Mon Nov 11 20:38:32 CST 2024 cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects /usr/local/freesurfer/8.0.0-beta/bin/recon-all -i T1.nii.gz -s sub-JS_test -all subjid sub-JS_test setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects FREESURFER_HOME /usr/local/freesurfer/8.0.0-beta Actual FREESURFER_HOME /usr/local/freesurfer/8.0.0-beta build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 127596 maxlocks unlimited maxsignal 127596 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 31Gi 721Mi 29Gi 6.0Mi 867Mi 30Gi Swap: 8.0Gi 0B 8.0Gi ######################################## program versions used 8.0.0-beta (freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc) 8.0.0-beta ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 8.0.0-beta ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 8.0.0-beta ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mris_convert -all-info ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 8.0.0-beta mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/11/11-12:38:32-GMT BuildTime: Nov 3 2024 00:08:22 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc User: root Machine: LXG Platform: Linux PlatformVersion: 5.15.153.1-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0 ####################################### GCADIR /usr/local/freesurfer/8.0.0-beta/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/8.0.0-beta/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test mri_convert /root/T1.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig/001.mgz mri_convert /root/T1.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=1) reading from /root/T1.nii.gz... WARNING: hdr.dim[4] = 0 (nframes), setting to 1 TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996165, -0.0700546, -0.0524091) j_ras = (0.0703331, 0.997517, 0.00348582) k_ras = (0.0520348, -0.00715855, 0.99862) writing to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig/001.mgz... @#@FSTIME 2024:11:11:20:38:32 mri_convert N 2 e 0.76 S 0.01 U 0.73 P 99% M 22220 F 8 R 600 W 0 c 2 w 4 I 760 O 14512 L 0.00 0.00 0.00 @#@FSLOADPOST 2024:11:11:20:38:33 mri_convert N 2 0.00 0.00 0.00 #-------------------------------------------- #@# MotionCor Mon Nov 11 20:38:33 CST 2024 Found 1 runs /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig/001.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz mri_info /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 176 x 256 x 170 voxel sizes: 1.000000, 1.000000, 1.000000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -88.0, xend: 88.0 ystart: -128.0, yend: 128.0 zstart: -85.0, zend: 85.0 TR: 1900.00 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 = 0.9962, y_r = 0.0703, z_r = 0.0520, c_r = 3.0034 : x_a = -0.0701, y_a = 0.9975, z_a = -0.0072, c_a = 7.7398 : x_s = -0.0524, y_s = 0.0035, z_s = 0.9986, c_s = 19.8414 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.9962 0.0703 0.0520 -98.0848 -0.0701 0.9975 -0.0072 -113.1691 -0.0524 0.0035 0.9986 -60.8755 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 0.9962 -0.0701 -0.0524 86.5902 0.0703 0.9975 0.0035 119.9990 0.0520 -0.0072 0.9986 65.0851 0.0000 0.0000 0.0000 1.0000 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test mri_convert /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --conform reading from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996165, -0.0700546, -0.0524091) j_ras = (0.0703331, 0.997517, 0.00348582) k_ras = (0.0520348, -0.00715855, 0.99862) volume geometry: valid : -658365376 extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) 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) : ( 3.0034, 7.7398, 19.8414) file : /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 1005 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz... @#@FSTIME 2024:11:11:20:38:36 mri_convert N 3 e 0.93 S 0.01 U 0.92 P 100% M 31316 F 0 R 6136 W 0 c 1 w 1 I 0 O 8792 L 0.00 0.00 0.00 @#@FSLOADPOST 2024:11:11:20:38:37 mri_convert N 3 0.08 0.02 0.01 mri_add_xform_to_header -c /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/talairach.xfm /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2024:11:11:20:38:37 mri_add_xform_to_header N 4 e 0.37 S 0.00 U 0.34 P 96% M 23172 F 17 R 973 W 0 c 1 w 16 I 3600 O 8792 L 0.08 0.02 0.01 @#@FSLOADPOST 2024:11:11:20:38:38 mri_add_xform_to_header N 4 0.08 0.02 0.01 mri_info /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz orig.mgz ======================================== Volume information for /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz type: MGH intent: MRI (0) dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1900.00 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 = 3.0034 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 7.7398 : x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 19.8414 talairach xfm : /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 131.0034 -0.0000 0.0000 1.0000 -120.2602 -0.0000 -1.0000 0.0000 147.8414 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 -0.0000 131.0034 0.0000 -0.0000 -1.0000 147.8414 -0.0000 1.0000 -0.0000 120.2602 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz --trg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --outlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg2orig.lta 8.0.0-beta --inlta: identity.nofile input LTA transform. --src: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg.mgz src image (geometry). --trg: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz trg image (geometry). --outlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg2orig.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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/rawavg2orig.lta... lta_convert successful. @#@FSTIME 2024:11:11:20:38:38 lta_convert N 8 e 0.09 S 0.00 U 0.08 P 97% M 6412 F 6 R 249 W 0 c 1 w 6 I 904 O 8 L 0.08 0.02 0.01 @#@FSLOADPOST 2024:11:11:20:38:38 lta_convert N 8 0.08 0.02 0.01 mri_synthstrip --threads 1 -i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz -o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 2024:11:11:20:38:38 mri_synthstrip N 6 e 17.84 S 2.06 U 15.87 P 100% M 5904820 F 1488 R 106435 W 0 c 22 w 3475 I 394168 O 3000 L 0.08 0.02 0.01 @#@FSLOADPOST 2024:11:11:20:38:56 mri_synthstrip N 6 0.28 0.07 0.02 mri_synthseg --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthseg.rca.mgz --threads 1 --vol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/stats/synthseg.vol.csv --keepgeom --addctab --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread addctab True predicting 1/1 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 232s 232s/step Reslicing to have same geom as the input [1. 1. 1.] segmentation saved in: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthseg.rca.mgz volumes saved in: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/stats/synthseg.vol.csv #@# mri_synthseg vmpeak 17831972 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 2024:11:11:20:38:56 mri_synthseg N 11 e 243.69 S 9.44 U 232.91 P 99% M 13991500 F 3758 R 424443 W 0 c 257 w 9228 I 834616 O 3048 L 0.28 0.07 0.02 @#@FSLOADPOST 2024:11:11:20:43:00 mri_synthseg N 11 1.02 0.62 0.27 Mon Nov 11 20:43:00 CST 2024 setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test /usr/local/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthstrip.mgz --t /usr/local/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz --affine-only --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305 --threads 1 -rwxr-xr-x 1 root root 30900 Nov 3 08:16 /usr/local/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3675 Mon Nov 11 20:43:00 CST 2024 mri_synthmorph -m affine -t /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/aff.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthstrip.mgz /usr/local/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz -j 1 #@# mri_synthmorph: affine, threads: 1, VmPeak: 6825004 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 2024:11:11:20:43:00 mri_synthmorph N 8 e 26.51 S 3.45 U 22.76 P 98% M 5498136 F 340 R 311520 W 0 c 71 w 2563 I 187824 O 432 L 1.02 0.62 0.27 @#@FSLOADPOST 2024:11:11:20:43:26 mri_synthmorph N 8 1.01 0.65 0.29 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test lta_convert --invert --inlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/aff.lta --outlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta 8.0.0-beta --invert: will invert transform. --inlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/aff.lta input LTA transform. --outlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta output LTA. LTA read, type : 1 1.01600 -0.10490 -0.05406 0.54325; 0.07942 1.00637 0.10112 -32.58241; 0.04790 -0.03962 1.04753 -20.03142; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta... lta_convert successful. @#@FSTIME 2024:11:11:20:43:26 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 0% M 5784 F 0 R 221 W 0 c 0 w 0 I 0 O 8 L 1.01 0.65 0.29 @#@FSLOADPOST 2024:11:11:20:43:26 lta_convert N 5 1.01 0.65 0.29 To check affine registration tkregisterfv --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthstrip.mgz --targ /usr/local/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz --reg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.mni305/aff.lta AffineOnly specified, so exiting now Started at Mon Nov 11 20:43:00 CST 2024 Ended at Mon Nov 11 20:43:26 CST 2024 Fs-Synthmorph-Reg-Run-Time-Sec 26 Fs-Synthmorph-Reg-Run-Time-Min 0.43 Fs-Synthmorph-Reg-Run-Time-Hours 0.01 fs-synthmorph-reg Done @#@FSTIME 2024:11:11:20:43:00 fs-synthmorph-reg N 9 e 26.57 S 3.46 U 22.79 P 98% M 5498136 F 342 R 333199 W 0 c 74 w 2782 I 187896 O 456 L 1.02 0.62 0.27 @#@FSLOADPOST 2024:11:11:20:43:26 fs-synthmorph-reg N 9 1.01 0.65 0.29 8.0.0-beta --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 1.01600 -0.10490 -0.05406 0.54325; 0.07942 1.00637 0.10112 -32.58241; 0.04790 -0.03962 1.04753 -20.03142; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file talairach.xfm.lta... lta_convert successful. 8.0.0-beta --inlta: talairach.xfm.lta input LTA transform. --outmni: talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.01600 -0.10490 -0.05406 0.54326; 0.07942 1.00637 0.10112 -32.58241; 0.04790 -0.03962 1.04753 -20.03142; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. fs-synthmorph-reg --s sub-JS_test --threads 1 --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --test Mon Nov 11 20:43:26 CST 2024 setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test /usr/local/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg --s sub-JS_test --threads 1 --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --test -rwxr-xr-x 1 root root 30900 Nov 3 08:16 /usr/local/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3949 mri_mask -bb 3 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 25 36 0 207 185 256 maskval=0, outval=0 Writing masked volume to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done. lta_convert --inlta identity.nofile --src /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --trg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --outlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta 8.0.0-beta --inlta: identity.nofile input LTA transform. --src: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz src image (geometry). --trg: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz trg image (geometry). --outlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta... lta_convert successful. Mon Nov 11 20:43:27 CST 2024 mri_synthmorph -m affine -t /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 [DEBUG] FSNifti1Extension.read(): esize = 1232 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1220 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1204 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1165 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1105 (tag = 31, length = 83) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1010 (tag = 3, length = 453) [DEBUG] FSNifti1Extension.read(): remaining taglen = 545 (tag = 3, length = 512) [DEBUG] FSNifti1Extension.read(): remaining taglen = 21 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 8 [DEBUG] FSNifti1Extension.read(): esize = 144 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 132 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 116 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 77 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 17 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 4 #@# mri_synthmorph: affine, threads: 1, VmPeak: 6768396 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 2024:11:11:20:43:27 mri_synthmorph N 8 e 26.13 S 3.38 U 22.66 P 99% M 5446724 F 47 R 292133 W 0 c 68 w 1499 I 24456 O 432 L 1.01 0.65 0.29 @#@FSLOADPOST 2024:11:11:20:43:53 mri_synthmorph N 8 1.00 0.68 0.31 Mon Nov 11 20:43:53 CST 2024 mri_concatenate_lta -invert1 -invertout /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta... mri_concatenate_lta successful. @#@FSTIME 2024:11:11:20:43:53 mri_concatenate_lta N 5 e 0.00 S 0.00 U 0.00 P 100% M 5588 F 0 R 220 W 0 c 0 w 1 I 0 O 8 L 1.00 0.68 0.31 @#@FSLOADPOST 2024:11:11:20:43:53 mri_concatenate_lta N 5 1.00 0.68 0.31 mri_concatenate_lta -invert2 /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta... mri_concatenate_lta successful. @#@FSTIME 2024:11:11:20:43:53 mri_concatenate_lta N 4 e 0.00 S 0.00 U 0.00 P 0% M 5384 F 0 R 216 W 0 c 0 w 1 I 8 O 8 L 1.00 0.68 0.31 @#@FSLOADPOST 2024:11:11:20:43:53 mri_concatenate_lta N 4 1.00 0.68 0.31 lta_convert --invert --inlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --outlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta 8.0.0-beta --invert: will invert transform. --inlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta input LTA transform. --outlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta output LTA. LTA read, type : 1 0.92801 0.10373 0.04106 4.03521; -0.07830 0.95396 -0.04446 28.99595; -0.04133 0.02823 0.89328 20.15619; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta... lta_convert successful. @#@FSTIME 2024:11:11:20:43:53 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 96% M 5948 F 0 R 223 W 0 c 0 w 1 I 0 O 8 L 1.00 0.68 0.31 @#@FSLOADPOST 2024:11:11:20:43:53 lta_convert N 5 1.00 0.68 0.31 lta_convert --inlta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta --outmni /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm 8.0.0-beta --inlta: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta input LTA transform. --outmni: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm output MNI/XFM matrix. LTA read, type : 1 1.06550 -0.11424 -0.05467 0.11495; 0.08962 1.03711 0.04750 -31.39115; 0.04646 -0.03806 1.11544 -21.56685; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. To check affine registration tkregisterfv --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz --targ /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --reg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta mri_synthmorph -m deform -t /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz -i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 -o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz [DEBUG] FSNifti1Extension.read(): esize = 1232 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1220 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1204 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1165 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1105 (tag = 31, length = 83) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1010 (tag = 3, length = 453) [DEBUG] FSNifti1Extension.read(): remaining taglen = 545 (tag = 3, length = 512) [DEBUG] FSNifti1Extension.read(): remaining taglen = 21 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 8 [DEBUG] FSNifti1Extension.read(): esize = 144 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 132 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 116 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 77 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 17 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 4 #@# mri_synthmorph: deform, threads: 1, VmPeak: 15529016 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 2024:11:11:20:43:53 mri_synthmorph N 12 e 538.44 S 13.37 U 524.28 P 99% M 14216052 F 61 R 808620 W 0 c 161 w 3412 I 6864264 O 121224 L 1.00 0.68 0.31 @#@FSLOADPOST 2024:11:11:20:52:51 mri_synthmorph N 12 1.01 0.97 0.64 mri_warp_convert --inras /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz --insrcgeom /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --outm3z /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz --vg-thresh 1e-5 --lta1-inv /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta --lta2 /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta 8.0.0-beta --inras: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz input RAS warp. --insrcgeom: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz atlas/source image (used for geometry). --outm3z: /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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(/usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 [256 x 256 x 256] [INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193] [INFO] Warpfield::convert(): total out of range voxel count: 0 volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) 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) : ( 3.0034, 7.7398, 19.8414) file : /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz volume geometry: extent : (193, 229, 193) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : ( 1.0000, -0.0000, 0.0000) y_(ras) : (-0.0000, 1.0000, 0.0000) z_(ras) : (-0.0000, -0.0000, 1.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /autofs/space/curv_001/users/fs-mni152-atlas/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz mri_warp_convert successful. @#@FSTIME 2024:11:11:20:52:51 mri_warp_convert N 12 e 5.68 S 0.68 U 4.96 P 99% M 3406464 F 21 R 851558 W 0 c 5 w 19 I 3792 O 90776 L 1.01 0.97 0.64 @#@FSLOADPOST 2024:11:11:20:52:57 mri_warp_convert N 12 1.01 0.97 0.64 mri_ca_register -invert-and-save /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 [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...(256, 256, 256) Saving inverse to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz GCAMwrite(/usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 [256 x 256 x 256] [INFO] Warpfield::convert(): gcam image [193 x 229 x 193] [INFO] Warpfield::convert(): gcam atlas [256 x 256 x 256] [INFO] Warpfield::convert(): total out of range voxel count: 0 volume geometry: extent : (193, 229, 193) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : ( 1.0000, -0.0000, 0.0000) y_(ras) : (-0.0000, 1.0000, 0.0000) z_(ras) : (-0.0000, -0.0000, 1.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /autofs/space/curv_001/users/fs-mni152-atlas/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) 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) : ( 3.0034, 7.7398, 19.8414) file : /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz @#@FSTIME 2024:11:11:20:52:57 mri_ca_register N 3 e 45.00 S 1.63 U 43.32 P 99% M 7132704 F 11 R 1709715 W 0 c 34 w 13 I 1824 O 277448 L 1.01 0.97 0.64 @#@FSLOADPOST 2024:11:11:20:53:42 mri_ca_register N 3 1.00 0.98 0.66 mri_vol2vol --regheader --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz --targ /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz movvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz targvol /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1732042020 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 2024:11:11:20:53:42 mri_vol2vol N 7 e 0.68 S 0.00 U 0.67 P 98% M 54712 F 6 R 1605 W 0 c 3 w 5 I 1272 O 32248 L 1.00 0.98 0.66 @#@FSLOADPOST 2024:11:11:20:53:43 mri_vol2vol N 7 1.00 0.98 0.66 mri_convert -rt nearest /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz -at /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz mri_convert -rt nearest /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz -at /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.84987e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (5.87897e-09, 1, 0) INFO: Reading transformation from file /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... INFO: Applying transformation from file /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... Applying morph_3d ... [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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz... @#@FSTIME 2024:11:11:20:53:43 mri_convert N 6 e 3.18 S 0.40 U 2.77 P 99% M 2367472 F 2 R 560813 W 0 c 5 w 2 I 256 O 7136 L 1.00 0.98 0.66 @#@FSLOADPOST 2024:11:11:20:53:46 mri_convert N 6 1.00 0.98 0.66 mri_diff --po /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz mri_diff --po /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz diffcount 4587825 Volumes differ in pixel data maxdiff 98.51811218 at 159 165 20 0 tkmeditfv -f /usr/local/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -aux /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz Started at Mon Nov 11 20:43:26 CST 2024 Ended at Mon Nov 11 20:53:46 CST 2024 Fs-Synthmorph-Reg-Run-Time-Sec 620 Fs-Synthmorph-Reg-Run-Time-Min 10.33 Fs-Synthmorph-Reg-Run-Time-Hours 0.17 fs-synthmorph-reg Done @#@FSTIME 2024:11:11:20:43:26 fs-synthmorph-reg N 7 e 620.26 S 19.49 U 599.77 P 99% M 14216052 F 157 R 4274400 W 0 c 283 w 5508 I 6898032 O 538040 L 1.01 0.65 0.29 @#@FSLOADPOST 2024:11:11:20:53:46 fs-synthmorph-reg N 7 1.00 0.98 0.66 #-------------------------------------------- #@# Nu Intensity Correction Mon Nov 11 20:53:46 CST 2024 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri /usr/local/freesurfer/8.0.0-beta/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 8.0.0-beta Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Mon Nov 11 20:53:46 CST 2024 tmpdir is ./tmp.mri_nu_correct.mni.6882 cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.6882/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.6882/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6882/ones.mgz 8.0.0-beta cwd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.6882/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6882/ones.mgz sysname Linux hostname LXG machine x86_64 user root input ./tmp.mri_nu_correct.mni.6882/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6882/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.6882/ones.mgz Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6882/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6882/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6882/input.mean.dat 8.0.0-beta cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6882/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6882/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6882/input.mean.dat sysname Linux hostname LXG machine x86_64 user root whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6882/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.6882/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6882/ones.mgz --i ./tmp.mri_nu_correct.mni.6882/nu0.mgz --sum ./tmp.mri_nu_correct.mni.6882/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6882/output.mean.dat 8.0.0-beta cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6882/ones.mgz --i ./tmp.mri_nu_correct.mni.6882/nu0.mgz --sum ./tmp.mri_nu_correct.mni.6882/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6882/output.mean.dat sysname Linux hostname LXG machine x86_64 user root whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6882/ones.mgz Loading ./tmp.mri_nu_correct.mni.6882/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.6882/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6882/nu0.mgz ./tmp.mri_nu_correct.mni.6882/nu0.mgz mul 1.10029752820351545759 Packing Done packing Unpacking Saving result to './tmp.mri_nu_correct.mni.6882/nu0.mgz' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 213648 mri_convert ./tmp.mri_nu_correct.mni.6882/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.6882/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.6882/nu0.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.84987e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (5.87897e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 2 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 1, i2 = 45 #mri_make_uchar# mapping 3 116 to 3 110 : b 0.107955 m 0.948088 : thresh -0.113866 maxsat 268.848 : nzero 0 nsat 0 Mon Nov 11 20:54:59 CST 2024 mri_nu_correct.mni done @#@FSTIME 2024:11:11:20:53:46 mri_nu_correct.mni N 9 e 72.13 S 0.19 U 71.86 P 99% M 614400 F 68 R 168808 W 0 c 37 w 200 I 12656 O 43544 L 1.00 0.98 0.66 @#@FSLOADPOST 2024:11:11:20:54:59 mri_nu_correct.mni N 9 1.00 0.98 0.69 mri_add_xform_to_header -c /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2024:11:11:20:54:59 mri_add_xform_to_header N 4 e 0.37 S 0.00 U 0.37 P 100% M 23440 F 2 R 993 W 0 c 1 w 2 I 512 O 8552 L 1.00 0.98 0.69 @#@FSLOADPOST 2024:11:11:20:54:59 mri_add_xform_to_header N 4 1.00 0.99 0.69 #-------------------------------------------- #@# Intensity Normalization Mon Nov 11 20:54:59 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.01600 -0.10490 -0.05406 0.54326; 0.07942 1.00637 0.10112 -32.58241; 0.04790 -0.03962 1.04753 -20.03142; 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 = 22 Starting OpenSpline(): npoints = 22 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 86 (86), valley at 55 (55) csf peak at 43, setting threshold to 71 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 78 (78), valley at 33 (33) csf peak at 40, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 0 minutes and 38 seconds. @#@FSTIME 2024:11:11:20:54:59 mri_normalize N 7 e 38.28 S 0.13 U 38.13 P 99% M 586320 F 10 R 15556 W 0 c 23 w 10 I 1736 O 8248 L 1.00 0.99 0.69 @#@FSLOADPOST 2024:11:11:20:55:37 mri_normalize N 7 1.00 0.99 0.70 #-------------------------------------- #@# MCADura Segmentation Mon Nov 11 20:55:37 CST 2024 mri_mcadura_seg --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/mca-dura.mgz --threads 1 --synthmorphdir /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm Mon Nov 11 20:55:37 CST 2024 setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri /usr/local/freesurfer/8.0.0-beta/bin/mri_mcadura_seg --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/mca-dura.mgz --threads 1 --synthmorphdir /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root root 13384 Nov 3 08:16 /usr/local/freesurfer/8.0.0-beta/bin/mri_mcadura_seg freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 7491 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_vol2vol --reg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/mcadura.prior.lh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.06550 0.11424 0.05467 -0.84615; 0.04646 -0.03806 1.11544 -18.09007; -0.08962 -1.03711 -0.04750 4.65238; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/mcadura.prior.lh.nii.gz regfile /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1732137148 Final tkRAS-to-tkRAS Matrix is: -1.06550 0.11424 0.05467 -0.84615; 0.04646 -0.03806 1.11544 -18.09007; -0.08962 -1.03711 -0.04750 4.65238; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.06550 0.05467 -0.11424 241.35637; -0.08962 -0.04750 1.03711 -5.35094; -0.04646 -1.11544 -0.03806 232.00438; 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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/mcadura.prior.lh.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/lh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 7035 voxels in mask (pct= 0.04) MRIcropToFoV(): thresh=0.001 FoV = (80,80,80) nhits=7035 centroid = (162.733,144.913,175.18) min = (135,120,157) max = (181,165,193) delta = (47,46,37) Region 123 105 135 80 80 80 123 105 135 80 80 80 maskval=0, outval=0 Writing masked volume to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/lh.crop.nii.gz...done. mri_vol2vol --regheader --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --targ /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/lh.crop.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.lh.crop.nii.gz movvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz targvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/lh.crop.nii.gz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/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 1732105278 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -35.00000; 0.00000 1.00000 0.00000 47.00000; 0.00000 0.00000 1.00000 -17.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 123.00000; 0.00000 1.00000 0.00000 105.00000; 0.00000 0.00000 1.00000 135.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_sclimbic_seg --model /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.lh.crop.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.mgz /usr/local/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.lh.crop.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.0.0-beta/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 [DEBUG] FSNifti1Extension.read(): esize = 1232 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1220 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1204 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1165 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1105 (tag = 31, length = 83) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1010 (tag = 3, length = 453) [DEBUG] FSNifti1Extension.read(): remaining taglen = 545 (tag = 3, length = 512) [DEBUG] FSNifti1Extension.read(): remaining taglen = 21 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 8 Loaded input image from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.lh.crop.nii.gz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 1s 989ms/step Wrote segmentation to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.mgz vmpcma: 4614988 done mri_vol2vol --regheader --interp nearest --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.mgz --targ /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.uncropped.mgz movvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.mgz targvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/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 1731504838 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 35.00000; 0.00000 1.00000 0.00000 -47.00000; 0.00000 0.00000 1.00000 17.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -123.00000; 0.00000 1.00000 0.00000 -105.00000; 0.00000 0.00000 1.00000 -135.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --reg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/mcadura.prior.rh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.06550 0.11424 0.05467 -0.84615; 0.04646 -0.03806 1.11544 -18.09007; -0.08962 -1.03711 -0.04750 4.65238; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/mcadura.prior.rh.nii.gz regfile /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1731792652 Final tkRAS-to-tkRAS Matrix is: -1.06550 0.11424 0.05467 -0.84615; 0.04646 -0.03806 1.11544 -18.09007; -0.08962 -1.03711 -0.04750 4.65238; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.06550 0.05467 -0.11424 241.35637; -0.08962 -0.04750 1.03711 -5.35094; -0.04646 -1.11544 -0.03806 232.00438; 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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/mcadura.prior.rh.nii.gz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/rh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 7506 voxels in mask (pct= 0.04) MRIcropToFoV(): thresh=0.001 FoV = (80,80,80) nhits=7506 centroid = (89.5771,148.294,170.275) min = (67,125,153) max = (116,167,189) delta = (50,43,37) Region 50 108 130 80 80 80 50 108 130 80 80 80 maskval=0, outval=0 Writing masked volume to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/rh.crop.nii.gz...done. mri_vol2vol --regheader --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --targ /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/rh.crop.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.nii.gz movvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz targvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/rh.crop.nii.gz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/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 1731736563 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 38.00000; 0.00000 1.00000 0.00000 42.00000; 0.00000 0.00000 1.00000 -20.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 50.00000; 0.00000 1.00000 0.00000 108.00000; 0.00000 0.00000 1.00000 130.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.nii.gz --left-right-reverse-pix /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.lrrev.nii.gz mri_convert /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.nii.gz --left-right-reverse-pix /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.lrrev.nii.gz reading from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/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=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.84987e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (5.87897e-09, 1, 0) writing to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.lrrev.nii.gz... mri_sclimbic_seg --model /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.lrrev.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.lrrev.mgz /usr/local/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.lrrev.nii.gz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.lrrev.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.0.0-beta/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 [DEBUG] FSNifti1Extension.read(): esize = 1856 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1844 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1828 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1789 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1729 (tag = 31, length = 83) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1634 (tag = 3, length = 453) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1169 (tag = 3, length = 512) [DEBUG] FSNifti1Extension.read(): remaining taglen = 645 (tag = 3, length = 605) [DEBUG] FSNifti1Extension.read(): remaining taglen = 28 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 15 (tag = 0, length = 0) Loaded input image from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/invol.rh.crop.lrrev.nii.gz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 1s 1s/step Wrote segmentation to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.lrrev.mgz vmpcma: 4614996 done mri_convert /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.lrrev.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.mgz --left-right-swap-label-table /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.index /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.rh.index --left-right-reverse-pix mri_convert /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.lrrev.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.mgz --left-right-swap-label-table /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.lh.index /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/dumca.rh.index --left-right-reverse-pix reading from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.lrrev.mgz... Performing left-right swap of labels MRIlrswapSeg(): nswaps 832 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=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.84987e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (5.87897e-09, 1, 0) writing to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.mgz... mri_vol2vol --regheader --interp nearest --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.mgz --targ /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.uncropped.mgz movvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.mgz targvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/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 1732257342 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -38.00000; 0.00000 1.00000 0.00000 -42.00000; 0.00000 0.00000 1.00000 20.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -50.00000; 0.00000 1.00000 0.00000 -108.00000; 0.00000 0.00000 1.00000 -130.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_concat /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.lh.uncropped.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.mri_mcadura_seg.7491/seg.rh.uncropped.mgz --sum --ctab /usr/local/freesurfer/8.0.0-beta/models/mca-dura.ctab --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/mca-dura.mgz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing sum across frames Writing to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/mca-dura.mgz fsvglrun freeview -neuro-view --hide-3d-slices --view coronal /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/mca-dura.mgz:isosurface=1:outline=1 Started at Mon Nov 11 20:55:37 CST 2024 Ended at Mon Nov 11 20:55:47 CST 2024 mri_mcadura_seg-Run-Time-Sec 10 mri_mcadura_seg Done #-------------------------------------- #@# VSinus Segmentation Mon Nov 11 20:55:47 CST 2024 mri_vsinus_seg --s sub-JS_test --rca-synthseg --threads 1 --synthmorphdir /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm Mon Nov 11 20:55:47 CST 2024 setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri /usr/local/freesurfer/8.0.0-beta/bin/mri_vsinus_seg --s sub-JS_test --rca-synthseg --threads 1 --synthmorphdir /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root root 20960 Nov 3 08:16 /usr/local/freesurfer/8.0.0-beta/bin/mri_vsinus_seg freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 7780 mri_vol2vol --mov /usr/local/freesurfer/8.0.0-beta/average/vsinus.no-sp.prior.mni152.1.0mm.mgz --lta /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --targ /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mgz Matrix from LTA: -1.06550 0.11424 0.05467 -0.84615; 0.04646 -0.03806 1.11544 -18.09010; -0.08962 -1.03711 -0.04750 4.65239; 0.00000 0.00000 0.00000 1.00000; /usr/local/freesurfer/8.0.0-beta/average/vsinus.no-sp.prior.mni152.1.0mm.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz movvol /usr/local/freesurfer/8.0.0-beta/average/vsinus.no-sp.prior.mni152.1.0mm.mgz targvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mgz regfile /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1731922781 Final tkRAS-to-tkRAS Matrix is: -1.06550 0.11424 0.05467 -0.84615; 0.04646 -0.03806 1.11544 -18.09009; -0.08962 -1.03711 -0.04750 4.65238; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.06550 0.05467 -0.11424 241.35638; -0.08962 -0.04750 1.03711 -5.35096; -0.04646 -1.11544 -0.03806 232.00438; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop 0 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz threshold mask volume at 0.001 cropping npad = 0 DoAbs = 0 Found 96638 voxels in mask (pct= 0.58) Computing bounding box, npad = 0, 0, 0, 0, 0, 0 69 41 42 128 124 97 maskval=0, outval=0 Writing masked volume to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz...done. mri_binarize --crop-around-ras /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz nolta cras /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz 0 144 144 144 Getting cras from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz final ras2vox matrix -1.00000 0.00000 -0.00000 131.00337; 0.00000 -0.00000 -1.00000 147.84140; -0.00000 1.00000 -0.00000 120.26017; -0.00000 -0.00000 -0.00000 1.00000; -------------------------- ostr LIA (144 144 144) (144 144 144) rasCenter -1.99663 -29.7602 44.8414 crsCenter 133 103 90.5 MRIcropAroundCRS() vol size 256 256 256 center 133 103 90.5 fov 144 144 144 limits 62 205 32 175 20 163 using MRIextractRegion() mri_sclimbic_seg --model /usr/local/freesurfer/8.0.0-beta/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1 --no-cite-sclimbic --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz /usr/local/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.0.0-beta/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1 --no-cite-sclimbic --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/vsinus.no-sp.ctab Loaded population stats /usr/local/freesurfer/8.0.0-beta/models/sclimbic.volstats.csv nb_labels 6 inshape (144, 144, 144) features 24 (None, 144, 144, 144, 1) Loading weights from /usr/local/freesurfer/8.0.0-beta/models/vsinus.no-sp.m.all.nstd10-070.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.0.0-beta/models/vsinus.no-sp.m.all.nstd10-070.h5 Segmenting image 1/1 Loaded input image from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 8s 8s/step Wrote segmentation to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz vmpcma: 6370064 done mri_binarize --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthseg.rca.mgz --match 3 42 --inv --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/ctxsegmask.mgz 8.0.0-beta cwd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri cmdline mri_binarize --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthseg.rca.mgz --match 3 42 --inv --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/ctxsegmask.mgz sysname Linux hostname LXG machine x86_64 user root input /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthseg.rca.mgz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 571120 values in range Counting number of voxels in first frame Found 571120 voxels in final mask Writing output to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/ctxsegmask.mgz Count: 571120 571120.000000 16777216 3.404140 mri_binarize done mri_vol2vol --mov /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz --targ /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --interp nearest --o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz --regheader movvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz targvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz outvol /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 1731708468 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 6.00000; 0.00000 1.00000 0.00000 36.00000; 0.00000 0.00000 1.00000 -24.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -62.00000; 0.00000 1.00000 0.00000 -32.00000; 0.00000 0.00000 1.00000 -20.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/tmp.vsinus/ctxsegmask.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz...done. mri_segstats --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --seg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz --sum /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/stats/vsinus.stats --subject sub-JS_test --etiv 8.0.0-beta cwd cmdline mri_segstats --i /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz --seg /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz --sum /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/stats/vsinus.stats --subject sub-JS_test --etiv sysname Linux hostname LXG machine x86_64 user root whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1793629 mm^3 (det: 1.086125 ) Loading /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz Using embedded color table (and excluding seg 0) Loading /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz Voxel Volume is 1 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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz:lock=1 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz:isosurface=1:outline=1 Started at Mon Nov 11 20:55:47 CST 2024 Ended at Mon Nov 11 20:56:03 CST 2024 Mri_Vsinus_Seg-Run-Time-Sec 16 Mri_Vsinus_Seg-Run-Time-Min 0.27 Mri_Vsinus_Seg-Run-Time-Hours 0.00 mri_vsinus_seg Done mri_mask /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/T1.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/synthstrip.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/brainmask.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/brainmask.mgz...done. #------------------------------------- #@# EM Registration Mon Nov 11 20:56:03 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/8.0.0-beta/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/8.0.0-beta/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 0 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=26.9 skull bounding box = (61, 51, 44) --> (200, 182, 222) finding center of left hemi white matter using (107, 95, 133) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (90,79,111) --> (124, 111,154) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.5 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.376 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.184039 @ (-10.526, -10.526, -10.526) max log p = -3.786440 @ (5.263, 5.263, -15.789) max log p = -3.669600 @ (2.632, 2.632, 2.632) max log p = -3.597603 @ (1.316, 3.947, 1.316) max log p = -3.592642 @ (-0.658, -1.974, 0.658) max log p = -3.581878 @ (-0.329, 0.329, -0.329) max log p = -3.581878 @ (0.000, 0.000, 0.000) max log p = -3.581878 @ (0.000, 0.000, 0.000) Found translation: (-2.3, -0.3, -22.0): log p = -3.582 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.550, old_max_log_p =-3.582 (thresh=-3.6) 0.98296 -0.14630 0.11127 3.21540; 0.12941 0.98074 0.14630 -33.37994; -0.13053 -0.12941 0.98296 12.46348; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.514, old_max_log_p =-3.550 (thresh=-3.5) 0.99352 -0.01593 0.11250 -13.90055; 0.01579 0.99987 0.00208 -2.61801; -0.11252 -0.00029 0.99365 -6.66872; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.514, old_max_log_p =-3.514 (thresh=-3.5) 0.99352 -0.01593 0.11250 -13.90055; 0.01579 0.99987 0.00208 -2.61801; -0.11252 -0.00029 0.99365 -6.66872; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.432, old_max_log_p =-3.514 (thresh=-3.5) 1.00943 -0.08267 0.10989 -9.51308; 0.06423 0.96872 0.13873 -26.37540; -0.11769 -0.12815 0.98459 10.69329; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.411, old_max_log_p =-3.432 (thresh=-3.4) 1.03093 -0.01907 0.11665 -21.04369; 0.00572 0.99669 0.06795 -11.21612; -0.11111 -0.06331 0.97296 3.32009; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.398, old_max_log_p =-3.411 (thresh=-3.4) 1.03093 -0.01907 0.11665 -21.04369; 0.00583 1.01468 0.06917 -13.57136; -0.11111 -0.06331 0.97296 3.32009; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.398, old_max_log_p =-3.398 (thresh=-3.4) 1.03093 -0.01907 0.11665 -21.04369; 0.00583 1.01468 0.06917 -13.57136; -0.11111 -0.06331 0.97296 3.32009; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.392, old_max_log_p =-3.398 (thresh=-3.4) 1.02852 -0.01903 0.11638 -20.69718; 0.00491 1.01294 0.07706 -14.24713; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.388, old_max_log_p =-3.392 (thresh=-3.4) 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.388, old_max_log_p =-3.388 (thresh=-3.4) 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 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) = -0.0 tol 0.000010 Resulting transform: 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.388 (old=-4.376) transform before final EM align: 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 4.0 tol 0.000000 final transform: 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 773836 FSRUNTIME@ mri_em_register 0.0784 hours 1 threads registration took 4 minutes and 42 seconds. @#@FSTIME 2024:11:11:20:56:03 mri_em_register N 7 e 282.40 S 0.22 U 282.11 P 99% M 616420 F 11 R 114892 W 0 c 20 w 288 I 141872 O 24 L 1.00 0.99 0.71 @#@FSLOADPOST 2024:11:11:21:00:46 mri_em_register N 7 1.00 1.02 0.82 #-------------------------------------- #@# CA Normalize Mon Nov 11 21:00:46 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/8.0.0-beta/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/8.0.0-beta/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=26.9 skull bounding box = (61, 51, 44) --> (200, 182, 222) finding center of left hemi white matter using (107, 95, 133) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,79,111) --> (124, 111,154) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.5 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246437 sample points... INFO: compute sample coordinates transform 1.02852 -0.01903 0.11638 -20.69718; 0.00492 1.01531 0.07724 -14.56011; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 55, 49) --> (197, 170, 220) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 3 of 7405 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 56, 46) --> (135, 172, 217) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 18 of 8729 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (135, 138, 75) --> (183, 183, 130) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 2 of 120 (1.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (92, 138, 68) --> (136, 183, 128) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 15 of 74 (20.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (115, 132, 109) --> (149, 200, 141) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 361 (0.3%) samples deleted using 16689 total control points for intensity normalization... bias field = 0.988 +- 0.049 161 of 16650 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 55, 49) --> (197, 170, 220) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 7597 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 56, 46) --> (135, 172, 217) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 20 of 8878 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (135, 138, 75) --> (183, 183, 130) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 146 (7.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (92, 138, 68) --> (136, 183, 128) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 31 of 108 (28.7%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (115, 132, 109) --> (149, 200, 141) Brain_Stem: limiting intensities to 88.0 --> 132.0 186 of 470 (39.6%) samples deleted using 17199 total control points for intensity normalization... bias field = 1.036 +- 0.044 80 of 16871 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 55, 49) --> (197, 170, 220) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 5 of 7569 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 56, 46) --> (135, 172, 217) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 25 of 8859 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (135, 138, 75) --> (183, 183, 130) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 76 of 219 (34.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (92, 138, 68) --> (136, 183, 128) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 93 of 151 (61.6%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (115, 132, 109) --> (149, 200, 141) Brain_Stem: limiting intensities to 88.0 --> 132.0 363 of 490 (74.1%) samples deleted using 17288 total control points for intensity normalization... bias field = 1.031 +- 0.038 42 of 16635 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 20 seconds. @#@FSTIME 2024:11:11:21:00:46 mri_ca_normalize N 8 e 20.20 S 0.18 U 20.00 P 99% M 930816 F 10 R 138478 W 0 c 23 w 8 I 1432 O 4112 L 1.00 1.02 0.82 @#@FSLOADPOST 2024:11:11:21:01:06 mri_ca_normalize N 8 1.00 1.01 0.82 #-------------------------------------- #@# EntoWM Segmentation Mon Nov 11 21:01:06 CST 2024 mri_entowm_seg --s sub-JS_test --conform --threads 1 mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer/8.0.0-beta/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer/8.0.0-beta/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-JS_test --conform --threads 1 /usr/local/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer/8.0.0-beta/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer/8.0.0-beta/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-JS_test --conform --threads 1 Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/8.0.0-beta/models/entowm.ctab Loaded population stats /usr/local/freesurfer/8.0.0-beta/models/sclimbic.volstats.csv nb_labels 5 inshape (160, 160, 160) features 24 (None, 160, 160, 160, 1) Loading weights from /usr/local/freesurfer/8.0.0-beta/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.0.0-beta/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 Using subject directory /usr/local/freesurfer/8.0.0-beta/subjects Computed eTIV from talairach Segmenting subject sub-JS_test 1/1 Loaded input image from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/nu.mgz 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 10s 10s/step Wrote segmentation to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/entowm.mgz Wrote volume stats to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/stats/entowm.stats Wrote summary of label volumes to /usr/local/freesurfer/8.0.0-beta/subjects/entowm_volumes_all.csv vmpcma: 7201928 done Started at Mon Nov 11 21:01:06 CST 2024 Started at Mon Nov 11 21:01:06 CST 2024 Ended at Mon Nov 11 21:01:18 CST 2024 Ended at Mon Nov 11 21:01:18 CST 2024 mri_entowm_seg-Run-Time-Sec 12 mri_entowm_seg-Run-Time-Sec 12 mri_entowm_seg-Run-Time-Min 0.24 mri_entowm_seg-Run-Time-Min 0.24 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 937 970.9924 wm-lh-entorhinal 2 3201 267 273.1433 wm-lh-gyrus-ambiens 3 4006 984 1019.1097 wm-rh-entorhinal 4 4201 281 294.4316 wm-rh-gyrus-ambiens #-------------------------------------- #@# CC Seg Mon Nov 11 21:01:18 CST 2024 seg2cc --s sub-JS_test Mon Nov 11 21:01:18 CST 2024 setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri /usr/local/freesurfer/8.0.0-beta/bin/seg2cc --s sub-JS_test freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc seg2cc 8.0.0-beta Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri IsConformed yes Mon Nov 11 21:01:18 CST 2024 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta sub-JS_test 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 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/norm.mgz 107757 voxels in left wm, 86817 in right wm, xrange [119, 139] searching rotation angles z=[-3 11], y=[-1 13] searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.7 global minimum found at slice 127.6, rotations (5.65, 3.95) final transformation (x=127.6, yr=5.649, zr=3.947): 0.99278 -0.06883 0.09820 -4.37653; 0.06849 0.99763 0.00677 13.61786; -0.09843 0.00000 0.99514 9.19701; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 124 min_x_fornix = 121 min_x_fornix = 119 min_x_fornix = 118 min_x_fornix = 119 cc center is found at 128 105 132 eigenvectors: 0.00018 0.00189 1.00000; 0.13050 -0.99145 0.00185; 0.99145 0.13050 -0.00043; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #VMPC# mri_cc VmPeak 440808 mri_cc done @#@FSTIME 2024:11:11:21:01:18 mri_cc N 7 e 22.86 S 0.04 U 22.77 P 99% M 344908 F 9 R 15415 W 0 c 12 w 8 I 1392 O 920 L 1.00 1.01 0.82 @#@FSLOADPOST 2024:11:11:21:01:41 mri_cc N 7 1.00 1.01 0.83 Mon Nov 11 21:01:41 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri Started at Mon Nov 11 21:01:18 CST 2024 Ended at Mon Nov 11 21:01:41 CST 2024 Seg2cc-Run-Time-Sec 23 Seg2cc-Run-Time-Hours 0.01 seg2cc Done @#@FSTIME 2024:11:11:21:01:18 seg2cc N 2 e 22.96 S 0.05 U 22.87 P 99% M 344908 F 9 R 30399 W 0 c 14 w 240 I 1416 O 968 L 1.00 1.01 0.82 @#@FSLOADPOST 2024:11:11:21:01:41 seg2cc N 2 1.00 1.01 0.83 #-------------------------------------- #@# Merge ASeg Mon Nov 11 21:01:41 CST 2024 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Nov 11 21:01:41 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 256 (src width 256) normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 684 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 85 (85), valley at 56 (56) csf peak at 43, setting threshold to 71 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 85 (85), valley at 56 (56) csf peak at 43, setting threshold to 71 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 0 minutes and 54 seconds. @#@FSTIME 2024:11:11:21:01:41 mri_normalize N 9 e 54.81 S 0.52 U 54.26 P 99% M 1169284 F 0 R 217933 W 0 c 33 w 1 I 0 O 2600 L 1.00 1.01 0.83 @#@FSLOADPOST 2024:11:11:21:02:36 mri_normalize N 9 1.03 1.02 0.84 #-------------------------------------------- #@# Mask BFS Mon Nov 11 21:02:36 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1750248 voxels in mask (pct= 10.43) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:11:11:21:02:36 mri_mask N 5 e 0.37 S 0.00 U 0.37 P 100% M 74068 F 0 R 2945 W 0 c 1 w 1 I 0 O 2600 L 1.03 1.02 0.84 @#@FSLOADPOST 2024:11:11:21:02:36 mri_mask N 5 1.03 1.02 0.84 mri_mask -oval 1 -invert brain.finalsurfs.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 16775542 Resetting threshold to 0.5 DoAbs = 0 Found 16775542 voxels in mask (pct= 99.99) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:11:11:21:02:36 mri_mask N 6 e 0.93 S 0.01 U 0.91 P 99% M 172596 F 0 R 3079 W 0 c 1 w 1 I 0 O 2600 L 1.03 1.02 0.84 @#@FSLOADPOST 2024:11:11:21:02:37 mri_mask N 6 1.03 1.02 0.84 mri_mask -oval 1 -invert brain.finalsurfs.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/vsinus.mgz brain.finalsurfs.mgz setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 16759976 Resetting threshold to 0.5 DoAbs = 0 Found 16759976 voxels in mask (pct= 99.90) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:11:11:21:02:37 mri_mask N 6 e 0.94 S 0.02 U 0.92 P 100% M 172632 F 0 R 3076 W 0 c 2 w 1 I 0 O 2584 L 1.03 1.02 0.84 @#@FSLOADPOST 2024:11:11:21:02:38 mri_mask N 6 1.03 1.02 0.84 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 = 548 @#@FSTIME 2024:11:11:21:02:38 mri_edit_wm_with_aseg N 7 e 0.61 S 0.03 U 0.57 P 98% M 90168 F 7 R 1753 W 0 c 2 w 6 I 1384 O 2584 L 1.03 1.02 0.84 @#@FSLOADPOST 2024:11:11:21:02:39 mri_edit_wm_with_aseg N 7 1.03 1.02 0.84 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 = 4208 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 730 @#@FSTIME 2024:11:11:21:02:39 mri_edit_wm_with_aseg N 6 e 0.67 S 0.00 U 0.67 P 100% M 88472 F 0 R 4570 W 0 c 2 w 1 I 0 O 2584 L 1.03 1.02 0.84 @#@FSLOADPOST 2024:11:11:21:02:39 mri_edit_wm_with_aseg N 6 1.03 1.02 0.84 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Mon Nov 11 21:02:39 CST 2024 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:11:11:21:02:39 AntsDenoiseImageFs N 4 e 14.40 S 0.06 U 14.32 P 99% M 351024 F 25 R 3700 W 0 c 7 w 22 I 4880 O 2600 L 1.03 1.02 0.84 @#@FSLOADPOST 2024:11:11:21:02:54 AntsDenoiseImageFs N 4 1.02 1.02 0.85 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 545458, nonwhite = 15687650, ambig = 544108, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (101.0): 101.0 +- 6.0 [79.0 --> 125.0] CCS GM (79.0) : 78.3 +- 10.3 [30.0 --> 95.0] white_mean 101.002 white_sigma 6.03539 gray_mean 78.3267 gray_sigma 10.3059 setting bottom of white matter range wm_low to 88.6 setting top of gray matter range gray_hi to 98.9 wm_low 88.6326 wm_hi 125 gray_low 30 gray_hi 98.9384 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=88.6326, wm_hi=125, gray_hi=98.9384 white = 566160, nonwhite = 15977211, ambig = 233845, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 88.6326 wm_hi 125 gray_low 30 gray_hi 98.9384 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 98.9384, wm_low = 88.6326 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=98.9384, wmlow=88.6326 183385 voxels processed (1.09%) 82052 voxels white (0.49%) 101333 voxels non-white (0.60%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=83.6326, gray_hi=98.9384, wsize=13 375594 voxels tested (2.24%) 69245 voxels changed (0.41%) 67807 multi-scale searches (0.40%) Recovering bright white MRIrecoverBrightWhite() wm_low 88.6326 wm_hi 125 slack 6.03539 pct_thresh 0.33 intensity_thresh 131.035 nvox_thresh 8.58 39 voxels tested (0.00%) 31 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=83.6326, hithr=98.9384 smoothing input volume with sigma = 0.250 148439 voxels tested (0.88%) 19696 voxels changed (0.12%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 3410 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1969 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4016 filled MRIfindBrightNonWM(): 29 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 0.5 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:11:11:21:02:54 mri_segment N 5 e 32.52 S 0.09 U 32.41 P 99% M 155624 F 5 R 78568 W 0 c 29 w 5 I 1208 O 928 L 1.02 1.02 0.85 @#@FSLOADPOST 2024:11:11:21:03:26 mri_segment N 5 1.01 1.02 0.85 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 0.28 minutes Fixing entowm 3 255 255 LabelAmygalaCortalJunction((): nhits = 4208 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 3506 additional wm voxels added 0 additional wm voxels added SEG EDIT: 353257 voxels turned on, 58337 voxels turned off. Dilating 1 voxels in 3d propagating editing to output volume from wm.seg.mgz MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 2469 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 730 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:11:11:21:03:26 mri_edit_wm_with_aseg N 17 e 16.61 S 0.08 U 16.52 P 99% M 653256 F 0 R 45195 W 0 c 16 w 1 I 0 O 792 L 1.01 1.02 0.85 @#@FSLOADPOST 2024:11:11:21:03:43 mri_edit_wm_with_aseg N 17 1.01 1.02 0.86 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 23 found - 23 modified | TOTAL: 23 pass 2 (xy+): 0 found - 23 modified | TOTAL: 23 pass 1 (xy-): 25 found - 25 modified | TOTAL: 48 pass 2 (xy-): 0 found - 25 modified | TOTAL: 48 pass 1 (yz+): 24 found - 24 modified | TOTAL: 72 pass 2 (yz+): 0 found - 24 modified | TOTAL: 72 pass 1 (yz-): 18 found - 18 modified | TOTAL: 90 pass 2 (yz-): 0 found - 18 modified | TOTAL: 90 pass 1 (xz+): 17 found - 17 modified | TOTAL: 107 pass 2 (xz+): 0 found - 17 modified | TOTAL: 107 pass 1 (xz-): 15 found - 15 modified | TOTAL: 122 pass 2 (xz-): 0 found - 15 modified | TOTAL: 122 Iteration Number : 1 pass 1 (+++): 11 found - 11 modified | TOTAL: 11 pass 2 (+++): 0 found - 11 modified | TOTAL: 11 pass 1 (+++): 4 found - 4 modified | TOTAL: 15 pass 2 (+++): 0 found - 4 modified | TOTAL: 15 pass 1 (+++): 16 found - 16 modified | TOTAL: 31 pass 2 (+++): 0 found - 16 modified | TOTAL: 31 pass 1 (+++): 6 found - 6 modified | TOTAL: 37 pass 2 (+++): 0 found - 6 modified | TOTAL: 37 Iteration Number : 1 pass 1 (++): 40 found - 40 modified | TOTAL: 40 pass 2 (++): 0 found - 40 modified | TOTAL: 40 pass 1 (+-): 32 found - 32 modified | TOTAL: 72 pass 2 (+-): 0 found - 32 modified | TOTAL: 72 pass 1 (--): 35 found - 35 modified | TOTAL: 107 pass 2 (--): 0 found - 35 modified | TOTAL: 107 pass 1 (-+): 97 found - 97 modified | TOTAL: 204 pass 2 (-+): 0 found - 97 modified | TOTAL: 204 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 3 found - 3 modified | TOTAL: 7 pass 2 (xz+): 0 found - 3 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 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 = 377 (out of 695200: 0.054229) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:11:21:03:43 mri_pretess N 4 e 1.14 S 0.00 U 1.12 P 98% M 56688 F 19 R 2201 W 0 c 1 w 18 I 4104 O 800 L 1.01 1.02 0.86 @#@FSLOADPOST 2024:11:11:21:03:44 mri_pretess N 4 1.01 1.02 0.86 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 = 2469 @#@FSTIME 2024:11:11:21:03:44 mri_edit_wm_with_aseg N 7 e 0.54 S 0.01 U 0.51 P 98% M 90120 F 0 R 1758 W 0 c 4 w 0 I 0 O 800 L 1.01 1.02 0.86 @#@FSLOADPOST 2024:11:11:21:03:45 mri_edit_wm_with_aseg N 7 1.01 1.02 0.86 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 = 4208 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 730 @#@FSTIME 2024:11:11:21:03:45 mri_edit_wm_with_aseg N 6 e 0.60 S 0.00 U 0.59 P 99% M 86468 F 0 R 4574 W 0 c 2 w 1 I 0 O 800 L 1.01 1.02 0.86 @#@FSLOADPOST 2024:11:11:21:03:45 mri_edit_wm_with_aseg N 6 1.01 1.02 0.86 #-------------------------------------------- #@# Fill Mon Nov 11 21:03:45 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/8.0.0-beta/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 1.02852 -0.01903 0.11638 -20.69717; 0.00492 1.01531 0.07724 -14.56010; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.02852 -0.01903 0.11638 -20.69717; 0.00492 1.01531 0.07724 -14.56010; -0.11128 -0.07167 0.97350 4.28955; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 3137 (min = 350, max = 1400), aspect = 1.18 (min = 0.10, max = 0.75) need search nearby using seed (124, 113, 92), TAL = (4.0, -36.0, 15.0) talairach voxel to voxel transform 0.95973 0.00983 -0.11551 20.50231; -0.01292 0.97930 -0.07615 14.31789; 0.10876 0.07322 1.00841 -1.00848; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 113, 92) --> (4.0, -36.0, 15.0) done. filling took 0.4 minutes talairach cc position changed to (4.00, -36.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -36.00, 15.00) SRC: (112.72, 116.60, 111.57) search lh wm seed point around talairach space (-14.00, -36.00, 15.00), SRC: (147.27, 116.14, 115.48) 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 2024:11:11:21:03:45 mri_fill N 10 e 23.80 S 0.27 U 23.51 P 99% M 936276 F 7 R 305003 W 0 c 18 w 7 I 1336 O 288 L 1.01 1.02 0.86 @#@FSLOADPOST 2024:11:11:21:04:09 mri_fill N 10 1.00 1.01 0.86 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Mon Nov 11 21:04:09 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 6 found - 6 modified | TOTAL: 6 pass 2 (yz+): 0 found - 6 modified | TOTAL: 6 pass 1 (yz-): 7 found - 7 modified | TOTAL: 13 pass 2 (yz-): 0 found - 7 modified | TOTAL: 13 pass 1 (xz+): 0 found - 0 modified | TOTAL: 13 pass 1 (xz-): 4 found - 4 modified | TOTAL: 17 pass 2 (xz-): 0 found - 4 modified | TOTAL: 17 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 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 21 (out of 336634: 0.006238) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:11:21:04:09 mri_pretess N 4 e 0.65 S 0.00 U 0.65 P 99% M 40436 F 1 R 1635 W 0 c 2 w 0 I 24 O 280 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:10 mri_pretess N 4 1.00 1.01 0.86 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 8.0.0-beta 8.0.0-beta slice 50: 1173 vertices, 1264 faces slice 60: 5366 vertices, 5533 faces slice 70: 11582 vertices, 11826 faces slice 80: 19503 vertices, 19806 faces slice 90: 29283 vertices, 29646 faces slice 100: 39947 vertices, 40292 faces slice 110: 50763 vertices, 51127 faces slice 120: 62884 vertices, 63363 faces slice 130: 76654 vertices, 77174 faces slice 140: 89157 vertices, 89581 faces slice 150: 100213 vertices, 100606 faces slice 160: 111446 vertices, 111800 faces slice 170: 120376 vertices, 120707 faces slice 180: 128637 vertices, 128929 faces slice 190: 135586 vertices, 135854 faces slice 200: 142022 vertices, 142248 faces slice 210: 147364 vertices, 147502 faces slice 220: 148836 vertices, 148864 faces slice 230: 148836 vertices, 148864 faces slice 240: 148836 vertices, 148864 faces slice 250: 148836 vertices, 148864 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:11:11:21:04:10 mri_tessellate N 3 e 0.49 S 0.00 U 0.48 P 97% M 43332 F 7 R 1991 W 0 c 1 w 4 I 1376 O 6984 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:10 mri_tessellate N 3 1.00 1.01 0.86 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 148836 voxel in cpt #1: X=-28 [v=148836,e=446592,f=297728] located at (-29.131460, 0.520109, 16.542826) For the whole surface: X=-28 [v=148836,e=446592,f=297728] One single component has been found nothing to do done @#@FSTIME 2024:11:11:21:04:10 mris_extract_main_component N 2 e 0.35 S 0.05 U 0.29 P 95% M 295088 F 19 R 29069 W 0 c 1 w 16 I 3352 O 10472 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:11 mris_extract_main_component N 2 1.00 1.01 0.86 #-------------------------------------------- #@# Tessellate rh Mon Nov 11 21:04:11 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 10 found - 10 modified | TOTAL: 11 pass 2 (yz+): 0 found - 10 modified | TOTAL: 11 pass 1 (yz-): 1 found - 1 modified | TOTAL: 12 pass 2 (yz-): 0 found - 1 modified | TOTAL: 12 pass 1 (xz+): 0 found - 0 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 Iteration Number : 1 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 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 17 (out of 336405: 0.005053) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:11:21:04:11 mri_pretess N 4 e 0.65 S 0.00 U 0.64 P 98% M 40532 F 0 R 1639 W 0 c 2 w 0 I 0 O 280 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:11 mri_pretess N 4 1.00 1.01 0.86 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 8.0.0-beta 8.0.0-beta slice 50: 567 vertices, 625 faces slice 60: 3984 vertices, 4190 faces slice 70: 10565 vertices, 10819 faces slice 80: 19588 vertices, 19922 faces slice 90: 30605 vertices, 30962 faces slice 100: 42244 vertices, 42633 faces slice 110: 54813 vertices, 55273 faces slice 120: 69180 vertices, 69670 faces slice 130: 82978 vertices, 83470 faces slice 140: 95452 vertices, 95856 faces slice 150: 106437 vertices, 106867 faces slice 160: 116871 vertices, 117199 faces slice 170: 125496 vertices, 125840 faces slice 180: 132980 vertices, 133258 faces slice 190: 139871 vertices, 140126 faces slice 200: 145843 vertices, 146117 faces slice 210: 150357 vertices, 150500 faces slice 220: 151354 vertices, 151396 faces slice 230: 151354 vertices, 151396 faces slice 240: 151354 vertices, 151396 faces slice 250: 151354 vertices, 151396 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:11:11:21:04:11 mri_tessellate N 3 e 0.48 S 0.01 U 0.45 P 97% M 43880 F 0 R 2105 W 0 c 1 w 0 I 0 O 7104 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:12 mri_tessellate N 3 1.00 1.01 0.86 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 151354 voxel in cpt #1: X=-42 [v=151354,e=454188,f=302792] located at (27.824358, -1.742848, 14.627092) For the whole surface: X=-42 [v=151354,e=454188,f=302792] One single component has been found nothing to do done @#@FSTIME 2024:11:11:21:04:12 mris_extract_main_component N 2 e 0.39 S 0.05 U 0.32 P 97% M 300268 F 0 R 28676 W 0 c 1 w 0 I 0 O 10648 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:12 mris_extract_main_component N 2 1.00 1.01 0.86 #-------------------------------------------- #@# Smooth1 lh Mon Nov 11 21:04:12 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 2024:11:11:21:04:12 mris_smooth N 5 e 1.25 S 0.06 U 1.17 P 99% M 235008 F 9 R 43894 W 0 c 2 w 6 I 984 O 10472 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:14 mris_smooth N 5 1.00 1.01 0.86 #-------------------------------------------- #@# Smooth1 rh Mon Nov 11 21:04:14 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/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 2024:11:11:21:04:14 mris_smooth N 5 e 1.30 S 0.02 U 1.28 P 100% M 238900 F 0 R 42571 W 0 c 5 w 1 I 0 O 10648 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:15 mris_smooth N 5 1.00 1.01 0.86 #-------------------------------------------- #@# Inflation1 lh Mon Nov 11 21:04:15 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.3 mm, total surface area = 79958 mm^2 step 000: RMS=0.149 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.1 minutes inflation complete. Not saving sulc mris_inflate utimesec 6.861436 mris_inflate stimesec 0.360075 mris_inflate ru_maxrss 237376 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 497381 mris_inflate ru_majflt 21 mris_inflate ru_nswap 0 mris_inflate ru_inblock 3712 mris_inflate ru_oublock 10472 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 18 mris_inflate ru_nivcsw 12 @#@FSTIME 2024:11:11:21:04:15 mris_inflate N 3 e 7.24 S 0.36 U 6.86 P 99% M 237376 F 22 R 497386 W 0 c 12 w 19 I 3968 O 10472 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:22 mris_inflate N 3 1.00 1.01 0.86 #-------------------------------------------- #@# Inflation1 rh Mon Nov 11 21:04:22 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.8 mm, total surface area = 81545 mm^2 step 000: RMS=0.148 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.037 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.1 minutes inflation complete. Not saving sulc mris_inflate utimesec 7.097466 mris_inflate stimesec 0.419850 mris_inflate ru_maxrss 241272 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 496563 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10648 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 10 @#@FSTIME 2024:11:11:21:04:22 mris_inflate N 3 e 7.52 S 0.41 U 7.09 P 99% M 241272 F 0 R 496569 W 0 c 10 w 1 I 0 O 10648 L 1.00 1.01 0.86 @#@FSLOADPOST 2024:11:11:21:04:30 mris_inflate N 3 1.00 1.01 0.87 #-------------------------------------------- #@# QSphere lh Mon Nov 11 21:04:30 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 8.0.0-beta available threads: 1 scaling brain by 0.297... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.54 (0.00-->7.63) (max @ vno 53808 --> 54945) face area 0.02 +- 0.03 (-0.15-->0.83) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.961, avgs=0 005/300: dt: 0.9000, rms radial error=176.702, avgs=0 010/300: dt: 0.9000, rms radial error=176.144, avgs=0 015/300: dt: 0.9000, rms radial error=175.411, avgs=0 020/300: dt: 0.9000, rms radial error=174.578, avgs=0 025/300: dt: 0.9000, rms radial error=173.687, avgs=0 030/300: dt: 0.9000, rms radial error=172.763, avgs=0 035/300: dt: 0.9000, rms radial error=171.821, avgs=0 040/300: dt: 0.9000, rms radial error=170.870, avgs=0 045/300: dt: 0.9000, rms radial error=169.917, avgs=0 050/300: dt: 0.9000, rms radial error=168.965, avgs=0 055/300: dt: 0.9000, rms radial error=168.015, avgs=0 060/300: dt: 0.9000, rms radial error=167.070, avgs=0 065/300: dt: 0.9000, rms radial error=166.129, avgs=0 070/300: dt: 0.9000, rms radial error=165.193, avgs=0 075/300: dt: 0.9000, rms radial error=164.262, avgs=0 080/300: dt: 0.9000, rms radial error=163.336, avgs=0 085/300: dt: 0.9000, rms radial error=162.416, avgs=0 090/300: dt: 0.9000, rms radial error=161.500, avgs=0 095/300: dt: 0.9000, rms radial error=160.589, avgs=0 100/300: dt: 0.9000, rms radial error=159.683, avgs=0 105/300: dt: 0.9000, rms radial error=158.783, avgs=0 110/300: dt: 0.9000, rms radial error=157.888, avgs=0 115/300: dt: 0.9000, rms radial error=156.999, avgs=0 120/300: dt: 0.9000, rms radial error=156.115, avgs=0 125/300: dt: 0.9000, rms radial error=155.235, avgs=0 130/300: dt: 0.9000, rms radial error=154.361, avgs=0 135/300: dt: 0.9000, rms radial error=153.493, avgs=0 140/300: dt: 0.9000, rms radial error=152.630, avgs=0 145/300: dt: 0.9000, rms radial error=151.772, avgs=0 150/300: dt: 0.9000, rms radial error=150.919, avgs=0 155/300: dt: 0.9000, rms radial error=150.071, avgs=0 160/300: dt: 0.9000, rms radial error=149.227, avgs=0 165/300: dt: 0.9000, rms radial error=148.387, avgs=0 170/300: dt: 0.9000, rms radial error=147.553, avgs=0 175/300: dt: 0.9000, rms radial error=146.722, avgs=0 180/300: dt: 0.9000, rms radial error=145.897, avgs=0 185/300: dt: 0.9000, rms radial error=145.076, avgs=0 190/300: dt: 0.9000, rms radial error=144.259, avgs=0 195/300: dt: 0.9000, rms radial error=143.447, avgs=0 200/300: dt: 0.9000, rms radial error=142.639, avgs=0 205/300: dt: 0.9000, rms radial error=141.836, avgs=0 210/300: dt: 0.9000, rms radial error=141.037, avgs=0 215/300: dt: 0.9000, rms radial error=140.243, avgs=0 220/300: dt: 0.9000, rms radial error=139.453, avgs=0 225/300: dt: 0.9000, rms radial error=138.668, avgs=0 230/300: dt: 0.9000, rms radial error=137.886, avgs=0 235/300: dt: 0.9000, rms radial error=137.110, avgs=0 240/300: dt: 0.9000, rms radial error=136.337, avgs=0 245/300: dt: 0.9000, rms radial error=135.569, avgs=0 250/300: dt: 0.9000, rms radial error=134.805, avgs=0 255/300: dt: 0.9000, rms radial error=134.045, avgs=0 260/300: dt: 0.9000, rms radial error=133.290, avgs=0 265/300: dt: 0.9000, rms radial error=132.539, avgs=0 270/300: dt: 0.9000, rms radial error=131.792, avgs=0 275/300: dt: 0.9000, rms radial error=131.049, avgs=0 280/300: dt: 0.9000, rms radial error=130.310, avgs=0 285/300: dt: 0.9000, rms radial error=129.576, avgs=0 290/300: dt: 0.9000, rms radial error=128.845, avgs=0 295/300: dt: 0.9000, rms radial error=128.119, avgs=0 300/300: dt: 0.9000, rms radial error=127.397, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17612.05 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00022 epoch 2 (K=40.0), pass 1, starting sse = 2956.55 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00029 epoch 3 (K=160.0), pass 1, starting sse = 291.82 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/14 = 0.00533 epoch 4 (K=640.0), pass 1, starting sse = 19.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/17 = 0.00517 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0131 hours FSRUNTIME@ mris_sphere 0.0131 hours 1 threads #VMPC# mris_sphere VmPeak 497080 mris_sphere done @#@FSTIME 2024:11:11:21:04:30 mris_sphere N 9 e 47.03 S 1.59 U 45.40 P 99% M 242928 F 13 R 1952083 W 0 c 69 w 9 I 1648 O 10472 L 1.00 1.01 0.87 @#@FSLOADPOST 2024:11:11:21:05:17 mris_sphere N 9 1.00 1.01 0.88 #-------------------------------------------- #@# QSphere rh Mon Nov 11 21:05:17 CST 2024 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 8.0.0-beta available threads: 1 scaling brain by 0.301... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.54 (0.00-->8.14) (max @ vno 55673 --> 55674) face area 0.02 +- 0.03 (-0.11-->1.17) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.586, avgs=0 005/300: dt: 0.9000, rms radial error=176.333, avgs=0 010/300: dt: 0.9000, rms radial error=175.788, avgs=0 015/300: dt: 0.9000, rms radial error=175.071, avgs=0 020/300: dt: 0.9000, rms radial error=174.239, avgs=0 025/300: dt: 0.9000, rms radial error=173.347, avgs=0 030/300: dt: 0.9000, rms radial error=172.424, avgs=0 035/300: dt: 0.9000, rms radial error=171.486, avgs=0 040/300: dt: 0.9000, rms radial error=170.541, avgs=0 045/300: dt: 0.9000, rms radial error=169.595, avgs=0 050/300: dt: 0.9000, rms radial error=168.649, avgs=0 055/300: dt: 0.9000, rms radial error=167.706, avgs=0 060/300: dt: 0.9000, rms radial error=166.766, avgs=0 065/300: dt: 0.9000, rms radial error=165.831, avgs=0 070/300: dt: 0.9000, rms radial error=164.900, avgs=0 075/300: dt: 0.9000, rms radial error=163.975, avgs=0 080/300: dt: 0.9000, rms radial error=163.054, avgs=0 085/300: dt: 0.9000, rms radial error=162.138, avgs=0 090/300: dt: 0.9000, rms radial error=161.227, avgs=0 095/300: dt: 0.9000, rms radial error=160.321, avgs=0 100/300: dt: 0.9000, rms radial error=159.420, avgs=0 105/300: dt: 0.9000, rms radial error=158.525, avgs=0 110/300: dt: 0.9000, rms radial error=157.634, avgs=0 115/300: dt: 0.9000, rms radial error=156.748, avgs=0 120/300: dt: 0.9000, rms radial error=155.867, avgs=0 125/300: dt: 0.9000, rms radial error=154.990, avgs=0 130/300: dt: 0.9000, rms radial error=154.118, avgs=0 135/300: dt: 0.9000, rms radial error=153.252, avgs=0 140/300: dt: 0.9000, rms radial error=152.389, avgs=0 145/300: dt: 0.9000, rms radial error=151.532, avgs=0 150/300: dt: 0.9000, rms radial error=150.679, avgs=0 155/300: dt: 0.9000, rms radial error=149.831, avgs=0 160/300: dt: 0.9000, rms radial error=148.988, avgs=0 165/300: dt: 0.9000, rms radial error=148.149, avgs=0 170/300: dt: 0.9000, rms radial error=147.314, avgs=0 175/300: dt: 0.9000, rms radial error=146.485, avgs=0 180/300: dt: 0.9000, rms radial error=145.660, avgs=0 185/300: dt: 0.9000, rms radial error=144.839, avgs=0 190/300: dt: 0.9000, rms radial error=144.023, avgs=0 195/300: dt: 0.9000, rms radial error=143.212, avgs=0 200/300: dt: 0.9000, rms radial error=142.405, avgs=0 205/300: dt: 0.9000, rms radial error=141.603, avgs=0 210/300: dt: 0.9000, rms radial error=140.806, avgs=0 215/300: dt: 0.9000, rms radial error=140.013, avgs=0 220/300: dt: 0.9000, rms radial error=139.224, avgs=0 225/300: dt: 0.9000, rms radial error=138.440, avgs=0 230/300: dt: 0.9000, rms radial error=137.661, avgs=0 235/300: dt: 0.9000, rms radial error=136.885, avgs=0 240/300: dt: 0.9000, rms radial error=136.115, avgs=0 245/300: dt: 0.9000, rms radial error=135.348, avgs=0 250/300: dt: 0.9000, rms radial error=134.585, avgs=0 255/300: dt: 0.9000, rms radial error=133.827, avgs=0 260/300: dt: 0.9000, rms radial error=133.073, avgs=0 265/300: dt: 0.9000, rms radial error=132.324, avgs=0 270/300: dt: 0.9000, rms radial error=131.578, avgs=0 275/300: dt: 0.9000, rms radial error=130.837, avgs=0 280/300: dt: 0.9000, rms radial error=130.100, avgs=0 285/300: dt: 0.9000, rms radial error=129.366, avgs=0 290/300: dt: 0.9000, rms radial error=128.637, avgs=0 295/300: dt: 0.9000, rms radial error=127.912, avgs=0 300/300: dt: 0.9000, rms radial error=127.191, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17817.95 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00025 epoch 2 (K=40.0), pass 1, starting sse = 2951.92 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00015 epoch 3 (K=160.0), pass 1, starting sse = 297.45 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/13 = 0.00579 epoch 4 (K=640.0), pass 1, starting sse = 21.49 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/23 = 0.00660 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0143 hours FSRUNTIME@ mris_sphere 0.0143 hours 1 threads #VMPC# mris_sphere VmPeak 501052 mris_sphere done @#@FSTIME 2024:11:11:21:05:17 mris_sphere N 9 e 51.33 S 1.98 U 49.32 P 99% M 246800 F 0 R 2290416 W 0 c 73 w 1 I 0 O 10656 L 1.00 1.01 0.88 @#@FSLOADPOST 2024:11:11:21:06:08 mris_sphere N 9 1.07 1.03 0.90 #@# Fix Topology lh Mon Nov 11 21:06:08 CST 2024 mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 sub-JS_test lh Setting OMP_NUM_THREADS=1 reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 Setting OMP_NUM_THREADS=1 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 8.0.0-beta 8.0.0-beta before topology correction, eno=-28 (nv=148836, nf=297728, ne=446592, g=15) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 7981 ambiguous faces found in tessellation segmenting defects... 18 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 9 into 6 17 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7446 (-4.3723) -vertex loglikelihood: -5.7937 (-2.8969) -normal dot loglikelihood: -3.6852 (-3.6852) -quad curv loglikelihood: -6.0197 (-3.0098) Total Loglikelihood : -24.2432 CORRECTING DEFECT 0 (vertices=162, convex hull=129, v0=810) After retessellation of defect 0 (v0=810), euler #=-15 (144487,432695,288193) : difference with theory (-14) = 1 CORRECTING DEFECT 1 (vertices=90, convex hull=105, v0=1436) After retessellation of defect 1 (v0=1436), euler #=-14 (144511,432809,288284) : difference with theory (-13) = 1 CORRECTING DEFECT 2 (vertices=60, convex hull=110, v0=15109) After retessellation of defect 2 (v0=15109), euler #=-13 (144547,432963,288403) : difference with theory (-12) = 1 CORRECTING DEFECT 3 (vertices=206, convex hull=101, v0=21139) After retessellation of defect 3 (v0=21139), euler #=-12 (144564,433059,288483) : difference with theory (-11) = 1 CORRECTING DEFECT 4 (vertices=47, convex hull=39, v0=38952) After retessellation of defect 4 (v0=38952), euler #=-11 (144571,433094,288512) : difference with theory (-10) = 1 CORRECTING DEFECT 5 (vertices=1654, convex hull=191, v0=46716) After retessellation of defect 5 (v0=46716), euler #=-10 (144581,433214,288623) : difference with theory (-9) = 1 CORRECTING DEFECT 6 (vertices=1383, convex hull=489, v0=54208) A large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 6 (v0=54208), euler #=-8 (144620,433578,288950) : difference with theory (-8) = 0 CORRECTING DEFECT 7 (vertices=8, convex hull=21, v0=58344) After retessellation of defect 7 (v0=58344), euler #=-7 (144624,433594,288963) : difference with theory (-7) = 0 CORRECTING DEFECT 8 (vertices=35, convex hull=95, v0=59819) After retessellation of defect 8 (v0=59819), euler #=-6 (144633,433662,289023) : difference with theory (-6) = 0 CORRECTING DEFECT 9 (vertices=83, convex hull=40, v0=95830) After retessellation of defect 9 (v0=95830), euler #=-5 (144642,433706,289059) : difference with theory (-5) = 0 CORRECTING DEFECT 10 (vertices=14, convex hull=24, v0=96980) After retessellation of defect 10 (v0=96980), euler #=-4 (144644,433719,289071) : difference with theory (-4) = 0 CORRECTING DEFECT 11 (vertices=374, convex hull=74, v0=103262) After retessellation of defect 11 (v0=103262), euler #=-3 (144670,433834,289161) : difference with theory (-3) = 0 CORRECTING DEFECT 12 (vertices=64, convex hull=74, v0=104479) After retessellation of defect 12 (v0=104479), euler #=-2 (144679,433899,289218) : difference with theory (-2) = 0 CORRECTING DEFECT 13 (vertices=18, convex hull=33, v0=108092) After retessellation of defect 13 (v0=108092), euler #=-1 (144685,433927,289241) : difference with theory (-1) = 0 CORRECTING DEFECT 14 (vertices=144, convex hull=167, v0=120123) After retessellation of defect 14 (v0=120123), euler #=0 (144758,434224,289466) : difference with theory (0) = 0 CORRECTING DEFECT 15 (vertices=30, convex hull=61, v0=145615) After retessellation of defect 15 (v0=145615), euler #=1 (144777,434304,289528) : difference with theory (1) = 0 CORRECTING DEFECT 16 (vertices=16, convex hull=58, v0=145915) After retessellation of defect 16 (v0=145915), euler #=2 (144782,434340,289560) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.02-->10.02) (max @ vno 62730 --> 74803) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.02-->10.02) (max @ vno 62730 --> 74803) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 118 mutations (38.8%), 186 crossovers (61.2%), 562 vertices were eliminated building final representation... 4054 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=144782, nf=289560, ne=434340, g=0) writing corrected surface to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 302 intersecting 001: 69 intersecting 002: 29 intersecting terminating search with 0 intersecting topology fixing took 4.1 minutes FSRUNTIME@ mris_fix_topology lh 0.0685 hours 1 threads #VMPC# mris_fix_topology VmPeak 769360 @#@FSTIME 2024:11:11:21:06:08 mris_fix_topology N 18 e 246.62 S 0.21 U 246.36 P 99% M 753024 F 17 R 178205 W 0 c 12 w 29 I 2056 O 13688 L 1.07 1.03 0.90 @#@FSLOADPOST 2024:11:11:21:10:15 mris_fix_topology N 18 1.00 1.01 0.93 #@# Fix Topology rh Mon Nov 11 21:10:15 CST 2024 mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 sub-JS_test rh Setting OMP_NUM_THREADS=1 reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 Setting OMP_NUM_THREADS=1 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 8.0.0-beta 8.0.0-beta before topology correction, eno=-42 (nv=151354, nf=302792, ne=454188, g=22) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 6805 ambiguous faces found in tessellation segmenting defects... 23 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 1 -merging segment 8 into 7 21 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.8449 (-4.4224) -vertex loglikelihood: -5.7815 (-2.8908) -normal dot loglikelihood: -3.6465 (-3.6465) -quad curv loglikelihood: -5.7393 (-2.8697) Total Loglikelihood : -24.0122 CORRECTING DEFECT 0 (vertices=28, convex hull=25, v0=36096) After retessellation of defect 0 (v0=36096), euler #=-19 (147253,440394,293122) : difference with theory (-18) = 1 CORRECTING DEFECT 1 (vertices=992, convex hull=492, v0=41023) A large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 1 (v0=41023), euler #=-17 (147456,441251,293778) : difference with theory (-17) = 0 CORRECTING DEFECT 2 (vertices=108, convex hull=118, v0=42326) After retessellation of defect 2 (v0=42326), euler #=-16 (147467,441339,293856) : difference with theory (-16) = 0 CORRECTING DEFECT 3 (vertices=207, convex hull=143, v0=47374) After retessellation of defect 3 (v0=47374), euler #=-16 (147499,441505,293990) : difference with theory (-15) = 1 CORRECTING DEFECT 4 (vertices=31, convex hull=58, v0=50858) After retessellation of defect 4 (v0=50858), euler #=-15 (147519,441584,294050) : difference with theory (-14) = 1 CORRECTING DEFECT 5 (vertices=560, convex hull=319, v0=51213) After retessellation of defect 5 (v0=51213), euler #=-14 (147632,442082,294436) : difference with theory (-13) = 1 CORRECTING DEFECT 6 (vertices=25, convex hull=54, v0=53615) After retessellation of defect 6 (v0=53615), euler #=-13 (147641,442128,294474) : difference with theory (-12) = 1 CORRECTING DEFECT 7 (vertices=1134, convex hull=852, v0=55151) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 7 (v0=55151), euler #=-11 (147855,443231,295365) : difference with theory (-11) = 0 CORRECTING DEFECT 8 (vertices=36, convex hull=45, v0=61725) After retessellation of defect 8 (v0=61725), euler #=-10 (147859,443258,295389) : difference with theory (-10) = 0 CORRECTING DEFECT 9 (vertices=75, convex hull=65, v0=101885) After retessellation of defect 9 (v0=101885), euler #=-9 (147882,443354,295463) : difference with theory (-9) = 0 CORRECTING DEFECT 10 (vertices=190, convex hull=84, v0=109528) After retessellation of defect 10 (v0=109528), euler #=-8 (147900,443451,295543) : difference with theory (-8) = 0 CORRECTING DEFECT 11 (vertices=10, convex hull=26, v0=109614) After retessellation of defect 11 (v0=109614), euler #=-7 (147902,443466,295557) : difference with theory (-7) = 0 CORRECTING DEFECT 12 (vertices=119, convex hull=125, v0=116025) After retessellation of defect 12 (v0=116025), euler #=-6 (147957,443687,295724) : difference with theory (-6) = 0 CORRECTING DEFECT 13 (vertices=296, convex hull=91, v0=120891) After retessellation of defect 13 (v0=120891), euler #=-5 (147971,443763,295787) : difference with theory (-5) = 0 CORRECTING DEFECT 14 (vertices=19, convex hull=51, v0=134943) After retessellation of defect 14 (v0=134943), euler #=-4 (147980,443810,295826) : difference with theory (-4) = 0 CORRECTING DEFECT 15 (vertices=81, convex hull=40, v0=135028) After retessellation of defect 15 (v0=135028), euler #=-3 (147992,443857,295862) : difference with theory (-3) = 0 CORRECTING DEFECT 16 (vertices=74, convex hull=80, v0=137210) After retessellation of defect 16 (v0=137210), euler #=-2 (148016,443962,295944) : difference with theory (-2) = 0 CORRECTING DEFECT 17 (vertices=35, convex hull=67, v0=145645) After retessellation of defect 17 (v0=145645), euler #=-1 (148035,444047,296011) : difference with theory (-1) = 0 CORRECTING DEFECT 18 (vertices=30, convex hull=27, v0=145837) After retessellation of defect 18 (v0=145837), euler #=0 (148038,444065,296027) : difference with theory (0) = 0 CORRECTING DEFECT 19 (vertices=17, convex hull=54, v0=146243) After retessellation of defect 19 (v0=146243), euler #=1 (148046,444110,296065) : difference with theory (1) = 0 CORRECTING DEFECT 20 (vertices=31, convex hull=54, v0=150494) After retessellation of defect 20 (v0=150494), euler #=2 (148060,444174,296116) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.08-->10.80) (max @ vno 57957 --> 58083) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.08-->10.80) (max @ vno 57957 --> 58083) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 88 mutations (32.6%), 182 crossovers (67.4%), 532 vertices were eliminated building final representation... 3294 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=148060, nf=296116, ne=444174, g=0) writing corrected surface to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 527 intersecting 001: 84 intersecting 002: 21 intersecting terminating search with 0 intersecting topology fixing took 1.8 minutes FSRUNTIME@ mris_fix_topology rh 0.0293 hours 1 threads #VMPC# mris_fix_topology VmPeak 772084 @#@FSTIME 2024:11:11:21:10:15 mris_fix_topology N 18 e 105.35 S 0.13 U 105.19 P 99% M 756512 F 0 R 177644 W 0 c 11 w 14 I 0 O 13968 L 1.00 1.01 0.93 @#@FSLOADPOST 2024:11:11:21:12:00 mris_fix_topology N 18 1.10 1.03 0.95 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 144782 - 434340 + 289560 = 2 --> 0 holes F =2V-4: 289560 = 289564-4 (0) 2E=3F: 868680 = 868680 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 148060 - 444174 + 296116 = 2 --> 0 holes F =2V-4: 296116 = 296120-4 (0) 2E=3F: 888348 = 888348 (0) total defect index = 0 Mon Nov 11 21:12:01 CST 2024 setenv SUBJECTS_DIR /usr/local/freesurfer/8.0.0-beta/subjects cd /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/scripts /usr/local/freesurfer/8.0.0-beta/bin/defect2seg --s sub-JS_test --cortex freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc defect2seg 8.0.0-beta Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 12901 mri_label2label --label-cortex /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.orig.nofix /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/aseg.presurf.mgz 0 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 8 non-cortical segments detected only using segment with 8931 vertices erasing segment 1 (vno[0] = 81627) erasing segment 2 (vno[0] = 96980) erasing segment 3 (vno[0] = 104490) erasing segment 4 (vno[0] = 104551) erasing segment 5 (vno[0] = 105609) erasing segment 6 (vno[0] = 105611) erasing segment 7 (vno[0] = 107956) mri_label2vol --defects /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.orig.nofix /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.defect_labels /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/orig.mgz 1000 0 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/surface.defects.mgz /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/surface.defects.mgz mris_defects_pointset -s /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.orig.nofix -d /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.defect_labels -o /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.defects.pointset --label /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/lh.nofix.cortex.label Reading in surface /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.orig.nofix Reading in defect segmentation /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/lh.defect_labels Reading in label /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 193716 mris_defects_pointset done mri_label2label --label-cortex /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/rh.orig.nofix /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/aseg.presurf.mgz 0 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/rh.nofix.cortex.label double free or corruption (out) Abort (core dumped) ERROR: Command exited with non-zero status 1 @#@FSTIME 2024:11:11:21:12:01 defect2seg N 3 e 10.78 S 0.17 U 9.96 P 93% M 357304 F 50 R 125299 W 0 c 11 w 19557 I 8200 O 12304 L 1.10 1.03 0.95 @#@FSLOADPOST 2024:11:11:21:12:11 defect2seg N 3 1.00 1.01 0.94 Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-JS_test exited with ERRORS at Mon Nov 11 21:12:11 CST 2024 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting