/test/sub-01/mri/nu.mgz --seg /mnt/data4/test/sub-01/mri/vsinus.mgz --sum /mnt/data4/test/sub-01/stats/vsinus.stats --subject sub-01 --etiv 8.1.0 cwd cmdline mri_segstats --i /mnt/data4/test/sub-01/mri/nu.mgz --seg /mnt/data4/test/sub-01/mri/vsinus.mgz --sum /mnt/data4/test/sub-01/stats/vsinus.stats --subject sub-01 --etiv sysname Linux hostname kami-image3 machine x86_64 user kami whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1694110 mm^3 (det: 1.149928 ) Loading /mnt/data4/test/sub-01/mri/vsinus.mgz Using embedded color table (and excluding seg 0) Loading /mnt/data4/test/sub-01/mri/nu.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 6 segmentations Computing statistics for each segmentation Reporting on 5 segmentations Using PrintSegStat mri_segstats done fsvglrun freeview --hide-3d-slices --view coronal -neuro-view /mnt/data4/test/sub-01/mri/nu.mgz:lock=1 /mnt/data4/test/sub-01/mri/vsinus.mgz:isosurface=1:outline=1 Started at Fri Apr 10 07:01:02 PM JST 2026 Ended at Fri Apr 10 07:01:25 PM JST 2026 Mri_Vsinus_Seg-Run-Time-Sec 23 Mri_Vsinus_Seg-Run-Time-Min 0.38 Mri_Vsinus_Seg-Run-Time-Hours 0.01 mri_vsinus_seg Done mri_mask /mnt/data4/test/sub-01/mri/T1.mgz /mnt/data4/test/sub-01/mri/synthstrip.mgz /mnt/data4/test/sub-01/mri/brainmask.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /mnt/data4/test/sub-01/mri/brainmask.mgz...done. #------------------------------------- #@# EM Registration Fri Apr 10 07:01:27 PM JST 2026 /mnt/data4/test/sub-01/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/8.1.0/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 = 8 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/8.1.0/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=13.0 skull bounding box = (76, 41, 43) --> (243, 210, 266) finding center of left hemi white matter using (132, 97, 155) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (111,76,127) --> (152, 117,182) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.5 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.380 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.130331 @ (-10.526, 10.526, -10.526) max log p = -3.774447 @ (5.263, 5.263, -5.263) max log p = -3.612269 @ (7.895, 2.632, 2.632) max log p = -3.612269 @ (0.000, 0.000, 0.000) max log p = -3.608076 @ (-1.974, 1.974, -0.658) max log p = -3.587554 @ (0.329, 0.329, 0.987) max log p = -3.587554 @ (0.000, 0.000, 0.000) max log p = -3.587554 @ (0.000, 0.000, 0.000) Found translation: (1.0, 20.7, -12.8): log p = -3.588 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.571, old_max_log_p =-3.588 (thresh=-3.6) 0.86000 0.00000 0.00000 -10.86310; 0.00000 0.86000 0.00000 11.05854; 0.00000 0.00000 0.80000 -12.82895; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 10 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.571, old_max_log_p =-3.571 (thresh=-3.6) 0.86000 0.00000 0.00000 -10.86310; 0.00000 0.86000 0.00000 11.05854; 0.00000 0.00000 0.80000 -12.82895; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 10 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.380, old_max_log_p =-3.571 (thresh=-3.6) 0.87305 -0.03400 0.04742 -14.92940; 0.02457 0.81030 0.04778 3.67847; -0.05932 -0.05115 0.78132 4.82840; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 9 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.378, old_max_log_p =-3.380 (thresh=-3.4) 0.87305 -0.03400 0.04742 -14.92940; 0.02503 0.82549 0.04868 0.94260; -0.05932 -0.05115 0.78132 4.82840; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 9 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.345, old_max_log_p =-3.378 (thresh=-3.4) 0.86991 -0.04686 0.04012 -11.30236; 0.03983 0.82814 0.04299 0.09273; -0.05194 -0.04468 0.78390 2.32778; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.337, old_max_log_p =-3.345 (thresh=-3.3) 0.86784 -0.05953 0.02652 -7.23432; 0.05388 0.82437 0.04328 -1.16714; -0.03779 -0.04554 0.78629 0.18544; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.332, old_max_log_p =-3.337 (thresh=-3.3) 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.332, old_max_log_p =-3.332 (thresh=-3.3) 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 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 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.332 (old=-4.380) transform before final EM align: 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 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 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.9 tol 0.000000 final transform: 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 1004652 FSRUNTIME@ mri_em_register 0.0337 hours 8 threads registration took 2 minutes and 1 seconds. @#@FSTIME 2026:04:10:19:01:27 mri_em_register N 7 e 121.48 S 1.33 U 621.50 P 512% M 787992 F 8 R 217556 W 0 c 1869 w 684 I 141632 O 24 L 1.85 1.66 1.55 @#@FSLOADPOST 2026:04:10:19:03:28 mri_em_register N 7 4.32 2.82 2.00 #-------------------------------------- #@# CA Normalize Fri Apr 10 07:03:28 PM JST 2026 /mnt/data4/test/sub-01/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/8.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/8.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=13.0 skull bounding box = (76, 41, 43) --> (243, 210, 266) finding center of left hemi white matter using (132, 97, 155) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (111,76,127) --> (152, 117,182) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.5 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246437 sample points... INFO: compute sample coordinates transform 0.86784 -0.05953 0.02652 -7.23432; 0.05382 0.82340 0.04323 -0.99047; -0.03792 -0.04570 0.78905 -0.27924; 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 (157, 45, 50) --> (236, 186, 262) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 2 of 8207 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (83, 48, 48) --> (159, 193, 261) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 1 of 8332 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (163, 147, 81) --> (220, 202, 149) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 272 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (113, 148, 76) --> (163, 205, 149) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 97 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (141, 141, 125) --> (182, 224, 163) Brain_Stem: limiting intensities to 91.0 --> 132.0 0 of 233 (0.0%) samples deleted using 17141 total control points for intensity normalization... bias field = 0.988 +- 0.047 193 of 17138 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (157, 45, 50) --> (236, 186, 262) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 4 of 8385 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (83, 48, 48) --> (159, 193, 261) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 2 of 8541 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (163, 147, 81) --> (220, 202, 149) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 312 (0.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (113, 148, 76) --> (163, 205, 149) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 119 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (141, 141, 125) --> (182, 224, 163) Brain_Stem: limiting intensities to 88.0 --> 132.0 8 of 329 (2.4%) samples deleted using 17686 total control points for intensity normalization... bias field = 1.027 +- 0.040 124 of 17601 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (157, 45, 50) --> (236, 186, 262) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 8390 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (83, 48, 48) --> (159, 193, 261) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 4 of 8547 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (163, 147, 81) --> (220, 202, 149) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 60 of 374 (16.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (113, 148, 76) --> (163, 205, 149) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 56 of 166 (33.7%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (141, 141, 125) --> (182, 224, 163) Brain_Stem: limiting intensities to 88.0 --> 132.0 66 of 369 (17.9%) samples deleted using 17846 total control points for intensity normalization... bias field = 1.022 +- 0.035 103 of 17531 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 40 seconds. @#@FSTIME 2026:04:10:19:03:28 mri_ca_normalize N 8 e 99.79 S 0.87 U 105.86 P 106% M 925332 F 9 R 683132 W 0 c 430 w 201 I 1464 O 7480 L 4.32 2.82 2.00 @#@FSLOADPOST 2026:04:10:19:05:08 mri_ca_normalize N 8 1.78 2.36 1.91 #-------------------------------------- #@# EntoWM Segmentation Fri Apr 10 07:05:08 PM JST 2026 mri_entowm_seg --s sub-01 --conform --threads 8 mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer/8.1.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-01 --conform --threads 8 /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer/8.1.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-01 --conform --threads 8 Keeping anterior commissure in vols and stats Using CPU Using 8 thread(s) Loaded lookup table /usr/local/freesurfer/8.1.0/models/entowm.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 5 inshape (160, 160, 160) features 24 (None, 160, 160, 160, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 Using subject directory /mnt/data4/test Computed eTIV from talairach Segmenting subject sub-01 1/1 Loaded input image from /mnt/data4/test/sub-01/mri/nu.mgz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 3s 3s/step Wrote segmentation to /mnt/data4/test/sub-01/mri/entowm.mgz Wrote volume stats to /mnt/data4/test/sub-01/stats/entowm.stats vmpcma: 16741176 done Started at Fri Apr 10 07:05:08 PM JST 2026 Started at Fri Apr 10 07:05:08 PM JST 2026 Ended at Fri Apr 10 07:05:16 PM JST 2026 Ended at Fri Apr 10 07:05:16 PM JST 2026 mri_entowm_seg-Run-Time-Sec 8 mri_entowm_seg-Run-Time-Sec 8 mri_entowm_seg-Run-Time-Min 0.16 mri_entowm_seg-Run-Time-Min 0.16 mri_entowm_seg-Run-Time-Hours 0.00 mri_entowm_seg-Run-Time-Hours 0.00 mri_entowm_seg Done mri_entowm_seg Done 1 3006 1989 1056.3920 wm-lh-entorhinal 2 3201 464 261.6664 wm-lh-gyrus-ambiens 3 4006 2226 1191.3365 wm-rh-entorhinal 4 4201 330 203.0359 wm-rh-gyrus-ambiens #-------------------------------------- #@# CC Seg Fri Apr 10 07:05:16 PM JST 2026 seg2cc --s sub-01 Fri Apr 10 07:05:16 PM JST 2026 setenv SUBJECTS_DIR /mnt/data4/test cd /mnt/data4/test/sub-01/mri /usr/local/freesurfer/8.1.0/bin/seg2cc --s sub-01 freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed seg2cc 8.1.0 Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux /mnt/data4/test/sub-01/mri /mnt/data4/test/sub-01/mri IsConformed yes Fri Apr 10 07:05:17 PM JST 2026 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta sub-01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as transforms/cc_up.lta reading aseg from /mnt/data4/test/sub-01/mri/aseg.auto_noCCseg.mgz reading norm from /mnt/data4/test/sub-01/mri/norm.mgz 97793 voxels in left wm, 59596 in right wm, xrange [154, 165] searching rotation angles z=[-6 8], y=[-5 9] searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.2 global minimum found at slice 157.9, rotations (2.36, 1.50) final transformation (x=157.9, yr=2.360, zr=1.497): 0.99881 -0.02612 0.04116 -33.06758; 0.02610 0.99966 0.00108 14.75396; -0.04117 0.00000 0.99915 -15.37040; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 min_x_fornix = 136 min_x_fornix = 138 min_x_fornix = 138 min_x_fornix = 134 min_x_fornix = 129 cc center is found at 128 109 150 eigenvectors: -0.00010 -0.00400 0.99999; 0.12452 -0.99221 -0.00396; 0.99222 0.12452 0.00060; error in mid anterior detected - correcting... writing aseg with callosum to /mnt/data4/test/sub-01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #VMPC# mri_cc VmPeak 898316 mri_cc done @#@FSTIME 2026:04:10:19:05:17 mri_cc N 7 e 53.37 S 0.69 U 55.33 P 104% M 668536 F 6 R 550147 W 0 c 271 w 66 I 1320 O 1336 L 2.28 2.45 1.94 @#@FSLOADPOST 2026:04:10:19:06:10 mri_cc N 7 1.75 2.30 1.92 Fri Apr 10 07:06:10 PM JST 2026 /mnt/data4/test/sub-01/mri Started at Fri Apr 10 07:05:16 PM JST 2026 Ended at Fri Apr 10 07:06:10 PM JST 2026 Seg2cc-Run-Time-Sec 54 Seg2cc-Run-Time-Hours 0.01 seg2cc Done @#@FSTIME 2026:04:10:19:05:16 seg2cc N 2 e 53.89 S 0.88 U 55.67 P 104% M 668536 F 7 R 562996 W 0 c 295 w 343 I 1432 O 1400 L 2.28 2.45 1.94 @#@FSLOADPOST 2026:04:10:19:06:10 seg2cc N 2 1.75 2.30 1.92 #-------------------------------------- #@# Merge ASeg Fri Apr 10 07:06:10 PM JST 2026 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Apr 10 07:06:10 PM JST 2026 /mnt/data4/test/sub-01/mri mri_normalize -seed 1234 -mprage -noconform -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 320 (src width 320) normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 449 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 76 (76), valley at 43 (43) csf peak at 28, setting threshold to 60 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 76 (76), valley at 43 (43) csf peak at 29, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 6 seconds. @#@FSTIME 2026:04:10:19:06:10 mri_normalize N 10 e 247.34 S 2.12 U 272.39 P 110% M 2215820 F 0 R 1203052 W 0 c 1177 w 98 I 0 O 4944 L 1.75 2.30 1.92 @#@FSLOADPOST 2026:04:10:19:10:18 mri_normalize N 10 1.17 1.66 1.74 #-------------------------------------------- #@# Mask BFS Fri Apr 10 07:10:18 PM JST 2026 /mnt/data4/test/sub-01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 3258695 voxels in mask (pct= 9.94) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2026:04:10:19:10:18 mri_mask N 5 e 1.40 S 0.06 U 2.77 P 201% M 137536 F 0 R 33184 W 0 c 22 w 15 I 0 O 4904 L 1.08 1.63 1.73 @#@FSLOADPOST 2026:04:10:19:10:19 mri_mask N 5 1.08 1.63 1.73 mri_mask -oval 1 -invert brain.finalsurfs.mgz /mnt/data4/test/sub-01/mri/mca-dura.mgz brain.finalsurfs.mgz setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 32765392 Resetting threshold to 0.5 DoAbs = 0 Found 32765392 voxels in mask (pct= 99.99) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2026:04:10:19:10:19 mri_mask N 6 e 3.38 S 0.13 U 4.85 P 147% M 329692 F 0 R 81305 W 0 c 21 w 23 I 0 O 4904 L 1.08 1.63 1.73 @#@FSLOADPOST 2026:04:10:19:10:23 mri_mask N 6 1.08 1.63 1.73 mri_mask -oval 1 -invert brain.finalsurfs.mgz /mnt/data4/test/sub-01/mri/vsinus.mgz brain.finalsurfs.mgz setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 32747106 Resetting threshold to 0.5 DoAbs = 0 Found 32747106 voxels in mask (pct= 99.94) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2026:04:10:19:10:23 mri_mask N 6 e 3.47 S 0.14 U 4.82 P 143% M 329728 F 0 R 81313 W 0 c 26 w 16 I 0 O 4888 L 1.08 1.63 1.73 @#@FSLOADPOST 2026:04:10:19:10:26 mri_mask N 6 1.07 1.62 1.73 mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 2 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 2 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz Fixing entowm 2 255 255 MRIfixEntoWM(): 255 255 Level=2 MRIfixEntoWM(): nchanged = 794 @#@FSTIME 2026:04:10:19:10:26 mri_edit_wm_with_aseg N 7 e 1.66 S 0.08 U 3.05 P 187% M 168528 F 4 R 40882 W 0 c 13 w 20 I 1424 O 4888 L 1.07 1.62 1.73 @#@FSLOADPOST 2026:04:10:19:10:28 mri_edit_wm_with_aseg N 7 1.07 1.61 1.72 mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 brain.finalsurfs.mgz brain.finalsurfs.mgz mri_edit_wm_wit supposed to be reproducible but seed not set LabelAmygalaCortalJunction((): nhits = 6171 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 1011 @#@FSTIME 2026:04:10:19:10:28 mri_edit_wm_with_aseg N 6 e 1.31 S 0.10 U 3.42 P 268% M 147616 F 0 R 75656 W 0 c 13 w 22 I 0 O 4888 L 1.07 1.61 1.72 @#@FSLOADPOST 2026:04:10:19:10:29 mri_edit_wm_with_aseg N 6 1.07 1.61 1.72 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Fri Apr 10 07:10:29 PM JST 2026 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2026:04:10:19:10:29 AntsDenoiseImageFs N 4 e 60.03 S 0.26 U 60.47 P 101% M 678720 F 21 R 168551 W 0 c 230 w 31 I 5024 O 4888 L 1.07 1.61 1.72 @#@FSLOADPOST 2026:04:10:19:11:29 AntsDenoiseImageFs N 4 1.02 1.50 1.67 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 0.8, wsize = 16 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 16 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 919299, nonwhite = 31092804, ambig = 755897, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (102.0): 102.2 +- 5.1 [79.0 --> 125.0] CCS GM (79.0) : 78.8 +- 9.2 [30.0 --> 95.0] white_mean 102.199 white_sigma 5.14894 gray_mean 78.8252 gray_sigma 9.21755 setting bottom of white matter range wm_low to 88.0 setting top of gray matter range gray_hi to 97.3 wm_low 88.0428 wm_hi 125 gray_low 30 gray_hi 97.2603 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=88.0428, wm_hi=125, gray_hi=97.2603 white = 973355, nonwhite = 31528509, ambig = 266136, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 88.0428 wm_hi 125 gray_low 30 gray_hi 97.2603 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 97.2603, wm_low = 88.0428 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=97.2603, wmlow=88.0428 197320 voxels processed (0.60%) 94749 voxels white (0.29%) 102571 voxels non-white (0.31%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=83.0428, gray_hi=97.2603, wsize=16 460203 voxels tested (1.40%) 67638 voxels changed (0.21%) 86830 multi-scale searches (0.26%) Recovering bright white MRIrecoverBrightWhite() wm_low 88.0428 wm_hi 125 slack 5.14894 pct_thresh 0.33 intensity_thresh 130.149 nvox_thresh 8.58 187 voxels tested (0.00%) 120 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=83.0428, hithr=97.2603 smoothing input volume with sigma = 0.250 167024 voxels tested (0.51%) 23855 voxels changed (0.07%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 2701 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1663 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 5420 filled MRIfindBrightNonWM(): 491 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... @#@FSTIME 2026:04:10:19:11:29 mri_segment N 5 e 109.75 S 0.62 U 111.09 P 101% M 271100 F 4 R 559140 W 0 c 543 w 29 I 1248 O 1424 L 1.02 1.50 1.67 @#@FSLOADPOST 2026:04:10:19:13:19 mri_segment N 5 1.06 1.36 1.60 mri_edit_wm_with_aseg -keep-in -fix-ento-wm entowm.mgz 3 255 255 -fix-acj aseg.presurf.mgz 255 255 -fill-seg-wm -fix-scm-ha 1 wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz mri_edit_wm_with_aseg -keep-in -fix-ento-wm entowm.mgz 3 255 255 -fix-acj aseg.presurf.mgz 255 255 -fill-seg-wm -fix-scm-ha 1 wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... mri_edit_wm_wit supposed to be reproducible but seed not set auto filling took 0.77 minutes Fixing entowm 3 255 255 LabelAmygalaCortalJunction((): nhits = 6171 Fixing ACJ 255 255 FixSCM HA 1 reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 45101 additional wm voxels added 0 additional wm voxels added SEG EDIT: 670258 voxels turned on, 90718 voxels turned off. Dilating 1 voxels in 3d propagating editing to output volume from wm.seg.mgz MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 5009 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 1011 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2026:04:10:19:13:19 mri_edit_wm_with_aseg N 17 e 46.27 S 1.29 U 70.03 P 154% M 1249068 F 0 R 900900 W 0 c 241 w 156 I 0 O 1256 L 1.06 1.36 1.60 @#@FSLOADPOST 2026:04:10:19:14:05 mri_edit_wm_with_aseg N 17 1.70 1.45 1.62 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 27 found - 27 modified | TOTAL: 27 pass 2 (xy+): 0 found - 27 modified | TOTAL: 27 pass 1 (xy-): 37 found - 37 modified | TOTAL: 64 pass 2 (xy-): 0 found - 37 modified | TOTAL: 64 pass 1 (yz+): 31 found - 31 modified | TOTAL: 95 pass 2 (yz+): 0 found - 31 modified | TOTAL: 95 pass 1 (yz-): 26 found - 26 modified | TOTAL: 121 pass 2 (yz-): 0 found - 26 modified | TOTAL: 121 pass 1 (xz+): 28 found - 28 modified | TOTAL: 149 pass 2 (xz+): 0 found - 28 modified | TOTAL: 149 pass 1 (xz-): 19 found - 19 modified | TOTAL: 168 pass 2 (xz-): 0 found - 19 modified | TOTAL: 168 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 18 found - 18 modified | TOTAL: 36 pass 2 (+++): 0 found - 18 modified | TOTAL: 36 pass 1 (+++): 18 found - 18 modified | TOTAL: 54 pass 2 (+++): 0 found - 18 modified | TOTAL: 54 pass 1 (+++): 12 found - 12 modified | TOTAL: 66 pass 2 (+++): 0 found - 12 modified | TOTAL: 66 Iteration Number : 1 pass 1 (++): 41 found - 41 modified | TOTAL: 41 pass 2 (++): 0 found - 41 modified | TOTAL: 41 pass 1 (+-): 38 found - 38 modified | TOTAL: 79 pass 2 (+-): 0 found - 38 modified | TOTAL: 79 pass 1 (--): 41 found - 41 modified | TOTAL: 120 pass 2 (--): 0 found - 41 modified | TOTAL: 120 pass 1 (-+): 43 found - 43 modified | TOTAL: 163 pass 2 (-+): 0 found - 43 modified | TOTAL: 163 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 3 found - 3 modified | TOTAL: 7 pass 2 (yz+): 0 found - 3 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 3 found - 3 modified | TOTAL: 12 pass 2 (xz+): 0 found - 3 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 1 found - 1 modified | TOTAL: 5 pass 2 (+++): 0 found - 1 modified | TOTAL: 5 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 3 found - 3 modified | TOTAL: 3 pass 2 (+-): 0 found - 3 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 1 found - 1 modified | TOTAL: 6 pass 2 (-+): 0 found - 1 modified | TOTAL: 6 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 422 (out of 1151974: 0.036633) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:04:10:19:14:06 mri_pretess N 4 e 5.14 S 0.04 U 6.52 P 127% M 104384 F 14 R 24881 W 0 c 26 w 31 I 3912 O 1256 L 1.70 1.45 1.62 @#@FSLOADPOST 2026:04:10:19:14:11 mri_pretess N 4 1.73 1.46 1.62 Fixing entowm in wm.mgz mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 3 255 255 wm.mgz wm.mgz mri_edit_wm_with_aseg -sa-fix-ento-wm entowm.mgz 3 255 255 wm.mgz wm.mgz Fixing entowm 3 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 5009 @#@FSTIME 2026:04:10:19:14:11 mri_edit_wm_with_aseg N 7 e 1.56 S 0.08 U 2.95 P 194% M 168620 F 0 R 40886 W 0 c 9 w 15 I 0 O 1256 L 1.73 1.46 1.62 @#@FSLOADPOST 2026:04:10:19:14:12 mri_edit_wm_with_aseg N 7 1.73 1.46 1.62 Fixing ACJ in wm.mgz mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 wm.mgz wm.mgz mri_edit_wm_with_aseg -sa-fix-acj aseg.presurf.mgz 255 255 wm.mgz wm.mgz mri_edit_wm_wit supposed to be reproducible but seed not set LabelAmygalaCortalJunction((): nhits = 6171 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 1011 @#@FSTIME 2026:04:10:19:14:12 mri_edit_wm_with_aseg N 6 e 1.48 S 0.10 U 3.62 P 250% M 147376 F 0 R 75660 W 0 c 20 w 22 I 0 O 1256 L 1.73 1.46 1.62 @#@FSLOADPOST 2026:04:10:19:14:14 mri_edit_wm_with_aseg N 6 1.67 1.45 1.62 #-------------------------------------------- #@# Fill Fri Apr 10 07:14:14 PM JST 2026 /mnt/data4/test/sub-01/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/8.1.0/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... done. searching for cutting planes...voxel to talairach voxel transform 1.08480 -0.07441 0.03315 -9.04286; 0.06727 1.02925 0.05404 -1.23808; -0.04740 -0.05713 0.98632 -0.34906; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.08480 -0.07441 0.03315 -9.04286; 0.06727 1.02925 0.05404 -1.23808; -0.04740 -0.05713 0.98632 -0.34906; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (546, 2188) area[0] = 4364 (min = 546, max = 2188), aspect = 1.32 (min = 0.10, max = 0.75) need search nearby using seed (159, 137, 114), TAL = (0.8, -36.8, 18.4) talairach voxel to voxel transform 0.91634 0.06434 -0.03432 8.35406; -0.06202 0.96428 -0.05074 0.61530; 0.04044 0.05895 1.00928 0.79100; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (159, 137, 114) --> (0.8, -36.8, 18.4) done. filling took 1.6 minutes talairach cc position changed to (0.80, -36.80, 18.40) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(18.80, -36.80, 18.40) SRC: (138.34, 118.47, 129.45) search lh wm seed point around talairach space (-17.20, -36.80, 18.40), SRC: (179.57, 115.68, 131.27) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2026:04:10:19:14:14 mri_fill N 10 e 97.36 S 1.51 U 97.32 P 101% M 1489656 F 6 R 797571 W 0 c 560 w 22 I 1368 O 448 L 1.67 1.45 1.62 @#@FSLOADPOST 2026:04:10:19:15:51 mri_fill N 10 1.29 1.38 1.58 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Fri Apr 10 07:15:51 PM JST 2026 /mnt/data4/test/sub-01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 20 found - 20 modified | TOTAL: 25 pass 2 (yz+): 0 found - 20 modified | TOTAL: 25 pass 1 (yz-): 8 found - 8 modified | TOTAL: 33 pass 2 (yz-): 0 found - 8 modified | TOTAL: 33 pass 1 (xz+): 3 found - 3 modified | TOTAL: 36 pass 2 (xz+): 0 found - 3 modified | TOTAL: 36 pass 1 (xz-): 4 found - 4 modified | TOTAL: 40 pass 2 (xz-): 0 found - 4 modified | TOTAL: 40 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 2 found - 2 modified | TOTAL: 7 pass 2 (-+): 0 found - 2 modified | TOTAL: 7 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 47 (out of 553676: 0.008489) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:04:10:19:15:51 mri_pretess N 4 e 2.25 S 0.03 U 3.67 P 164% M 71904 F 0 R 16768 W 0 c 27 w 15 I 0 O 440 L 1.29 1.38 1.58 @#@FSLOADPOST 2026:04:10:19:15:54 mri_pretess N 4 1.27 1.38 1.57 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix.predec 8.1.0 8.1.0 slice 50: 1377 vertices, 1496 faces slice 60: 6788 vertices, 7023 faces slice 70: 14859 vertices, 15130 faces slice 80: 23715 vertices, 24051 faces slice 90: 34478 vertices, 34875 faces slice 100: 46024 vertices, 46468 faces slice 110: 58656 vertices, 59092 faces slice 120: 70900 vertices, 71350 faces slice 130: 83984 vertices, 84449 faces slice 140: 98511 vertices, 99011 faces slice 150: 112537 vertices, 113028 faces slice 160: 126525 vertices, 127013 faces slice 170: 139984 vertices, 140477 faces slice 180: 153194 vertices, 153694 faces slice 190: 166785 vertices, 167226 faces slice 200: 178122 vertices, 178525 faces slice 210: 187458 vertices, 187788 faces slice 220: 196079 vertices, 196396 faces slice 230: 204268 vertices, 204579 faces slice 240: 211461 vertices, 211718 faces slice 250: 217323 vertices, 217562 faces slice 260: 220969 vertices, 221038 faces slice 270: 221172 vertices, 221202 faces slice 280: 221172 vertices, 221202 faces slice 290: 221172 vertices, 221202 faces slice 300: 221172 vertices, 221202 faces slice 310: 221172 vertices, 221202 faces slice 320: 221172 vertices, 221202 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix.predec using vox2ras matrix: -0.80000 0.00000 0.00000 128.00000; 0.00000 0.00000 0.80000 -128.00000; 0.00000 -0.80000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2026:04:10:19:15:54 mri_tessellate N 3 e 2.52 S 0.03 U 3.23 P 129% M 61600 F 3 R 14734 W 0 c 18 w 12 I 1128 O 10376 L 1.27 1.38 1.57 @#@FSLOADPOST 2026:04:10:19:15:56 mri_tessellate N 3 1.27 1.38 1.57 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix.predec ../surf/lh.orig.nofix.predec counting number of connected components... 221172 voxel in cpt #1: X=-30 [v=221172,e=663606,f=442404] located at (-25.145000, -9.207247, 32.405563) For the whole surface: X=-30 [v=221172,e=663606,f=442404] One single component has been found nothing to do done @#@FSTIME 2026:04:10:19:15:56 mris_extract_main_component N 2 e 1.22 S 0.24 U 1.74 P 162% M 433360 F 15 R 115675 W 0 c 11 w 60 I 3352 O 15560 L 1.27 1.38 1.57 @#@FSLOADPOST 2026:04:10:19:15:58 mris_extract_main_component N 2 1.27 1.38 1.57 mris_remesh --desired-face-area 0.5 --input ../surf/lh.orig.nofix.predec --output ../surf/lh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.32 decimation level = 0.64 target vertices = 141550 Remesher::remeshBKV( 5 , 141550 ) vcount = 221172 vnum: 141550 area = 141569 avel: 0.910457 s0 = 0.859714 st: 1.07464 Targetn: 205247 points: 221172 Targetl: 0.943294 avg l: 0.910457 points: 221172 Maxndown:17517 Points: 221172 avg edge: 0.863603 Targetn: 189323 points: 221172 Targetl: 0.976131 avg l: 0.863603 points: 221194 Maxndown:35058 Points: 186136 avg edge: 0.911685 Targetn: 173398 points: 186136 Targetl: 1.00897 avg l: 0.911685 points: 186252 Maxndown:14139 Points: 172113 avg edge: 0.933875 Targetn: 157474 points: 172113 Targetl: 1.04181 avg l: 0.933875 points: 172142 Maxndown:16134 Points: 156008 avg edge: 0.966714 Targetn: 141550 points: 156008 Targetl: 1.07464 avg l: 0.966714 points: 156037 Maxndown:14487 Points: 141550 avg edge: 1.00244 Final Points: 141550 final avg edge: 1.00244 avg qual before : 0.866025 after: 0.965099 Removing intersections removing intersecting faces 000: 7 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 221172 nv = 141550 0.64 Area 283160 0.42736 0.05174 0.025294 0.9885 Corner 849480 60.00000 8.51401 10.141702 155.1213 Edge 424740 1.00241 0.10311 0.179049 1.6607 Hinge 424740 33.42726 29.58746 0.000000 178.0351 mris_remesh done @#@FSTIME 2026:04:10:19:15:58 mris_remesh N 6 e 14.49 S 0.64 U 17.12 P 122% M 853304 F 18 R 343861 W 0 c 126 w 114 I 3944 O 9960 L 1.27 1.38 1.57 @#@FSLOADPOST 2026:04:10:19:16:12 mris_remesh N 6 1.21 1.36 1.56 #-------------------------------------------- #@# Tessellate rh Fri Apr 10 07:16:12 PM JST 2026 /mnt/data4/test/sub-01/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 11 found - 11 modified | TOTAL: 14 pass 2 (yz+): 0 found - 11 modified | TOTAL: 14 pass 1 (yz-): 11 found - 11 modified | TOTAL: 25 pass 2 (yz-): 0 found - 11 modified | TOTAL: 25 pass 1 (xz+): 0 found - 0 modified | TOTAL: 25 pass 1 (xz-): 3 found - 3 modified | TOTAL: 28 pass 2 (xz-): 0 found - 3 modified | TOTAL: 28 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 2 found - 2 modified | TOTAL: 2 pass 2 (-+): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 30 (out of 557617: 0.005380) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:04:10:19:16:12 mri_pretess N 4 e 2.06 S 0.03 U 3.48 P 170% M 71904 F 0 R 16771 W 0 c 21 w 16 I 0 O 440 L 1.21 1.36 1.56 @#@FSLOADPOST 2026:04:10:19:16:14 mri_pretess N 4 1.19 1.35 1.56 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix.predec 8.1.0 8.1.0 slice 50: 1099 vertices, 1201 faces slice 60: 5845 vertices, 6063 faces slice 70: 13786 vertices, 14092 faces slice 80: 23017 vertices, 23378 faces slice 90: 33547 vertices, 33947 faces slice 100: 45944 vertices, 46446 faces slice 110: 59350 vertices, 59771 faces slice 120: 71718 vertices, 72137 faces slice 130: 85366 vertices, 85872 faces slice 140: 100139 vertices, 100639 faces slice 150: 114526 vertices, 115025 faces slice 160: 128634 vertices, 129173 faces slice 170: 142103 vertices, 142579 faces slice 180: 155391 vertices, 155910 faces slice 190: 167901 vertices, 168336 faces slice 200: 178781 vertices, 179172 faces slice 210: 188113 vertices, 188469 faces slice 220: 197301 vertices, 197592 faces slice 230: 205630 vertices, 205933 faces slice 240: 212872 vertices, 213160 faces slice 250: 219045 vertices, 219264 faces slice 260: 222576 vertices, 222668 faces slice 270: 222836 vertices, 222868 faces slice 280: 222836 vertices, 222868 faces slice 290: 222836 vertices, 222868 faces slice 300: 222836 vertices, 222868 faces slice 310: 222836 vertices, 222868 faces slice 320: 222836 vertices, 222868 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix.predec using vox2ras matrix: -0.80000 0.00000 0.00000 128.00000; 0.00000 0.00000 0.80000 -128.00000; 0.00000 -0.80000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2026:04:10:19:16:14 mri_tessellate N 3 e 2.48 S 0.03 U 3.19 P 129% M 61824 F 0 R 14789 W 0 c 12 w 9 I 0 O 10456 L 1.19 1.35 1.56 @#@FSLOADPOST 2026:04:10:19:16:17 mri_tessellate N 3 1.19 1.35 1.56 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix.predec ../surf/rh.orig.nofix.predec counting number of connected components... 222836 voxel in cpt #1: X=-32 [v=222836,e=668604,f=445736] located at (27.588877, -9.152300, 31.427916) For the whole surface: X=-32 [v=222836,e=668604,f=445736] One single component has been found nothing to do done @#@FSTIME 2026:04:10:19:16:17 mris_extract_main_component N 2 e 1.36 S 0.22 U 1.97 P 161% M 437712 F 0 R 116628 W 0 c 16 w 47 I 0 O 15672 L 1.19 1.35 1.56 @#@FSLOADPOST 2026:04:10:19:16:18 mris_extract_main_component N 2 1.17 1.35 1.56 mris_remesh --desired-face-area 0.5 --input ../surf/rh.orig.nofix.predec --output ../surf/rh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.32 decimation level = 0.64 target vertices = 142615 Remesher::remeshBKV( 5 , 142615 ) vcount = 222836 vnum: 142615 area = 142636 avel: 0.910457 s0 = 0.859718 st: 1.07465 Targetn: 206791 points: 222836 Targetl: 0.943295 avg l: 0.910457 points: 222836 Maxndown:17649 Points: 222836 avg edge: 0.863451 Targetn: 190747 points: 222836 Targetl: 0.976133 avg l: 0.863451 points: 222852 Maxndown:35315 Points: 187537 avg edge: 0.911838 Targetn: 174703 points: 187537 Targetl: 1.00897 avg l: 0.911838 points: 187651 Maxndown:14242 Points: 173409 avg edge: 0.934233 Targetn: 158659 points: 173409 Targetl: 1.04181 avg l: 0.934233 points: 173431 Maxndown:16249 Points: 157182 avg edge: 0.966925 Targetn: 142615 points: 157182 Targetl: 1.07465 avg l: 0.966925 points: 157217 Maxndown:14602 Points: 142615 avg edge: 1.00258 Final Points: 142615 final avg edge: 1.00258 avg qual before : 0.866025 after: 0.965019 Removing intersections removing intersecting faces 000: 6 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 222836 nv = 142615 0.64 Area 285294 0.42748 0.05222 0.058827 0.8807 Corner 855882 60.00000 8.51776 13.199040 143.4805 Edge 427941 1.00254 0.10352 0.234106 1.6242 Hinge 427941 34.03906 29.97549 0.000000 177.5221 mris_remesh done @#@FSTIME 2026:04:10:19:16:18 mris_remesh N 6 e 14.57 S 0.62 U 17.24 P 122% M 860996 F 0 R 331439 W 0 c 72 w 109 I 0 O 10032 L 1.17 1.35 1.56 @#@FSLOADPOST 2026:04:10:19:16:33 mris_remesh N 6 1.13 1.33 1.55 #-------------------------------------------- #@# Smooth1 lh Fri Apr 10 07:16:33 PM JST 2026 /mnt/data4/test/sub-01/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2026:04:10:19:16:33 mris_smooth N 5 e 2.32 S 0.16 U 3.45 P 155% M 219460 F 5 R 66323 W 0 c 24 w 58 I 1008 O 9960 L 1.13 1.33 1.55 @#@FSLOADPOST 2026:04:10:19:16:35 mris_smooth N 5 1.13 1.33 1.55 #-------------------------------------------- #@# Smooth1 rh Fri Apr 10 07:16:35 PM JST 2026 /mnt/data4/test/sub-01/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2026:04:10:19:16:35 mris_smooth N 5 e 2.31 S 0.16 U 3.48 P 158% M 221168 F 0 R 66918 W 0 c 33 w 66 I 0 O 10032 L 1.13 1.33 1.55 @#@FSLOADPOST 2026:04:10:19:16:38 mris_smooth N 5 1.13 1.33 1.55 #-------------------------------------------- #@# Inflation1 lh Fri Apr 10 07:16:38 PM JST 2026 /mnt/data4/test/sub-01/scripts mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 100 ** failed to open GIFTI XML file '100.gii' mrisReadGIFTIdanum: ERROR reading gifti 100.gii [INFO] read, cannot find 100, trying 100.gii ... error: No such file or directory error: mris_inflate: could not read surface file 100 Command exited with non-zero status 255 @#@FSTIME 2026:04:10:19:16:38 mris_inflate N 4 e 0.02 S 0.00 U 0.00 P 34% M 6272 F 16 R 234 W 0 c 0 w 18 I 3696 O 0 L 1.13 1.33 1.55 @#@FSLOADPOST 2026:04:10:19:16:38 mris_inflate N 4 1.20 1.34 1.55 Linux kami-image3 6.8.0-107-generic #107~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 18 23:40:43 UTC x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-01 exited with ERRORS at Fri Apr 10 07:16:38 PM JST 2026 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting