Sun 29 Dec 2024 11:25:09 AM GMT cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 /usr/local/freesurfer-8.0.0/bin/recon-all -all -subject sub-31 -sd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 -hires -i /data/DANCE-AE/work/sub-31/7t-struct/sub-31_uni_masked.nii.gz -T2 /data/DANCE-AE/work/sub-31/7t-struct/sub-31_t2w_registered.nii.gz -T2pial -expert /home/me18/Dropbox/DANCE-AE/preproc/structural/7T/fs_experts_file.txt -openmp 20 subjid sub-31 setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 FREESURFER_HOME /usr/local/freesurfer-8.0.0 Actual FREESURFER_HOME /usr/local/freesurfer-8.0.0 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 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 255214 maxlocks unlimited maxsignal 255214 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 62Gi 4.3Gi 14Gi 11Mi 43Gi 57Gi Swap: 14Gi 1.8Gi 13Gi ######################################## program versions used 8.0.0-beta (freesurfer-linux-ubuntu20_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: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic 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: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic 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: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic 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: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 mris_convert -all-info ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:09-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 8.0.0-beta TimeStamp: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic 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: 2024/12/29-11:25:10-GMT BuildTime: Nov 3 2024 00:00:46 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc User: me18 Machine: bioeng427-pc Platform: Linux PlatformVersion: 5.15.0-125-generic CompilerName: GCC CompilerVersion: 8.4.0 ####################################### GCADIR /usr/local/freesurfer-8.0.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer-8.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 mri_convert /data/DANCE-AE/work/sub-31/7t-struct/sub-31_uni_masked.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/001.mgz mri_convert /data/DANCE-AE/work/sub-31/7t-struct/sub-31_uni_masked.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=2) reading from /data/DANCE-AE/work/sub-31/7t-struct/sub-31_uni_masked.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0444867, -0.998793, 0.0208355) j_ras = (-0.101745, -0.016218, -0.994678) k_ras = (0.993815, -0.0463699, -0.1009) writing to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/001.mgz... @#@FSTIME 2024:12:29:11:25:10 mri_convert N 2 e 1.80 S 0.04 U 3.38 P 190% M 110380 F 0 R 26182 W 0 c 48 w 21 I 0 O 33504 L 1.04 1.01 1.00 @#@FSLOADPOST 2024:12:29:11:25:12 mri_convert N 2 1.04 1.01 1.00 #-------------------------------------------- #@# T2/FLAIR Input Sun 29 Dec 2024 11:25:12 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 mri_convert --no_scale 1 /data/DANCE-AE/work/sub-31/7t-struct/sub-31_t2w_registered.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/T2raw.mgz mri_convert --no_scale 1 /data/DANCE-AE/work/sub-31/7t-struct/sub-31_t2w_registered.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/T2raw.mgz INFO: using NIfTI-1 sform (sform_code=2) reading from /data/DANCE-AE/work/sub-31/7t-struct/sub-31_t2w_registered.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0444867, -0.998793, 0.0208355) j_ras = (-0.101745, -0.016218, -0.994678) k_ras = (0.993815, -0.0463699, -0.1009) writing to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/T2raw.mgz... @#@FSTIME 2024:12:29:11:25:12 mri_convert N 4 e 7.68 S 0.08 U 10.26 P 134% M 176960 F 0 R 42785 W 0 c 90 w 22 I 0 O 284888 L 1.04 1.01 1.00 @#@FSLOADPOST 2024:12:29:11:25:20 mri_convert N 4 1.04 1.01 1.00 #-------------------------------------------- #@# MotionCor Sun 29 Dec 2024 11:25:20 AM GMT Found 1 runs /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig/001.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz mri_info /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 320 x 320 x 256 voxel sizes: 0.650000, 0.650000, 0.650000 type: FLOAT (3) fov: 208.000 dof: 1 xstart: -104.0, xend: 104.0 ystart: -104.0, yend: 104.0 zstart: -83.2, zend: 83.2 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.0445, y_r = -0.1017, z_r = 0.9938, c_r = -1.0050 : x_a = -0.9988, y_a = -0.0162, z_a = -0.0464, c_a = 14.5081 : x_s = 0.0208, y_s = -0.9947, z_s = -0.1009, c_s = -21.9837 talairach xfm : Orientation : PIR Primary Slice Direction: sagittal voxel to ras transform: -0.0289 -0.0661 0.6460 -68.4824 -0.6492 -0.0105 -0.0301 123.9271 0.0135 -0.6465 -0.0656 87.6909 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.274625 ras to voxel transform: -0.0684 -1.5366 0.0321 182.9290 -0.1565 -0.0250 -1.5303 126.5636 1.5289 -0.0713 -0.1552 127.1590 0.0000 0.0000 0.0000 1.0000 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 mri_convert /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --conform_min mri_convert /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --conform_min reading from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0444867, -0.998793, 0.0208355) j_ras = (-0.101745, -0.016218, -0.994678) k_ras = (0.993815, -0.0463699, -0.1009) volume geometry: valid : -2080947440 extent : (320, 320, 320) voxel : ( 0.6500, 0.6500, 0.6500) 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) : (-1.0050, 14.5081, -21.9837) file : /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram -16.7694 6734.02 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz... @#@FSTIME 2024:12:29:11:25:23 mri_convert N 3 e 6.64 S 0.06 U 8.21 P 124% M 136128 F 17 R 48830 W 0 c 88 w 41 I 0 O 8784 L 0.95 1.00 1.00 @#@FSLOADPOST 2024:12:29:11:25:30 mri_convert N 3 0.96 1.00 1.00 mri_add_xform_to_header -c /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/talairach.xfm /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2024:12:29:11:25:30 mri_add_xform_to_header N 4 e 0.39 S 0.04 U 1.68 P 437% M 39328 F 17 R 8582 W 0 c 31 w 40 I 0 O 8784 L 0.96 1.00 1.00 @#@FSLOADPOST 2024:12:29:11:25:31 mri_add_xform_to_header N 4 0.96 1.00 1.00 mri_info /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz orig.mgz ======================================== Volume information for /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz type: MGH intent: MRI (0) dimensions: 320 x 320 x 320 voxel sizes: 0.650000, 0.650000, 0.650000 type: UCHAR (0) fov: 208.000 dof: 1 xstart: -104.0, xend: 104.0 ystart: -104.0, yend: 104.0 zstart: -104.0, zend: 104.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0050 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 14.5081 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -21.9837 talairach xfm : /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -0.6500 0.0000 0.0000 102.9950 -0.0000 0.0000 0.6500 -89.4919 0.0000 -0.6500 0.0000 82.0163 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.274625 ras to voxel transform: -1.5385 0.0000 -0.0000 158.4538 -0.0000 0.0000 -1.5385 126.1789 -0.0000 1.5385 -0.0000 137.6799 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz --trg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --outlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg2orig.lta 8.0.0-beta --inlta: identity.nofile input LTA transform. --src: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg.mgz src image (geometry). --trg: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz trg image (geometry). --outlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/rawavg2orig.lta... lta_convert successful. @#@FSTIME 2024:12:29:11:25:31 lta_convert N 8 e 0.28 S 0.00 U 0.27 P 99% M 6084 F 0 R 254 W 0 c 2 w 1 I 0 O 8 L 0.96 1.00 1.00 @#@FSLOADPOST 2024:12:29:11:25:31 lta_convert N 8 0.96 1.00 1.00 mri_synthstrip --threads 20 -i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz -o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 2024:12:29:11:25:31 mri_synthstrip N 6 e 6.69 S 13.20 U 38.80 P 776% M 3525924 F 11 R 3439612 W 0 c 1055 w 597 I 0 O 8576 L 0.96 1.00 1.00 @#@FSLOADPOST 2024:12:29:11:25:38 mri_synthstrip N 6 2.36 1.31 1.10 mri_synthseg --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthseg.rca.mgz --threads 20 --vol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/stats/synthseg.vol.csv --keepgeom --addctab --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 20 threads addctab True predicting 1/1 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 43s 43s/step Reslicing to have same geom as the input [0.64999998 0.64999998 0.64999998] segmentation saved in: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthseg.rca.mgz volumes saved in: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/stats/synthseg.vol.csv #@# mri_synthseg vmpeak 67325420 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 2024:12:29:11:25:38 mri_synthseg N 11 e 59.62 S 42.76 U 790.65 P 1397% M 13082652 F 21 R 13718397 W 0 c 511922 w 22519 I 0 O 3008 L 2.36 1.31 1.10 @#@FSLOADPOST 2024:12:29:11:26:37 mri_synthseg N 11 10.12 3.85 1.99 Sun 29 Dec 2024 11:26:37 AM GMT setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 /usr/local/freesurfer-8.0.0/bin/fs-synthmorph-reg --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthstrip.mgz --t /usr/local/freesurfer-8.0.0/average/mni305.cor.stripped.mgz --affine-only --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305 --threads 20 -rwxrwxr-x 1 501 1590 30900 Nov 3 00:09 /usr/local/freesurfer-8.0.0/bin/fs-synthmorph-reg freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3529376 Sun 29 Dec 2024 11:26:37 AM GMT mri_synthmorph -m affine -t /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/aff.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthstrip.mgz /usr/local/freesurfer-8.0.0/average/mni305.cor.stripped.mgz -j 20 #@# mri_synthmorph: affine, threads: 20, VmPeak: 10941140 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 2024:12:29:11:26:38 mri_synthmorph N 8 e 13.84 S 32.99 U 94.17 P 918% M 5506368 F 23 R 9204688 W 0 c 396444 w 18347 I 0 O 432 L 10.12 3.85 1.99 @#@FSLOADPOST 2024:12:29:11:26:51 mri_synthmorph N 8 9.69 4.08 2.10 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 lta_convert --invert --inlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/aff.lta --outlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta 8.0.0-beta --invert: will invert transform. --inlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/aff.lta input LTA transform. --outlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta output LTA. LTA read, type : 1 1.14492 -0.08020 -0.11634 -0.97079; 0.08910 1.07373 0.09040 -22.50744; 0.12099 -0.00756 1.17611 10.43274; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta... lta_convert successful. @#@FSTIME 2024:12:29:11:26:51 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 100% M 5872 F 0 R 226 W 0 c 0 w 1 I 0 O 8 L 9.69 4.08 2.10 @#@FSLOADPOST 2024:12:29:11:26:51 lta_convert N 5 9.69 4.08 2.10 To check affine registration tkregisterfv --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthstrip.mgz --targ /usr/local/freesurfer-8.0.0/average/mni305.cor.stripped.mgz --reg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.mni305/aff.lta AffineOnly specified, so exiting now Started at Sun 29 Dec 2024 11:26:37 AM GMT Ended at Sun 29 Dec 2024 11:26:51 AM GMT Fs-Synthmorph-Reg-Run-Time-Sec 14 Fs-Synthmorph-Reg-Run-Time-Min 0.23 Fs-Synthmorph-Reg-Run-Time-Hours 0.00 fs-synthmorph-reg Done @#@FSTIME 2024:12:29:11:26:37 fs-synthmorph-reg N 9 e 14.08 S 33.09 U 94.34 P 904% M 5506368 F 23 R 9228326 W 0 c 396451 w 18663 I 0 O 448 L 10.12 3.85 1.99 @#@FSLOADPOST 2024:12:29:11:26:51 fs-synthmorph-reg N 9 9.69 4.08 2.10 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 1.14492 -0.08020 -0.11634 -0.97079; 0.08910 1.07373 0.09040 -22.50744; 0.12099 -0.00756 1.17611 10.43274; 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 1.14492 -0.08020 -0.11634 -0.97079; 0.08910 1.07373 0.09040 -22.50745; 0.12099 -0.00756 1.17611 10.43275; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. fs-synthmorph-reg --s sub-31 --threads 20 --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --test Sun 29 Dec 2024 11:26:52 AM GMT setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31 /usr/local/freesurfer-8.0.0/bin/fs-synthmorph-reg --s sub-31 --threads 20 --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --test -rwxrwxr-x 1 501 1590 30900 Nov 3 00:09 /usr/local/freesurfer-8.0.0/bin/fs-synthmorph-reg freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3529643 mri_mask -bb 3 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 58 21 15 200 222 265 maskval=0, outval=0 Writing masked volume to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done. lta_convert --inlta identity.nofile --src /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --trg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --outlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta 8.0.0-beta --inlta: identity.nofile input LTA transform. --src: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz src image (geometry). --trg: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz trg image (geometry). --outlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta... lta_convert successful. Sun 29 Dec 2024 11:26:53 AM GMT mri_synthmorph -m affine -t /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 20 [DEBUG] FSNifti1Extension.read(): esize = 1280 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1268 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1252 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1213 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1153 (tag = 31, length = 85) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1056 (tag = 3, length = 494) [DEBUG] FSNifti1Extension.read(): remaining taglen = 550 (tag = 3, length = 513) [DEBUG] FSNifti1Extension.read(): remaining taglen = 25 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 12 (tag = 0, length = 0) [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: 20, VmPeak: 10850708 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 2024:12:29:11:26:53 mri_synthmorph N 8 e 13.67 S 32.93 U 93.46 P 924% M 5418584 F 16 R 9325147 W 0 c 354063 w 18274 I 0 O 432 L 9.69 4.08 2.10 @#@FSLOADPOST 2024:12:29:11:27:06 mri_synthmorph N 8 9.88 4.30 2.19 Sun 29 Dec 2024 11:27:06 AM GMT mri_concatenate_lta -invert1 -invertout /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta... mri_concatenate_lta successful. @#@FSTIME 2024:12:29:11:27:06 mri_concatenate_lta N 5 e 0.00 S 0.00 U 0.00 P 50% M 5368 F 0 R 222 W 0 c 0 w 1 I 0 O 8 L 9.88 4.30 2.19 @#@FSLOADPOST 2024:12:29:11:27:06 mri_concatenate_lta N 5 9.88 4.30 2.19 mri_concatenate_lta -invert2 /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta... mri_concatenate_lta successful. @#@FSTIME 2024:12:29:11:27:06 mri_concatenate_lta N 4 e 0.00 S 0.00 U 0.00 P 50% M 5148 F 0 R 220 W 0 c 0 w 1 I 0 O 8 L 9.88 4.30 2.19 @#@FSLOADPOST 2024:12:29:11:27:06 mri_concatenate_lta N 4 9.88 4.30 2.19 lta_convert --invert --inlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --outlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta 8.0.0-beta --invert: will invert transform. --inlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta input LTA transform. --outlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta output LTA. LTA read, type : 1 0.82449 0.07000 0.07469 1.76487; -0.06571 0.89839 -0.03915 20.96025; -0.07972 0.00178 0.79831 -8.39758; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta... lta_convert successful. @#@FSTIME 2024:12:29:11:27:06 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 100% M 5856 F 0 R 226 W 0 c 0 w 1 I 0 O 8 L 9.88 4.30 2.19 @#@FSLOADPOST 2024:12:29:11:27:06 lta_convert N 5 9.88 4.30 2.19 lta_convert --inlta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta --outmni /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm 8.0.0-beta --inlta: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta input LTA transform. --outmni: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm output MNI/XFM matrix. LTA read, type : 1 1.19424 -0.09282 -0.11628 -1.13861; 0.09254 1.10581 0.04557 -22.95865; 0.11905 -0.01174 1.24094 10.45682; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. To check affine registration tkregisterfv --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz --targ /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --reg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta mri_synthmorph -m deform -t /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz -i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 20 -o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz [DEBUG] FSNifti1Extension.read(): esize = 1280 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1268 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1252 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1213 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1153 (tag = 31, length = 85) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1056 (tag = 3, length = 494) [DEBUG] FSNifti1Extension.read(): remaining taglen = 550 (tag = 3, length = 513) [DEBUG] FSNifti1Extension.read(): remaining taglen = 25 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 12 (tag = 0, length = 0) [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: 20, VmPeak: 23119320 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 2024:12:29:11:27:06 mri_synthmorph N 12 e 161.86 S 129.28 U 2550.24 P 1655% M 14552984 F 18 R 40407839 W 0 c 482923 w 129707 I 0 O 108064 L 9.25 4.26 2.19 @#@FSLOADPOST 2024:12:29:11:29:48 mri_synthmorph N 12 16.21 9.65 4.57 mri_warp_convert --inras /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz --insrcgeom /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --outm3z /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz --vg-thresh 1e-5 --lta1-inv /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta --lta2 /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta 8.0.0-beta --inras: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz input RAS warp. --insrcgeom: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz atlas/source image (used for geometry). --outm3z: /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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(/data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [193 x 229 x 193] [INFO] Warpfield::convert(): gcam image [320 x 320 x 320] [INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193] [INFO] Warpfield::convert(): total out of range voxel count: 0 volume geometry: extent : (320, 320, 320) voxel : ( 0.6500, 0.6500, 0.6500) 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) : (-1.0050, 14.5081, -21.9837) file : /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 2024:12:29:11:29:48 mri_warp_convert N 12 e 9.20 S 0.98 U 9.33 P 112% M 3406844 F 0 R 866900 W 0 c 55 w 39 I 0 O 92768 L 16.21 9.65 4.57 @#@FSLOADPOST 2024:12:29:11:29:57 mri_warp_convert N 12 13.87 9.36 4.53 mri_ca_register -invert-and-save /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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...(320, 320, 320) Saving inverse to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz GCAMwrite(/data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [320 x 320 x 320] [INFO] Warpfield::convert(): gcam image [193 x 229 x 193] [INFO] Warpfield::convert(): gcam atlas [320 x 320 x 320] [INFO] Warpfield::convert(): total out of range voxel count: 0 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 : (320, 320, 320) voxel : ( 0.6500, 0.6500, 0.6500) 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) : (-1.0050, 14.5081, -21.9837) file : /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz @#@FSTIME 2024:12:29:11:29:57 mri_ca_register N 3 e 117.78 S 3.06 U 316.44 P 271% M 11696360 F 0 R 3146207 W 0 c 4730 w 5417 I 0 O 469400 L 13.87 9.36 4.53 @#@FSLOADPOST 2024:12:29:11:31:55 mri_ca_register N 3 4.74 7.48 4.40 mri_vol2vol --regheader --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz --targ /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz movvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz targvol /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 1736264461 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 2024:12:29:11:31:55 mri_vol2vol N 7 e 0.53 S 0.03 U 1.56 P 297% M 49376 F 0 R 27356 W 0 c 68 w 25 I 0 O 15760 L 4.74 7.48 4.40 @#@FSLOADPOST 2024:12:29:11:31:56 mri_vol2vol N 7 4.74 7.48 4.40 mri_convert -rt nearest /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz -at /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz mri_convert -rt nearest /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz -at /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.86561e-09, 0) j_ras = (2.29249e-08, 0, -1) k_ras = (5.73122e-09, 1, 3.58201e-10) INFO: Reading transformation from file /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... INFO: Applying transformation from file /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz... @#@FSTIME 2024:12:29:11:31:56 mri_convert N 6 e 3.55 S 0.72 U 21.07 P 614% M 2383164 F 0 R 602215 W 0 c 474 w 124 I 0 O 3928 L 4.74 7.48 4.40 @#@FSLOADPOST 2024:12:29:11:31:59 mri_convert N 6 5.96 7.69 4.49 mri_diff --po /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz mri_diff --po /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz diffcount 2219395 Volumes differ in pixel data maxdiff 111.71781158 at 121 159 45 0 tkmeditfv -f /usr/local/freesurfer-8.0.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -aux /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz Started at Sun 29 Dec 2024 11:26:52 AM GMT Ended at Sun 29 Dec 2024 11:32:00 AM GMT Fs-Synthmorph-Reg-Run-Time-Sec 308 Fs-Synthmorph-Reg-Run-Time-Min 5.13 Fs-Synthmorph-Reg-Run-Time-Hours 0.09 fs-synthmorph-reg Done @#@FSTIME 2024:12:29:11:26:51 fs-synthmorph-reg N 7 e 308.29 S 167.28 U 2997.20 P 1026% M 14552984 F 37 R 54468102 W 0 c 842462 w 154338 I 0 O 699064 L 9.69 4.08 2.10 @#@FSLOADPOST 2024:12:29:11:32:00 fs-synthmorph-reg N 7 5.96 7.69 4.49 #-------------------------------------------- #@# Nu Intensity Correction Sun 29 Dec 2024 11:32:00 AM GMT mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 /usr/bin/bc /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri /usr/local/freesurfer-8.0.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 8.0.0-beta Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Sun 29 Dec 2024 11:32:00 AM GMT tmpdir is ./tmp.mri_nu_correct.mni.3530320 cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.3530320/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.3530320/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.3530320/ones.mgz 8.0.0-beta cwd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.3530320/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.3530320/ones.mgz sysname Linux hostname bioeng427-pc machine x86_64 user me18 input ./tmp.mri_nu_correct.mni.3530320/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.3530320/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 32768000 values in range Counting number of voxels in first frame Found 32768000 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.3530320/ones.mgz Count: 32768000 8998911.132812 32768000 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3530320/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3530320/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3530320/input.mean.dat 8.0.0-beta cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3530320/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3530320/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3530320/input.mean.dat sysname Linux hostname bioeng427-pc machine x86_64 user me18 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3530320/ones.mgz Loading orig.mgz Voxel Volume is 0.274625 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.3530320/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3530320/ones.mgz --i ./tmp.mri_nu_correct.mni.3530320/nu0.mgz --sum ./tmp.mri_nu_correct.mni.3530320/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3530320/output.mean.dat 8.0.0-beta cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3530320/ones.mgz --i ./tmp.mri_nu_correct.mni.3530320/nu0.mgz --sum ./tmp.mri_nu_correct.mni.3530320/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3530320/output.mean.dat sysname Linux hostname bioeng427-pc machine x86_64 user me18 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3530320/ones.mgz Loading ./tmp.mri_nu_correct.mni.3530320/nu0.mgz Voxel Volume is 0.274625 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.3530320/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.3530320/nu0.mgz ./tmp.mri_nu_correct.mni.3530320/nu0.mgz mul .90735657652672899245 Packing Done packing Unpacking Saving result to './tmp.mri_nu_correct.mni.3530320/nu0.mgz' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 557120 mri_convert ./tmp.mri_nu_correct.mni.3530320/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.3530320/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.3530320/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.86561e-09, 0) j_ras = (2.29249e-08, 0, -1) k_ras = (5.73122e-09, 1, 3.58201e-10) 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 7 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 3, i2 = 68 #mri_make_uchar# mapping 7 159 to 3 110 : b -2.40923 m 0.708462 : thresh 3.40065 maxsat 363.335 : nzero 27923759 nsat 0 Sun 29 Dec 2024 11:37:11 AM GMT mri_nu_correct.mni done @#@FSTIME 2024:12:29:11:32:00 mri_nu_correct.mni N 10 e 311.64 S 2.78 U 331.17 P 107% M 1192760 F 35 R 1478510 W 0 c 1666 w 435 I 0 O 59480 L 5.96 7.69 4.49 @#@FSLOADPOST 2024:12:29:11:37:11 mri_nu_correct.mni N 10 1.04 3.37 3.49 mri_add_xform_to_header -c /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2024:12:29:11:37:11 mri_add_xform_to_header N 4 e 0.40 S 0.01 U 1.73 P 427% M 39492 F 0 R 8579 W 0 c 37 w 20 I 0 O 7888 L 1.04 3.37 3.49 @#@FSLOADPOST 2024:12:29:11:37:12 mri_add_xform_to_header N 4 1.03 3.33 3.48 #-------------------------------------------- #@# Intensity Normalization Sun 29 Dec 2024 11:37:12 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.14492 -0.08020 -0.11634 -0.97079; 0.08910 1.07373 0.09040 -22.50745; 0.12099 -0.00756 1.17611 10.43275; 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 = 21 Starting OpenSpline(): npoints = 21 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 63 (63), valley at 20 (20) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 62 (62), valley at 21 (21) csf peak at 31, setting threshold to 51 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 3 seconds. @#@FSTIME 2024:12:29:11:37:12 mri_normalize N 8 e 183.88 S 0.53 U 218.18 P 118% M 1130632 F 0 R 513845 W 0 c 1425 w 78 I 0 O 7208 L 1.03 3.33 3.48 @#@FSLOADPOST 2024:12:29:11:40:16 mri_normalize N 8 1.04 2.28 3.04 #-------------------------------------- #@# MCADura Segmentation Sun 29 Dec 2024 11:40:16 AM GMT mri_mcadura_seg --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/mca-dura.mgz --threads 20 --synthmorphdir /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm Sun 29 Dec 2024 11:40:16 AM GMT setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri /usr/local/freesurfer-8.0.0/bin/mri_mcadura_seg --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/mca-dura.mgz --threads 20 --synthmorphdir /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm -rwxrwxr-x 1 501 1590 13384 Nov 3 00:09 /usr/local/freesurfer-8.0.0/bin/mri_mcadura_seg freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3530707 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_vol2vol --reg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer-8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/mcadura.prior.lh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.19424 0.09282 0.11628 1.62916; 0.11905 -0.01174 1.24094 -35.61357; -0.09254 -1.10581 -0.04557 -9.48975; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer-8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/mcadura.prior.lh.nii.gz regfile /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 1735921811 Final tkRAS-to-tkRAS Matrix is: -1.19424 0.09282 0.11628 1.62916; 0.11905 -0.01174 1.24094 -35.61357; -0.09254 -1.10581 -0.04557 -9.48975; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.77625 0.07558 -0.06033 216.63132; -0.06015 -0.02962 0.71877 23.34901; -0.07738 -0.80661 -0.00763 203.54555; 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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/mcadura.prior.lh.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/lh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 19261 voxels in mask (pct= 0.06) MRIcropToFoV(): thresh=0.001 FoV = (124,124,124) nhits=19261 centroid = (206.759,160.916,206.902) min = (169,125,181) max = (232,190,233) delta = (64,66,53) Region 145 99 145 124 124 124 145 99 145 124 124 124 maskval=0, outval=0 Writing masked volume to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/lh.crop.nii.gz...done. mri_vol2vol --regheader --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --targ /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/lh.crop.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.lh.crop.nii.gz movvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz targvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/lh.crop.nii.gz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/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 1735649750 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -30.55000; 0.00000 1.00000 0.00000 30.55000; 0.00000 -0.00000 1.00000 -0.64999; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 145.00003; 0.00000 1.00000 0.00000 99.00000; 0.00000 0.00000 1.00000 145.00002; 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/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 20 --fov 72 --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.lh.crop.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.mgz /usr/local/freesurfer-8.0.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 20 --fov 72 --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.lh.crop.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 20 thread(s) Loaded lookup table /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.ctab Loaded population stats /usr/local/freesurfer-8.0.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 [DEBUG] FSNifti1Extension.read(): esize = 1280 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1268 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1252 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1213 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1153 (tag = 31, length = 85) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1056 (tag = 3, length = 494) [DEBUG] FSNifti1Extension.read(): remaining taglen = 550 (tag = 3, length = 513) [DEBUG] FSNifti1Extension.read(): remaining taglen = 25 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 12 (tag = 0, length = 0) Loaded input image from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.lh.crop.nii.gz The input image has resolution ['0.65', '0.65', '0.65'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 420ms/step Wrote segmentation to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.mgz vmpcma: 8706288 done mri_vol2vol --regheader --interp nearest --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.mgz --targ /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.uncropped.mgz movvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.mgz targvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/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 1735638173 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 30.54999; 0.00000 1.00000 0.00000 -30.54999; 0.00000 -0.00000 1.00000 0.65001; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 -144.99997; 0.00000 1.00000 0.00000 -99.00000; 0.00000 0.00000 1.00000 -144.99997; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --reg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer-8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/mcadura.prior.rh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.19424 0.09282 0.11628 1.62916; 0.11905 -0.01174 1.24094 -35.61357; -0.09254 -1.10581 -0.04557 -9.48975; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer-8.0.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/mcadura.prior.rh.nii.gz regfile /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 1735805199 Final tkRAS-to-tkRAS Matrix is: -1.19424 0.09282 0.11628 1.62916; 0.11905 -0.01174 1.24094 -35.61357; -0.09254 -1.10581 -0.04557 -9.48975; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.77625 0.07558 -0.06033 216.63132; -0.06015 -0.02962 0.71877 23.34901; -0.07738 -0.80661 -0.00763 203.54555; 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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/mcadura.prior.rh.nii.gz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/rh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 20352 voxels in mask (pct= 0.06) MRIcropToFoV(): thresh=0.001 FoV = (124,124,124) nhits=20352 centroid = (106.745,170.822,200.746) min = (75,140,176) max = (144,195,229) delta = (70,56,54) Region 45 109 139 124 124 124 45 109 139 124 124 124 maskval=0, outval=0 Writing masked volume to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/rh.crop.nii.gz...done. mri_vol2vol --regheader --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --targ /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/rh.crop.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.nii.gz movvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz targvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/rh.crop.nii.gz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/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 1735507355 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 34.45000; 0.00000 1.00000 0.00000 26.64999; 0.00000 -0.00000 1.00000 -7.15000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 45.00003; 0.00000 1.00000 0.00000 109.00002; 0.00000 0.00000 1.00000 139.00002; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.nii.gz --left-right-reverse-pix /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.lrrev.nii.gz mri_convert /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.nii.gz --left-right-reverse-pix /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.lrrev.nii.gz reading from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/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=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.86561e-09, 0) j_ras = (2.29249e-08, 0, -1) k_ras = (5.73122e-09, 1, 3.58201e-10) writing to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.lrrev.nii.gz... mri_sclimbic_seg --model /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 20 --fov 72 --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.lrrev.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.lrrev.mgz /usr/local/freesurfer-8.0.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 20 --fov 72 --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.lrrev.nii.gz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.lrrev.mgz Keeping anterior commissure in vols and stats Using CPU Using 20 thread(s) Loaded lookup table /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.ctab Loaded population stats /usr/local/freesurfer-8.0.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer-8.0.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 [DEBUG] FSNifti1Extension.read(): esize = 1888 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1876 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1860 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1821 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1761 (tag = 31, length = 85) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1664 (tag = 3, length = 494) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1158 (tag = 3, length = 513) [DEBUG] FSNifti1Extension.read(): remaining taglen = 633 (tag = 3, length = 608) [DEBUG] FSNifti1Extension.read(): remaining taglen = 13 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 0 Loaded input image from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/invol.rh.crop.lrrev.nii.gz The input image has resolution ['0.65', '0.65', '0.65'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 426ms/step Wrote segmentation to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.lrrev.mgz vmpcma: 8639000 done mri_convert /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.lrrev.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.mgz --left-right-swap-label-table /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.index /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.rh.index --left-right-reverse-pix mri_convert /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.lrrev.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.mgz --left-right-swap-label-table /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.lh.index /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/dumca.rh.index --left-right-reverse-pix reading from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.lrrev.mgz... Performing left-right swap of labels MRIlrswapSeg(): nswaps 2 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=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.86561e-09, 0) j_ras = (2.29249e-08, 0, -1) k_ras = (5.73122e-09, 1, 3.58201e-10) writing to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.mgz... mri_vol2vol --regheader --interp nearest --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.mgz --targ /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.uncropped.mgz movvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.mgz targvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/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 1735940256 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -34.45001; 0.00000 1.00000 0.00000 -26.64998; 0.00000 -0.00000 1.00000 7.15001; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 -44.99996; 0.00000 1.00000 0.00000 -109.00000; 0.00000 0.00000 1.00000 -138.99995; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_concat /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.lh.uncropped.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.mri_mcadura_seg.3530707/seg.rh.uncropped.mgz --sum --ctab /usr/local/freesurfer-8.0.0/models/mca-dura.ctab --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/mca-dura.mgz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing sum across frames Writing to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/mca-dura.mgz fsvglrun freeview -neuro-view --hide-3d-slices --view coronal /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/mca-dura.mgz:isosurface=1:outline=1 Started at Sun 29 Dec 2024 11:40:16 AM GMT Ended at Sun 29 Dec 2024 11:40:37 AM GMT mri_mcadura_seg-Run-Time-Sec 21 mri_mcadura_seg Done #-------------------------------------- #@# VSinus Segmentation Sun 29 Dec 2024 11:40:37 AM GMT mri_vsinus_seg --s sub-31 --rca-synthseg --threads 20 --synthmorphdir /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm Sun 29 Dec 2024 11:40:37 AM GMT setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri /usr/local/freesurfer-8.0.0/bin/mri_vsinus_seg --s sub-31 --rca-synthseg --threads 20 --synthmorphdir /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm -rwxrwxr-x 1 501 1590 20960 Nov 3 00:09 /usr/local/freesurfer-8.0.0/bin/mri_vsinus_seg freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc $Id$ Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3531334 mri_vol2vol --mov /usr/local/freesurfer-8.0.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz --lta /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --targ /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mgz Matrix from LTA: -1.19424 0.09282 0.11628 1.62917; 0.11905 -0.01174 1.24094 -35.61354; -0.09254 -1.10581 -0.04557 -9.48975; 0.00000 0.00000 0.00000 1.00000; /usr/local/freesurfer-8.0.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz movvol /usr/local/freesurfer-8.0.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz targvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mgz regfile /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 1736146562 Final tkRAS-to-tkRAS Matrix is: -1.19424 0.09282 0.11628 1.62920; 0.11905 -0.01174 1.24094 -35.61356; -0.09254 -1.10581 -0.04557 -9.48975; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.77625 0.07558 -0.06033 216.63132; -0.06015 -0.02962 0.71877 23.34901; -0.07738 -0.80661 -0.00763 203.54556; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop 0 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz threshold mask volume at 0.001 cropping npad = 0 DoAbs = 0 Found 263746 voxels in mask (pct= 0.80) Computing bounding box, npad = 0, 0, 0, 0, 0, 0 77 18 15 175 174 141 maskval=0, outval=0 Writing masked volume to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz...done. mri_binarize --crop-around-ras /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz nolta cras /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz 0 144 144 144 Getting cras from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz final ras2vox matrix -1.53846 0.00000 -0.00000 158.45383; -0.00000 0.00000 -1.53846 126.17895; -0.00000 1.53846 -0.00000 137.67990; -0.00000 -0.00000 -0.00000 1.00000; -------------------------- ostr LIA (144 144 144) (144 144 144) rasCenter -3.93002 -33.9169 13.7663 crsCenter 164.5 105 85.5 MRIcropAroundCRS() vol size 320 320 320 center 164.5 105 85.5 fov 144 144 144 limits 94 237 34 177 15 158 using MRIextractRegion() mri_sclimbic_seg --model /usr/local/freesurfer-8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 20 --no-cite-sclimbic --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz /usr/local/freesurfer-8.0.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer-8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 20 --no-cite-sclimbic --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz Keeping anterior commissure in vols and stats Using CPU Using 20 thread(s) Loaded lookup table /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/vsinus.no-sp.ctab Loaded population stats /usr/local/freesurfer-8.0.0/models/sclimbic.volstats.csv nb_labels 6 inshape (144, 144, 144) features 24 (None, 144, 144, 144, 1) Loading weights from /usr/local/freesurfer-8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer-8.0.0/models/vsinus.no-sp.m.all.nstd10-070.h5 Segmenting image 1/1 Loaded input image from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz The input image has resolution ['0.65', '0.65', '0.65'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 2s 2s/step Wrote segmentation to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz vmpcma: 15663684 done mri_binarize --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthseg.rca.mgz --match 3 42 --inv --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/ctxsegmask.mgz 8.0.0-beta cwd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri cmdline mri_binarize --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthseg.rca.mgz --match 3 42 --inv --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/ctxsegmask.mgz sysname Linux hostname bioeng427-pc machine x86_64 user me18 input /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthseg.rca.mgz frame 0 nErode3d 0 nErode2d 0 output /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 1719980 values in range Counting number of voxels in first frame Found 1719980 voxels in final mask Writing output to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/ctxsegmask.mgz Count: 1719980 472349.461982 32768000 5.248962 mri_binarize done mri_vol2vol --mov /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz --targ /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --interp nearest --o /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz --regheader movvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz targvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz outvol /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 1736187936 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 3.89999; 0.00000 1.00000 0.00000 47.45001; 0.00000 -0.00000 1.00000 -35.09999; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 -0.00000 -93.99997; 0.00000 1.00000 0.00000 -34.00000; 0.00000 0.00000 1.00000 -14.99995; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/tmp.vsinus/ctxsegmask.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz...done. mri_segstats --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --seg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz --sum /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/stats/vsinus.stats --subject sub-31 --etiv 8.0.0-beta cwd cmdline mri_segstats --i /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz --seg /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz --sum /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/stats/vsinus.stats --subject sub-31 --etiv sysname Linux hostname bioeng427-pc machine x86_64 user me18 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1325841 mm^3 (det: 1.469336 ) Loading /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz Using embedded color table (and excluding seg 0) Loading /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz Voxel Volume is 0.274625 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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz:lock=1 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz:isosurface=1:outline=1 Started at Sun 29 Dec 2024 11:40:37 AM GMT Ended at Sun 29 Dec 2024 11:40:55 AM GMT Mri_Vsinus_Seg-Run-Time-Sec 18 Mri_Vsinus_Seg-Run-Time-Min 0.30 Mri_Vsinus_Seg-Run-Time-Hours 0.00 mri_vsinus_seg Done mri_mask /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/T1.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/synthstrip.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/brainmask.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/brainmask.mgz...done. #------------------------------------- #@# EM Registration Sun 29 Dec 2024 11:40:56 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer-8.0.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 20 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer-8.0.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (64, 24, 19) --> (253, 216, 274) finding center of left hemi white matter using (127, 88, 147) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (104,64,115) --> (150, 111,178) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.785 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.073908 @ (31.579, 31.579, 10.526) max log p = -4.007856 @ (-5.263, 5.263, 5.263) max log p = -3.979446 @ (2.632, -2.632, 2.632) max log p = -3.952944 @ (-1.316, -1.316, 1.316) max log p = -3.927320 @ (-1.974, 1.974, -0.658) max log p = -3.927320 @ (0.000, 0.000, 0.000) max log p = -3.921606 @ (-0.164, -0.164, 0.164) max log p = -3.914239 @ (-0.082, -0.247, -0.082) Found translation: (25.4, 34.5, 19.2): log p = -3.914 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.553, old_max_log_p =-3.914 (thresh=-3.9) 0.73476 -0.09757 0.08412 11.11090; 0.09673 0.74111 0.01107 4.45882; -0.10489 0.00000 0.69277 26.15953; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.541, old_max_log_p =-3.553 (thresh=-3.5) 0.73476 -0.09757 0.08412 11.11090; 0.10960 0.73476 -0.07945 18.72297; -0.09136 0.09673 0.68829 8.36942; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.541, old_max_log_p =-3.541 (thresh=-3.5) 0.73476 -0.09757 0.08412 11.11090; 0.10960 0.73476 -0.07945 18.72297; -0.09136 0.09673 0.68829 8.36942; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.348, old_max_log_p =-3.541 (thresh=-3.5) 0.76780 -0.10101 0.04008 12.67858; 0.10036 0.76890 0.01149 2.85213; -0.05554 -0.00626 0.68373 20.63580; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.346, old_max_log_p =-3.348 (thresh=-3.3) 0.76780 -0.10101 0.04008 12.67858; 0.10036 0.76890 0.01149 2.85213; -0.05450 -0.00614 0.67091 22.61286; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 9 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.317, old_max_log_p =-3.346 (thresh=-3.3) 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04840 -0.00699 0.67357 21.05496; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 9 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.317, old_max_log_p =-3.317 (thresh=-3.3) 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.317 (old=-4.785) transform before final EM align: 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 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: 011: -log(p) = 3.9 tol 0.000000 final transform: 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 1101888 FSRUNTIME@ mri_em_register 0.0293 hours 20 threads registration took 1 minutes and 45 seconds. @#@FSTIME 2024:12:29:11:40:56 mri_em_register N 7 e 105.52 S 0.77 U 1228.14 P 1164% M 788912 F 18 R 217636 W 0 c 26080 w 2900 I 0 O 32 L 3.08 2.64 3.12 @#@FSLOADPOST 2024:12:29:11:42:42 mri_em_register N 7 11.33 5.89 4.25 #-------------------------------------- #@# CA Normalize Sun 29 Dec 2024 11:42:42 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer-8.0.0/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer-8.0.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (64, 24, 19) --> (253, 216, 274) finding center of left hemi white matter using (127, 88, 147) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (104,64,115) --> (150, 111,178) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.1 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 0.76732 -0.10084 0.03453 13.70223; 0.10071 0.77160 0.01153 1.87516; -0.04846 -0.00700 0.67436 20.93189; 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 (153, 41, 21) --> (246, 189, 271) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 8 of 8140 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (72, 45, 19) --> (161, 203, 268) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 6 of 8682 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (165, 148, 55) --> (232, 206, 136) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 43 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (112, 149, 49) --> (167, 211, 135) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 66 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (140, 142, 107) --> (188, 231, 153) Brain_Stem: limiting intensities to 89.0 --> 120.0 1 of 159 (0.6%) samples deleted using 17090 total control points for intensity normalization... bias field = 0.993 +- 0.042 197 of 17075 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (153, 41, 21) --> (246, 189, 271) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 12 of 8208 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (72, 45, 19) --> (161, 203, 268) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 6 of 8752 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (165, 148, 55) --> (232, 206, 136) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 93 (8.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (112, 149, 49) --> (167, 211, 135) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 107 (9.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (140, 142, 107) --> (188, 231, 153) Brain_Stem: limiting intensities to 88.0 --> 111.0 12 of 213 (5.6%) samples deleted using 17373 total control points for intensity normalization... bias field = 1.019 +- 0.038 137 of 17255 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (153, 41, 21) --> (246, 189, 271) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 11 of 8192 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (72, 45, 19) --> (161, 203, 268) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 11 of 8735 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (165, 148, 55) --> (232, 206, 136) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 57 of 128 (44.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (112, 149, 49) --> (167, 211, 135) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 125 (32.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (140, 142, 107) --> (188, 231, 153) Brain_Stem: limiting intensities to 88.0 --> 108.0 71 of 300 (23.7%) samples deleted using 17480 total control points for intensity normalization... bias field = 1.014 +- 0.035 94 of 17229 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 28 seconds. @#@FSTIME 2024:12:29:11:42:42 mri_ca_normalize N 8 e 87.82 S 0.66 U 102.44 P 117% M 941432 F 0 R 683291 W 0 c 829 w 532 I 0 O 9824 L 11.33 5.89 4.25 @#@FSLOADPOST 2024:12:29:11:44:09 mri_ca_normalize N 8 3.39 4.65 3.96 #-------------------------------------- #@# EntoWM Segmentation Sun 29 Dec 2024 11:44:09 AM GMT mri_entowm_seg --s sub-31 --conform --threads 20 mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer-8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer-8.0.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-31 --conform --threads 20 /usr/local/freesurfer-8.0.0/python/scripts/mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer-8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer-8.0.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-31 --conform --threads 20 Keeping anterior commissure in vols and stats Using CPU Using 20 thread(s) Loaded lookup table /usr/local/freesurfer-8.0.0/models/entowm.ctab Loaded population stats /usr/local/freesurfer-8.0.0/models/sclimbic.volstats.csv nb_labels 5 inshape (160, 160, 160) features 24 (None, 160, 160, 160, 1) Loading weights from /usr/local/freesurfer-8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer-8.0.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 Using subject directory /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 Computed eTIV from talairach Segmenting subject sub-31 1/1 Loaded input image from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/nu.mgz The input image has resolution ['0.65', '0.65', '0.65'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 3s 3s/step Wrote segmentation to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/entowm.mgz Wrote volume stats to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/stats/entowm.stats Wrote summary of label volumes to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/entowm_volumes_all.csv vmpcma: 18438316 done Started at Sun 29 Dec 2024 11:44:09 AM GMT Started at Sun 29 Dec 2024 11:44:09 AM GMT Ended at Sun 29 Dec 2024 11:44:16 AM GMT Ended at Sun 29 Dec 2024 11:44:16 AM GMT mri_entowm_seg-Run-Time-Sec 7 mri_entowm_seg-Run-Time-Sec 7 mri_entowm_seg-Run-Time-Min 0.14 mri_entowm_seg-Run-Time-Min 0.14 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 959 314.5776 wm-lh-entorhinal 2 3201 476 150.8730 wm-lh-gyrus-ambiens 3 4006 2129 641.6566 wm-rh-entorhinal 4 4201 470 165.3415 wm-rh-gyrus-ambiens #-------------------------------------- #@# CC Seg Sun 29 Dec 2024 11:44:16 AM GMT seg2cc --s sub-31 Sun 29 Dec 2024 11:44:16 AM GMT setenv SUBJECTS_DIR /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8 cd /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri /usr/local/freesurfer-8.0.0/bin/seg2cc --s sub-31 freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc seg2cc 8.0.0-beta Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri IsConformed yes Sun 29 Dec 2024 11:44:17 AM GMT mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta sub-31 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 /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/aseg.auto_noCCseg.mgz reading norm from /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/norm.mgz 268093 voxels in left wm, 183626 in right wm, xrange [145, 168] searching rotation angles z=[-1 13], y=[-3 11] 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 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.7 searching scale 1 Z rot 11.9 searching scale 1 Z rot 12.2 searching scale 1 Z rot 12.4 searching scale 1 Z rot 12.7 global minimum found at slice 153.7, rotations (3.90, 5.93) final transformation (x=153.7, yr=3.900, zr=5.930): 0.99234 -0.10332 0.06766 -23.98372; 0.10308 0.99465 0.00703 4.63651; -0.06802 0.00000 0.99768 -16.18424; 0.00000 0.00000 0.00000 1.00000; updating x range to be [123, 130] in xformed coordinates best xformed slice 127 min_x_fornix = 126 min_x_fornix = 144 min_x_fornix = 130 min_x_fornix = 129 min_x_fornix = 145 cc center is found at 127 107 155 eigenvectors: 0.00057 -0.00310 1.00000; 0.13570 -0.99074 -0.00315; 0.99075 0.13570 -0.00014; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/aseg.auto.mgz... corpus callosum segmentation took 1.6 minutes #VMPC# mri_cc VmPeak 997940 mri_cc done @#@FSTIME 2024:12:29:11:44:17 mri_cc N 7 e 93.96 S 0.42 U 98.10 P 104% M 655276 F 0 R 542943 W 0 c 394 w 134 I 0 O 1448 L 3.20 4.58 3.94 @#@FSLOADPOST 2024:12:29:11:45:51 mri_cc N 7 1.92 3.87 3.76 Sun 29 Dec 2024 11:45:51 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri Started at Sun 29 Dec 2024 11:44:16 AM GMT Ended at Sun 29 Dec 2024 11:45:51 AM GMT Seg2cc-Run-Time-Sec 95 Seg2cc-Run-Time-Hours 0.03 seg2cc Done @#@FSTIME 2024:12:29:11:44:16 seg2cc N 2 e 94.33 S 0.50 U 98.40 P 104% M 655276 F 1 R 559338 W 0 c 399 w 411 I 0 O 1576 L 3.20 4.58 3.94 @#@FSLOADPOST 2024:12:29:11:45:51 seg2cc N 2 1.92 3.87 3.76 #-------------------------------------- #@# Merge ASeg Sun 29 Dec 2024 11:45:51 AM GMT cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun 29 Dec 2024 11:45:51 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_normalize -seed 1234 -mprage -noconform -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 320 (src width 320) normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 1724 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 57 (57), valley at 14 (14) csf peak at 29, setting threshold to 47 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 56 (56), valley at 20 (20) csf peak at 29, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 21 seconds. @#@FSTIME 2024:12:29:11:45:51 mri_normalize N 10 e 262.32 S 1.67 U 311.11 P 119% M 2204064 F 17 R 1200711 W 0 c 2455 w 243 I 0 O 7064 L 1.92 3.87 3.76 @#@FSLOADPOST 2024:12:29:11:50:13 mri_normalize N 10 1.01 2.18 3.06 #-------------------------------------------- #@# Mask BFS Sun 29 Dec 2024 11:50:13 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 4682127 voxels in mask (pct= 14.29) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:12:29:11:50:13 mri_mask N 5 e 1.15 S 0.03 U 3.77 P 331% M 138028 F 18 R 33210 W 0 c 67 w 56 I 0 O 6984 L 1.01 2.18 3.06 @#@FSLOADPOST 2024:12:29:11:50:14 mri_mask N 5 1.01 2.18 3.06 mri_mask -oval 1 -invert brain.finalsurfs.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 32767978 Resetting threshold to 0.5 DoAbs = 0 Found 32767978 voxels in mask (pct=100.00) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:12:29:11:50:14 mri_mask N 6 e 3.23 S 0.11 U 6.51 P 204% M 330120 F 0 R 81329 W 0 c 108 w 39 I 0 O 6984 L 1.01 2.18 3.06 @#@FSLOADPOST 2024:12:29:11:50:18 mri_mask N 6 1.01 2.16 3.05 mri_mask -oval 1 -invert brain.finalsurfs.mgz /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri/vsinus.mgz brain.finalsurfs.mgz setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 32754308 Resetting threshold to 0.5 DoAbs = 0 Found 32754308 voxels in mask (pct= 99.96) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:12:29:11:50:18 mri_mask N 6 e 3.17 S 0.08 U 6.41 P 204% M 329760 F 0 R 81323 W 0 c 93 w 39 I 0 O 6976 L 1.01 2.16 3.05 @#@FSLOADPOST 2024:12:29:11:50:21 mri_mask N 6 1.01 2.16 3.05 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 = 946 @#@FSTIME 2024:12:29:11:50:21 mri_edit_wm_with_aseg N 7 e 1.59 S 0.03 U 5.02 P 317% M 169272 F 0 R 40944 W 0 c 107 w 40 I 0 O 6976 L 1.01 2.16 3.05 @#@FSLOADPOST 2024:12:29:11:50:22 mri_edit_wm_with_aseg N 7 1.01 2.16 3.05 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 = 8908 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 1324 @#@FSTIME 2024:12:29:11:50:22 mri_edit_wm_with_aseg N 6 e 1.44 S 0.07 U 6.92 P 485% M 145608 F 0 R 75235 W 0 c 162 w 59 I 0 O 6976 L 1.01 2.16 3.05 @#@FSLOADPOST 2024:12:29:11:50:24 mri_edit_wm_with_aseg N 6 1.01 2.14 3.04 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Sun 29 Dec 2024 11:50:24 AM GMT AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:12:29:11:50:24 AntsDenoiseImageFs N 4 e 67.26 S 0.17 U 68.41 P 101% M 679356 F 0 R 168589 W 0 c 218 w 20 I 0 O 7112 L 1.01 2.14 3.04 @#@FSLOADPOST 2024:12:29:11:51:31 AntsDenoiseImageFs N 4 1.00 1.91 2.90 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 0.65, wsize = 20 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 20 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 = 1148501, nonwhite = 31026750, ambig = 592749, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (104.0): 104.5 +- 4.6 [79.0 --> 125.0] CCS GM (70.0) : 67.7 +- 11.7 [30.0 --> 95.0] white_mean 104.502 white_sigma 4.63805 gray_mean 67.6609 gray_sigma 11.6741 setting bottom of white matter range wm_low to 79.3 setting top of gray matter range gray_hi to 91.0 wm_low 79.335 wm_hi 125 gray_low 30 gray_hi 91.0091 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=79.335, wm_hi=125, gray_hi=91.0091 white = 1369870, nonwhite = 31059696, ambig = 338434, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 79.335 wm_hi 125 gray_low 30 gray_hi 91.0091 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 91.0091, wm_low = 79.335 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.0091, wmlow=79.335 329220 voxels processed (1.00%) 153324 voxels white (0.47%) 175896 voxels non-white (0.54%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=74.335, gray_hi=91.0091, wsize=20 518816 voxels tested (1.58%) 117196 voxels changed (0.36%) 109162 multi-scale searches (0.33%) Recovering bright white MRIrecoverBrightWhite() wm_low 79.335 wm_hi 125 slack 4.63805 pct_thresh 0.33 intensity_thresh 129.638 nvox_thresh 8.58 1157 voxels tested (0.00%) 786 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=74.335, hithr=91.0091 smoothing input volume with sigma = 0.250 223876 voxels tested (0.68%) 38946 voxels changed (0.12%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 14177 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 4383 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 19013 filled MRIfindBrightNonWM(): 8200 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:12:29:11:51:31 mri_segment N 5 e 144.61 S 0.36 U 147.33 P 102% M 278112 F 9 R 558660 W 0 c 498 w 66 I 0 O 2048 L 1.00 1.91 2.90 @#@FSLOADPOST 2024:12:29:11:53:56 mri_segment N 5 1.00 1.56 2.62 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 0.68 minutes Fixing entowm 3 255 255 LabelAmygalaCortalJunction((): nhits = 8908 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 102021 additional wm voxels added 0 additional wm voxels added SEG EDIT: 1061001 voxels turned on, 102450 voxels turned off. Dilating 1 voxels in 3d propagating editing to output volume from wm.seg.mgz MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 4034 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 1324 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:12:29:11:53:56 mri_edit_wm_with_aseg N 17 e 40.86 S 1.66 U 90.00 P 224% M 1240912 F 0 R 1013535 W 0 c 1551 w 394 I 0 O 1784 L 1.00 1.56 2.62 @#@FSLOADPOST 2024:12:29:11:54:37 mri_edit_wm_with_aseg N 17 1.85 1.77 2.65 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 68 found - 68 modified | TOTAL: 68 pass 2 (xy+): 0 found - 68 modified | TOTAL: 68 pass 1 (xy-): 76 found - 76 modified | TOTAL: 144 pass 2 (xy-): 0 found - 76 modified | TOTAL: 144 pass 1 (yz+): 71 found - 71 modified | TOTAL: 215 pass 2 (yz+): 0 found - 71 modified | TOTAL: 215 pass 1 (yz-): 64 found - 64 modified | TOTAL: 279 pass 2 (yz-): 0 found - 64 modified | TOTAL: 279 pass 1 (xz+): 54 found - 54 modified | TOTAL: 333 pass 2 (xz+): 0 found - 54 modified | TOTAL: 333 pass 1 (xz-): 59 found - 59 modified | TOTAL: 392 pass 2 (xz-): 0 found - 59 modified | TOTAL: 392 Iteration Number : 1 pass 1 (+++): 40 found - 40 modified | TOTAL: 40 pass 2 (+++): 0 found - 40 modified | TOTAL: 40 pass 1 (+++): 71 found - 71 modified | TOTAL: 111 pass 2 (+++): 0 found - 71 modified | TOTAL: 111 pass 1 (+++): 78 found - 78 modified | TOTAL: 189 pass 2 (+++): 0 found - 78 modified | TOTAL: 189 pass 1 (+++): 65 found - 65 modified | TOTAL: 254 pass 2 (+++): 0 found - 65 modified | TOTAL: 254 Iteration Number : 1 pass 1 (++): 151 found - 151 modified | TOTAL: 151 pass 2 (++): 0 found - 151 modified | TOTAL: 151 pass 1 (+-): 233 found - 233 modified | TOTAL: 384 pass 2 (+-): 1 found - 234 modified | TOTAL: 385 pass 3 (+-): 0 found - 234 modified | TOTAL: 385 pass 1 (--): 282 found - 282 modified | TOTAL: 667 pass 2 (--): 0 found - 282 modified | TOTAL: 667 pass 1 (-+): 227 found - 227 modified | TOTAL: 894 pass 2 (-+): 0 found - 227 modified | TOTAL: 894 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 12 found - 12 modified | TOTAL: 18 pass 2 (xy-): 0 found - 12 modified | TOTAL: 18 pass 1 (yz+): 11 found - 11 modified | TOTAL: 29 pass 2 (yz+): 0 found - 11 modified | TOTAL: 29 pass 1 (yz-): 13 found - 13 modified | TOTAL: 42 pass 2 (yz-): 0 found - 13 modified | TOTAL: 42 pass 1 (xz+): 8 found - 8 modified | TOTAL: 50 pass 2 (xz+): 0 found - 8 modified | TOTAL: 50 pass 1 (xz-): 9 found - 9 modified | TOTAL: 59 pass 2 (xz-): 0 found - 9 modified | TOTAL: 59 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 2 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 6 found - 6 modified | TOTAL: 13 pass 2 (+-): 0 found - 6 modified | TOTAL: 13 pass 1 (--): 6 found - 6 modified | TOTAL: 19 pass 2 (--): 0 found - 6 modified | TOTAL: 19 pass 1 (-+): 8 found - 8 modified | TOTAL: 27 pass 2 (-+): 0 found - 8 modified | TOTAL: 27 Iteration Number : 3 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+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 = 1645 (out of 1688965: 0.097397) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:12:29:11:54:37 mri_pretess N 4 e 4.90 S 0.03 U 7.53 P 154% M 104884 F 0 R 24949 W 0 c 93 w 40 I 0 O 1792 L 1.85 1.77 2.65 @#@FSLOADPOST 2024:12:29:11:54:42 mri_pretess N 4 1.86 1.77 2.64 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 = 4034 @#@FSTIME 2024:12:29:11:54:42 mri_edit_wm_with_aseg N 7 e 1.53 S 0.07 U 4.95 P 328% M 169152 F 0 R 40944 W 0 c 90 w 40 I 0 O 1792 L 1.86 1.77 2.64 @#@FSLOADPOST 2024:12:29:11:54:43 mri_edit_wm_with_aseg N 7 1.79 1.76 2.63 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 = 8908 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 1324 @#@FSTIME 2024:12:29:11:54:43 mri_edit_wm_with_aseg N 6 e 1.10 S 0.08 U 6.68 P 614% M 145756 F 0 R 75235 W 0 c 153 w 59 I 0 O 1792 L 1.79 1.76 2.63 @#@FSLOADPOST 2024:12:29:11:54:44 mri_edit_wm_with_aseg N 6 1.79 1.76 2.63 #-------------------------------------------- #@# Fill Sun 29 Dec 2024 11:54:44 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer-8.0.0/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... done. searching for cutting planes...voxel to talairach voxel transform 1.18050 -0.15514 0.05313 -15.84273; 0.15495 1.18708 0.01774 -34.03824; -0.07455 -0.01077 1.03748 -4.72018; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.18050 -0.15514 0.05313 -15.84273; 0.15495 1.18708 0.01774 -34.03824; -0.07455 -0.01077 1.03748 -4.72018; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (828, 3314) area[0] = 16313 (min = 828, max = 3314), aspect = 1.14 (min = 0.10, max = 0.75) need search nearby using seed (144, 170, 148), TAL = (10.4, -7.8, -6.5) talairach voxel to voxel transform 0.83011 0.10808 -0.04435 16.62080; -0.10923 0.82805 -0.00856 26.41457; 0.05852 0.01636 0.96060 6.01833; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (144, 170, 148) --> (10.4, -7.8, -6.5) done. filling took 1.5 minutes badRH = 86216/811042, badLH=0/778128 talairach cc position changed to (10.40, -7.80, -6.50) Erasing brainstem...done. seed_search_size = 14, min_neighbors = 5 search rh wm seed point around talairach space:(28.40, -7.80, -6.50) SRC: (124.98, 153.21, 157.77) search lh wm seed point around talairach space (-7.60, -7.80, -6.50), SRC: (170.95, 147.16, 161.02) 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... error: Please check filled volume. Cerebellum may be included. @#@FSTIME 2024:12:29:11:54:44 mri_fill N 10 e 93.33 S 1.22 U 95.46 P 103% M 1534164 F 0 R 819505 W 0 c 373 w 40 I 0 O 544 L 1.79 1.76 2.63 @#@FSLOADPOST 2024:12:29:11:56:18 mri_fill N 10 1.17 1.56 2.48 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Sun 29 Dec 2024 11:56:18 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 7 found - 7 modified | TOTAL: 10 pass 2 (xy-): 0 found - 7 modified | TOTAL: 10 pass 1 (yz+): 14 found - 14 modified | TOTAL: 24 pass 2 (yz+): 0 found - 14 modified | TOTAL: 24 pass 1 (yz-): 13 found - 13 modified | TOTAL: 37 pass 2 (yz-): 0 found - 13 modified | TOTAL: 37 pass 1 (xz+): 10 found - 10 modified | TOTAL: 47 pass 2 (xz+): 0 found - 10 modified | TOTAL: 47 pass 1 (xz-): 6 found - 6 modified | TOTAL: 53 pass 2 (xz-): 0 found - 6 modified | TOTAL: 53 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 7 found - 7 modified | TOTAL: 9 pass 2 (+-): 0 found - 7 modified | TOTAL: 9 pass 1 (--): 1 found - 1 modified | TOTAL: 10 pass 2 (--): 0 found - 1 modified | TOTAL: 10 pass 1 (-+): 2 found - 2 modified | TOTAL: 12 pass 2 (-+): 0 found - 2 modified | TOTAL: 12 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 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 = 72 (out of 778200: 0.009252) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:12:29:11:56:18 mri_pretess N 4 e 2.77 S 0.03 U 5.40 P 196% M 72508 F 0 R 16824 W 0 c 99 w 40 I 0 O 536 L 1.17 1.56 2.48 @#@FSLOADPOST 2024:12:29:11:56:20 mri_pretess N 4 1.16 1.55 2.47 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix.predec 8.0.0-beta 8.0.0-beta slice 30: 1178 vertices, 1267 faces slice 40: 5863 vertices, 6081 faces slice 50: 12906 vertices, 13236 faces slice 60: 22065 vertices, 22443 faces slice 70: 32475 vertices, 32847 faces slice 80: 42676 vertices, 43106 faces slice 90: 56095 vertices, 56581 faces slice 100: 69194 vertices, 69654 faces slice 110: 83788 vertices, 84285 faces slice 120: 98155 vertices, 98674 faces slice 130: 114746 vertices, 115330 faces slice 140: 131289 vertices, 131882 faces slice 150: 147827 vertices, 148439 faces slice 160: 163323 vertices, 163912 faces slice 170: 179329 vertices, 179942 faces slice 180: 195097 vertices, 195654 faces slice 190: 207234 vertices, 207698 faces slice 200: 218758 vertices, 219217 faces slice 210: 228860 vertices, 229270 faces slice 220: 238139 vertices, 238542 faces slice 230: 247584 vertices, 247951 faces slice 240: 256373 vertices, 256719 faces slice 250: 263221 vertices, 263534 faces slice 260: 269368 vertices, 269598 faces slice 270: 272109 vertices, 272201 faces slice 280: 272198 vertices, 272270 faces slice 290: 272198 vertices, 272270 faces slice 300: 272198 vertices, 272270 faces slice 310: 272198 vertices, 272270 faces slice 320: 272198 vertices, 272270 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix.predec using vox2ras matrix: -0.65000 0.00000 0.00000 104.00000; 0.00000 0.00000 0.65000 -104.00000; 0.00000 -0.65000 0.00000 104.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:12:29:11:56:20 mri_tessellate N 3 e 1.61 S 0.01 U 2.93 P 182% M 67144 F 17 R 15928 W 0 c 52 w 38 I 0 O 12768 L 1.16 1.55 2.47 @#@FSLOADPOST 2024:12:29:11:56:22 mri_tessellate N 3 1.16 1.55 2.47 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix.predec ../surf/lh.orig.nofix.predec counting number of connected components... 272198 voxel in cpt #1: X=-72 [v=272198,e=816810,f=544540] located at (-21.209955, -10.850398, 29.120296) For the whole surface: X=-72 [v=272198,e=816810,f=544540] One single component has been found nothing to do done @#@FSTIME 2024:12:29:11:56:22 mris_extract_main_component N 2 e 1.30 S 0.21 U 2.86 P 235% M 529716 F 17 R 142025 W 0 c 42 w 974 I 0 O 19144 L 1.16 1.55 2.47 @#@FSLOADPOST 2024:12:29:11:56:23 mris_extract_main_component N 2 1.15 1.54 2.46 mris_remesh --desired-face-area 0.5 --input ../surf/lh.orig.nofix.predec --output ../surf/lh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.21125 decimation level = 0.4225 target vertices = 115004 Remesher::remeshBKV( 5 , 115004 ) vcount = 272198 vnum: 115004 area = 115034 avel: 0.739746 s0 = 0.698563 st: 1.07471 Targetn: 240759 points: 272198 Targetl: 0.806739 avg l: 0.739746 points: 272198 Maxndown:34582 Points: 272198 avg edge: 0.703664 Targetn: 209320 points: 272198 Targetl: 0.873732 avg l: 0.703664 points: 272198 Maxndown:69165 Points: 203033 avg edge: 0.781254 Targetn: 177881 points: 203033 Targetl: 0.940725 avg l: 0.781254 points: 203052 Maxndown:27688 Points: 175364 avg edge: 0.823339 Targetn: 146442 points: 175364 Targetl: 1.00772 avg l: 0.823339 points: 175371 Maxndown:31821 Points: 143550 avg edge: 0.89134 Targetn: 115004 points: 143550 Targetl: 1.07471 avg l: 0.89134 points: 143555 Maxndown:28551 Points: 115004 avg edge: 0.976602 Final Points: 115004 final avg edge: 0.976602 avg qual before : 0.866025 after: 0.948787 Removing intersections removing intersecting faces 000: 4 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 272198 nv = 115004 0.422501 Area 230152 0.40286 0.05533 0.006993 0.9323 Corner 690456 60.00000 9.98060 7.115998 161.0620 Edge 345228 0.97657 0.11545 0.111603 1.6819 Hinge 345228 30.70777 25.53149 0.000000 178.0453 mris_remesh done @#@FSTIME 2024:12:29:11:56:23 mris_remesh N 6 e 14.29 S 0.63 U 20.51 P 147% M 903460 F 22 R 381459 W 0 c 240 w 5320 I 0 O 8096 L 1.15 1.54 2.46 @#@FSLOADPOST 2024:12:29:11:56:38 mris_remesh N 6 1.12 1.52 2.45 #-------------------------------------------- #@# Tessellate rh Sun 29 Dec 2024 11:56:38 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 15 found - 15 modified | TOTAL: 22 pass 2 (yz+): 0 found - 15 modified | TOTAL: 22 pass 1 (yz-): 10 found - 10 modified | TOTAL: 32 pass 2 (yz-): 0 found - 10 modified | TOTAL: 32 pass 1 (xz+): 3 found - 3 modified | TOTAL: 35 pass 2 (xz+): 0 found - 3 modified | TOTAL: 35 pass 1 (xz-): 2 found - 2 modified | TOTAL: 37 pass 2 (xz-): 0 found - 2 modified | TOTAL: 37 Iteration Number : 1 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 : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 4 found - 4 modified | TOTAL: 4 pass 2 (+-): 0 found - 4 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 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-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 = 49 (out of 811091: 0.006041) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:12:29:11:56:38 mri_pretess N 4 e 2.72 S 0.03 U 5.34 P 197% M 72548 F 0 R 16825 W 0 c 89 w 40 I 0 O 536 L 1.12 1.52 2.45 @#@FSLOADPOST 2024:12:29:11:56:40 mri_pretess N 4 1.11 1.51 2.44 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix.predec 8.0.0-beta 8.0.0-beta slice 30: 1249 vertices, 1366 faces slice 40: 7157 vertices, 7404 faces slice 50: 15849 vertices, 16195 faces slice 60: 26461 vertices, 26870 faces slice 70: 38333 vertices, 38778 faces slice 80: 52438 vertices, 52959 faces slice 90: 68382 vertices, 68924 faces slice 100: 85687 vertices, 86340 faces slice 110: 103366 vertices, 103960 faces slice 120: 121403 vertices, 122024 faces slice 130: 139958 vertices, 140595 faces slice 140: 156861 vertices, 157498 faces slice 150: 174933 vertices, 175561 faces slice 160: 191582 vertices, 192178 faces slice 170: 208403 vertices, 209062 faces slice 180: 225370 vertices, 225970 faces slice 190: 240582 vertices, 241219 faces slice 200: 254943 vertices, 255495 faces slice 210: 268012 vertices, 268501 faces slice 220: 277722 vertices, 278115 faces slice 230: 287658 vertices, 288068 faces slice 240: 295126 vertices, 295469 faces slice 250: 302488 vertices, 302836 faces slice 260: 307497 vertices, 307727 faces slice 270: 309326 vertices, 309424 faces slice 280: 309326 vertices, 309424 faces slice 290: 309326 vertices, 309424 faces slice 300: 309326 vertices, 309424 faces slice 310: 309326 vertices, 309424 faces slice 320: 309326 vertices, 309424 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix.predec using vox2ras matrix: -0.65000 0.00000 0.00000 104.00000; 0.00000 0.00000 0.65000 -104.00000; 0.00000 -0.65000 0.00000 104.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:12:29:11:56:40 mri_tessellate N 3 e 1.65 S 0.02 U 2.95 P 180% M 70260 F 0 R 16757 W 0 c 53 w 21 I 0 O 14504 L 1.11 1.51 2.44 @#@FSLOADPOST 2024:12:29:11:56:42 mri_tessellate N 3 1.11 1.51 2.44 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix.predec ../surf/rh.orig.nofix.predec counting number of connected components... 309326 voxel in cpt #1: X=-98 [v=309326,e=928272,f=618848] located at (27.795698, -13.329223, 28.078024) For the whole surface: X=-98 [v=309326,e=928272,f=618848] One single component has been found nothing to do done @#@FSTIME 2024:12:29:11:56:42 mris_extract_main_component N 2 e 1.90 S 0.23 U 3.60 P 201% M 602188 F 19 R 161627 W 0 c 45 w 1100 I 0 O 21760 L 1.11 1.51 2.44 @#@FSLOADPOST 2024:12:29:11:56:44 mris_extract_main_component N 2 1.18 1.52 2.44 mris_remesh --desired-face-area 0.5 --input ../surf/rh.orig.nofix.predec --output ../surf/rh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.21125 decimation level = 0.4225 target vertices = 130690 Remesher::remeshBKV( 5 , 130690 ) vcount = 309326 vnum: 130690 area = 130732 avel: 0.739746 s0 = 0.698581 st: 1.07474 Targetn: 273598 points: 309326 Targetl: 0.806745 avg l: 0.739746 points: 309326 Maxndown:39300 Points: 309326 avg edge: 0.703078 Targetn: 237871 points: 309326 Targetl: 0.873744 avg l: 0.703078 points: 309326 Maxndown:78600 Points: 230726 avg edge: 0.78004 Targetn: 202144 points: 230726 Targetl: 0.940743 avg l: 0.78004 points: 230756 Maxndown:31473 Points: 199283 avg edge: 0.821749 Targetn: 166417 points: 199283 Targetl: 1.00774 avg l: 0.821749 points: 199286 Maxndown:36155 Points: 163131 avg edge: 0.889088 Targetn: 130690 points: 163131 Targetl: 1.07474 avg l: 0.889088 points: 163137 Maxndown:32447 Points: 130690 avg edge: 0.973445 Final Points: 130690 final avg edge: 0.973445 avg qual before : 0.866025 after: 0.948946 Removing intersections removing intersecting faces 000: 12 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 309326 nv = 130690 0.422499 Area 261576 0.40027 0.05537 0.031589 1.0179 Corner 784728 60.00000 9.97774 9.987763 154.2347 Edge 392364 0.97338 0.11522 0.240753 1.7012 Hinge 392364 31.11927 25.82588 0.000000 178.2490 mris_remesh done @#@FSTIME 2024:12:29:11:56:44 mris_remesh N 6 e 17.13 S 0.74 U 24.03 P 144% M 1027684 F 21 R 412131 W 0 c 244 w 5762 I 0 O 9200 L 1.18 1.52 2.44 @#@FSLOADPOST 2024:12:29:11:57:01 mris_remesh N 6 1.14 1.49 2.41 #-------------------------------------------- #@# Smooth1 lh Sun 29 Dec 2024 11:57:01 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 2024:12:29:11:57:01 mris_smooth N 5 e 1.65 S 0.08 U 4.09 P 252% M 178116 F 17 R 54378 W 0 c 88 w 393 I 0 O 8096 L 1.14 1.49 2.41 @#@FSLOADPOST 2024:12:29:11:57:03 mris_smooth N 5 1.13 1.48 2.41 #-------------------------------------------- #@# Smooth1 rh Sun 29 Dec 2024 11:57:03 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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 2024:12:29:11:57:03 mris_smooth N 5 e 1.95 S 0.08 U 4.57 P 238% M 202460 F 18 R 61724 W 0 c 109 w 460 I 0 O 9200 L 1.13 1.48 2.41 @#@FSLOADPOST 2024:12:29:11:57:05 mris_smooth N 5 1.13 1.48 2.41 #-------------------------------------------- #@# Inflation1 lh Sun 29 Dec 2024 11:57:05 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 100 Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.1 mm, total surface area = 61395 mm^2 resetting # of iterations to 15 for highres volume step 000: RMS=0.147 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.042 (target=0.015) step 065: RMS=0.041 (target=0.015) step 070: RMS=0.041 (target=0.015) step 075: RMS=0.040 (target=0.015) step 080: RMS=0.041 (target=0.015) step 085: RMS=0.041 (target=0.015) step 090: RMS=0.041 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 119.163801 mris_inflate stimesec 1.416336 mris_inflate ru_maxrss 180092 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 690926 mris_inflate ru_majflt 17 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8096 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 11908 mris_inflate ru_nivcsw 2807 @#@FSTIME 2024:12:29:11:57:05 mris_inflate N 4 e 10.64 S 1.42 U 119.16 P 1133% M 180092 F 17 R 690932 W 0 c 2808 w 11909 I 0 O 8096 L 1.13 1.48 2.41 @#@FSLOADPOST 2024:12:29:11:57:16 mris_inflate N 4 2.51 1.78 2.49 #-------------------------------------------- #@# Inflation1 rh Sun 29 Dec 2024 11:57:16 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 100 Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.3 mm, total surface area = 68371 mm^2 resetting # of iterations to 15 for highres volume step 000: RMS=0.154 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.072 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.064 (target=0.015) step 035: RMS=0.062 (target=0.015) step 040: RMS=0.062 (target=0.015) step 045: RMS=0.061 (target=0.015) step 050: RMS=0.059 (target=0.015) step 055: RMS=0.058 (target=0.015) step 060: RMS=0.058 (target=0.015) step 065: RMS=0.058 (target=0.015) step 070: RMS=0.058 (target=0.015) step 075: RMS=0.058 (target=0.015) step 080: RMS=0.058 (target=0.015) step 085: RMS=0.059 (target=0.015) step 090: RMS=0.060 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 129.556322 mris_inflate stimesec 1.571324 mris_inflate ru_maxrss 204156 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 814845 mris_inflate ru_majflt 16 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9200 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 15072 mris_inflate ru_nivcsw 2848 @#@FSTIME 2024:12:29:11:57:16 mris_inflate N 4 e 12.32 S 1.57 U 129.55 P 1064% M 204156 F 16 R 814851 W 0 c 2848 w 15073 I 0 O 9200 L 2.51 1.78 2.49 @#@FSLOADPOST 2024:12:29:11:57:28 mris_inflate N 4 6.45 2.69 2.78 #-------------------------------------------- #@# QSphere lh Sun 29 Dec 2024 11:57:28 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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: 20 scaling brain by 0.324... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.58 (0.00-->8.93) (max @ vno 45032 --> 46371) face area 0.03 +- 0.03 (-0.32-->0.73) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.909, avgs=0 005/300: dt: 0.9000, rms radial error=176.651, avgs=0 010/300: dt: 0.9000, rms radial error=176.096, avgs=0 015/300: dt: 0.9000, rms radial error=175.367, avgs=0 020/300: dt: 0.9000, rms radial error=174.537, avgs=0 025/300: dt: 0.9000, rms radial error=173.648, avgs=0 030/300: dt: 0.9000, rms radial error=172.726, avgs=0 035/300: dt: 0.9000, rms radial error=171.787, avgs=0 040/300: dt: 0.9000, rms radial error=170.840, avgs=0 045/300: dt: 0.9000, rms radial error=169.891, avgs=0 050/300: dt: 0.9000, rms radial error=168.943, avgs=0 055/300: dt: 0.9000, rms radial error=167.997, avgs=0 060/300: dt: 0.9000, rms radial error=167.055, avgs=0 065/300: dt: 0.9000, rms radial error=166.117, avgs=0 070/300: dt: 0.9000, rms radial error=165.184, avgs=0 075/300: dt: 0.9000, rms radial error=164.256, avgs=0 080/300: dt: 0.9000, rms radial error=163.332, avgs=0 085/300: dt: 0.9000, rms radial error=162.413, avgs=0 090/300: dt: 0.9000, rms radial error=161.500, avgs=0 095/300: dt: 0.9000, rms radial error=160.591, avgs=0 100/300: dt: 0.9000, rms radial error=159.688, avgs=0 105/300: dt: 0.9000, rms radial error=158.790, avgs=0 110/300: dt: 0.9000, rms radial error=157.897, avgs=0 115/300: dt: 0.9000, rms radial error=157.009, avgs=0 120/300: dt: 0.9000, rms radial error=156.126, avgs=0 125/300: dt: 0.9000, rms radial error=155.247, avgs=0 130/300: dt: 0.9000, rms radial error=154.374, avgs=0 135/300: dt: 0.9000, rms radial error=153.505, avgs=0 140/300: dt: 0.9000, rms radial error=152.641, avgs=0 145/300: dt: 0.9000, rms radial error=151.781, avgs=0 150/300: dt: 0.9000, rms radial error=150.927, avgs=0 155/300: dt: 0.9000, rms radial error=150.077, avgs=0 160/300: dt: 0.9000, rms radial error=149.231, avgs=0 165/300: dt: 0.9000, rms radial error=148.391, avgs=0 170/300: dt: 0.9000, rms radial error=147.555, avgs=0 175/300: dt: 0.9000, rms radial error=146.724, avgs=0 180/300: dt: 0.9000, rms radial error=145.898, 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=143.446, avgs=0 200/300: dt: 0.9000, rms radial error=142.638, avgs=0 205/300: dt: 0.9000, rms radial error=141.834, avgs=0 210/300: dt: 0.9000, rms radial error=141.035, avgs=0 215/300: dt: 0.9000, rms radial error=140.240, avgs=0 220/300: dt: 0.9000, rms radial error=139.450, avgs=0 225/300: dt: 0.9000, rms radial error=138.665, avgs=0 230/300: dt: 0.9000, rms radial error=137.883, avgs=0 235/300: dt: 0.9000, rms radial error=137.107, avgs=0 240/300: dt: 0.9000, rms radial error=136.334, avgs=0 245/300: dt: 0.9000, rms radial error=135.566, avgs=0 250/300: dt: 0.9000, rms radial error=134.802, avgs=0 255/300: dt: 0.9000, rms radial error=134.042, avgs=0 260/300: dt: 0.9000, rms radial error=133.287, avgs=0 265/300: dt: 0.9000, rms radial error=132.535, avgs=0 270/300: dt: 0.9000, rms radial error=131.788, avgs=0 275/300: dt: 0.9000, rms radial error=131.046, avgs=0 280/300: dt: 0.9000, rms radial error=130.307, avgs=0 285/300: dt: 0.9000, rms radial error=129.573, avgs=0 290/300: dt: 0.9000, rms radial error=128.843, avgs=0 295/300: dt: 0.9000, rms radial error=128.116, avgs=0 300/300: dt: 0.9000, rms radial error=127.394, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13204.97 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00043 epoch 2 (K=40.0), pass 1, starting sse = 2024.45 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00046 epoch 3 (K=160.0), pass 1, starting sse = 165.81 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/15 = 0.00862 epoch 4 (K=640.0), pass 1, starting sse = 10.48 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/16 = 0.00677 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0122 hours FSRUNTIME@ mris_sphere 0.0122 hours 20 threads #VMPC# mris_sphere VmPeak 2976468 mris_sphere done @#@FSTIME 2024:12:29:11:57:28 mris_sphere N 9 e 43.80 S 6.19 U 523.77 P 1209% M 183596 F 17 R 2730578 W 0 c 11449 w 14346 I 0 O 8096 L 6.45 2.69 2.78 @#@FSLOADPOST 2024:12:29:11:58:12 mris_sphere N 9 11.20 4.29 3.31 #-------------------------------------------- #@# QSphere rh Sun 29 Dec 2024 11:58:12 AM GMT /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/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: 20 scaling brain by 0.317... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.58 (0.00-->7.85) (max @ vno 78458 --> 78459) face area 0.03 +- 0.03 (-0.33-->0.65) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.196, avgs=0 005/300: dt: 0.9000, rms radial error=175.939, avgs=0 010/300: dt: 0.9000, rms radial error=175.388, avgs=0 015/300: dt: 0.9000, rms radial error=174.663, avgs=0 020/300: dt: 0.9000, rms radial error=173.838, avgs=0 025/300: dt: 0.9000, rms radial error=172.953, avgs=0 030/300: dt: 0.9000, rms radial error=172.035, avgs=0 035/300: dt: 0.9000, rms radial error=171.100, avgs=0 040/300: dt: 0.9000, rms radial error=170.155, avgs=0 045/300: dt: 0.9000, rms radial error=169.207, avgs=0 050/300: dt: 0.9000, rms radial error=168.258, avgs=0 055/300: dt: 0.9000, rms radial error=167.313, avgs=0 060/300: dt: 0.9000, rms radial error=166.379, avgs=0 065/300: dt: 0.9000, rms radial error=165.449, avgs=0 070/300: dt: 0.9000, rms radial error=164.523, avgs=0 075/300: dt: 0.9000, rms radial error=163.602, avgs=0 080/300: dt: 0.9000, rms radial error=162.686, avgs=0 085/300: dt: 0.9000, rms radial error=161.775, avgs=0 090/300: dt: 0.9000, rms radial error=160.869, avgs=0 095/300: dt: 0.9000, rms radial error=159.967, avgs=0 100/300: dt: 0.9000, rms radial error=159.071, avgs=0 105/300: dt: 0.9000, rms radial error=158.179, avgs=0 110/300: dt: 0.9000, rms radial error=157.292, avgs=0 115/300: dt: 0.9000, rms radial error=156.410, avgs=0 120/300: dt: 0.9000, rms radial error=155.533, avgs=0 125/300: dt: 0.9000, rms radial error=154.661, avgs=0 130/300: dt: 0.9000, rms radial error=153.793, avgs=0 135/300: dt: 0.9000, rms radial error=152.930, avgs=0 140/300: dt: 0.9000, rms radial error=152.072, avgs=0 145/300: dt: 0.9000, rms radial error=151.218, avgs=0 150/300: dt: 0.9000, rms radial error=150.369, avgs=0 155/300: dt: 0.9000, rms radial error=149.525, avgs=0 160/300: dt: 0.9000, rms radial error=148.686, avgs=0 165/300: dt: 0.9000, rms radial error=147.851, avgs=0 170/300: dt: 0.9000, rms radial error=147.021, avgs=0 175/300: dt: 0.9000, rms radial error=146.195, avgs=0 180/300: dt: 0.9000, rms radial error=145.374, avgs=0 185/300: dt: 0.9000, rms radial error=144.557, avgs=0 190/300: dt: 0.9000, rms radial error=143.745, avgs=0 195/300: dt: 0.9000, rms radial error=142.937, avgs=0 200/300: dt: 0.9000, rms radial error=142.134, avgs=0 205/300: dt: 0.9000, rms radial error=141.336, avgs=0 210/300: dt: 0.9000, rms radial error=140.541, avgs=0 215/300: dt: 0.9000, rms radial error=139.752, avgs=0 220/300: dt: 0.9000, rms radial error=138.966, avgs=0 225/300: dt: 0.9000, rms radial error=138.185, avgs=0 230/300: dt: 0.9000, rms radial error=137.409, avgs=0 235/300: dt: 0.9000, rms radial error=136.636, avgs=0 240/300: dt: 0.9000, rms radial error=135.868, avgs=0 245/300: dt: 0.9000, rms radial error=135.104, avgs=0 250/300: dt: 0.9000, rms radial error=134.345, avgs=0 255/300: dt: 0.9000, rms radial error=133.590, avgs=0 260/300: dt: 0.9000, rms radial error=132.839, avgs=0 265/300: dt: 0.9000, rms radial error=132.092, avgs=0 270/300: dt: 0.9000, rms radial error=131.349, avgs=0 275/300: dt: 0.9000, rms radial error=130.611, avgs=0 280/300: dt: 0.9000, rms radial error=129.876, avgs=0 285/300: dt: 0.9000, rms radial error=129.146, avgs=0 290/300: dt: 0.9000, rms radial error=128.420, avgs=0 295/300: dt: 0.9000, rms radial error=127.698, avgs=0 300/300: dt: 0.9000, rms radial error=126.980, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15215.94 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00034 epoch 2 (K=40.0), pass 1, starting sse = 2497.18 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00056 epoch 3 (K=160.0), pass 1, starting sse = 289.37 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/13 = 0.00325 epoch 4 (K=640.0), pass 1, starting sse = 46.73 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/16 = 0.00636 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0136 hours FSRUNTIME@ mris_sphere 0.0136 hours 20 threads #VMPC# mris_sphere VmPeak 3015176 mris_sphere done @#@FSTIME 2024:12:29:11:58:12 mris_sphere N 9 e 49.02 S 6.91 U 562.80 P 1162% M 208468 F 22 R 3040988 W 0 c 12567 w 14834 I 0 O 9200 L 11.20 4.29 3.31 @#@FSLOADPOST 2024:12:29:11:59:01 mris_sphere N 9 11.88 5.39 3.73 #@# Fix Topology lh Sun 29 Dec 2024 11:59:01 AM GMT mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 -threads 1 sub-31 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 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=-72 (nv=115004, nf=230152, ne=345228, g=37) 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 6 iterations marking ambiguous vertices... 5353 ambiguous faces found in tessellation segmenting defects... 34 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 9 into 8 -merging segment 29 into 26 31 defects to be corrected 0 vertices coincident reading input surface /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.8115 (-4.9057) -vertex loglikelihood: -7.2065 (-3.6032) -normal dot loglikelihood: -3.4703 (-3.4703) -quad curv loglikelihood: -5.8237 (-2.9118) Total Loglikelihood : -26.3120 CORRECTING DEFECT 0 (vertices=1178, convex hull=375, v0=0) After retessellation of defect 0 (v0=0), euler #=-26 (111939,334891,222926) : difference with theory (-28) = -2 CORRECTING DEFECT 1 (vertices=51, convex hull=89, v0=604) After retessellation of defect 1 (v0=604), euler #=-25 (111960,334993,223008) : difference with theory (-27) = -2 CORRECTING DEFECT 2 (vertices=21, convex hull=59, v0=5299) After retessellation of defect 2 (v0=5299), euler #=-24 (111969,335040,223047) : difference with theory (-26) = -2 CORRECTING DEFECT 3 (vertices=21, convex hull=29, v0=14521) After retessellation of defect 3 (v0=14521), euler #=-23 (111972,335059,223064) : difference with theory (-25) = -2 CORRECTING DEFECT 4 (vertices=47, convex hull=49, v0=18614) After retessellation of defect 4 (v0=18614), euler #=-22 (111986,335120,223112) : difference with theory (-24) = -2 CORRECTING DEFECT 5 (vertices=564, convex hull=534, v0=22332) After retessellation of defect 5 (v0=22332), euler #=-21 (112185,335975,223769) : difference with theory (-23) = -2 CORRECTING DEFECT 6 (vertices=171, convex hull=87, v0=45851) After retessellation of defect 6 (v0=45851), euler #=-21 (112200,336067,223846) : difference with theory (-22) = -1 CORRECTING DEFECT 7 (vertices=95, convex hull=85, v0=47073) After retessellation of defect 7 (v0=47073), euler #=-20 (112223,336178,223935) : difference with theory (-21) = -1 CORRECTING DEFECT 8 (vertices=41, convex hull=65, v0=52727) After retessellation of defect 8 (v0=52727), euler #=-19 (112245,336271,224007) : difference with theory (-20) = -1 CORRECTING DEFECT 9 (vertices=28, convex hull=30, v0=60434) After retessellation of defect 9 (v0=60434), euler #=-18 (112248,336293,224027) : difference with theory (-19) = -1 CORRECTING DEFECT 10 (vertices=38, convex hull=63, v0=63168) After retessellation of defect 10 (v0=63168), euler #=-17 (112257,336348,224074) : difference with theory (-18) = -1 CORRECTING DEFECT 11 (vertices=10, convex hull=27, v0=64074) After retessellation of defect 11 (v0=64074), euler #=-16 (112258,336359,224085) : difference with theory (-17) = -1 CORRECTING DEFECT 12 (vertices=27, convex hull=24, v0=64354) After retessellation of defect 12 (v0=64354), euler #=-15 (112263,336382,224104) : difference with theory (-16) = -1 CORRECTING DEFECT 13 (vertices=19, convex hull=35, v0=65340) After retessellation of defect 13 (v0=65340), euler #=-14 (112271,336415,224130) : difference with theory (-15) = -1 CORRECTING DEFECT 14 (vertices=102, convex hull=109, v0=68576) After retessellation of defect 14 (v0=68576), euler #=-15 (112302,336568,224251) : difference with theory (-14) = 1 CORRECTING DEFECT 15 (vertices=22, convex hull=29, v0=71764) After retessellation of defect 15 (v0=71764), euler #=-14 (112305,336587,224268) : difference with theory (-13) = 1 CORRECTING DEFECT 16 (vertices=28, convex hull=65, v0=74529) After retessellation of defect 16 (v0=74529), euler #=-13 (112321,336662,224328) : difference with theory (-12) = 1 CORRECTING DEFECT 17 (vertices=63, convex hull=108, v0=76490) After retessellation of defect 17 (v0=76490), euler #=-12 (112330,336733,224391) : difference with theory (-11) = 1 CORRECTING DEFECT 18 (vertices=110, convex hull=93, v0=78169) After retessellation of defect 18 (v0=78169), euler #=-11 (112349,336829,224469) : difference with theory (-10) = 1 CORRECTING DEFECT 19 (vertices=34, convex hull=28, v0=78401) After retessellation of defect 19 (v0=78401), euler #=-10 (112354,336854,224490) : difference with theory (-9) = 1 CORRECTING DEFECT 20 (vertices=22, convex hull=48, v0=79195) After retessellation of defect 20 (v0=79195), euler #=-9 (112358,336881,224514) : difference with theory (-8) = 1 CORRECTING DEFECT 21 (vertices=32, convex hull=41, v0=80545) After retessellation of defect 21 (v0=80545), euler #=-8 (112364,336913,224541) : difference with theory (-7) = 1 CORRECTING DEFECT 22 (vertices=17, convex hull=44, v0=80717) After retessellation of defect 22 (v0=80717), euler #=-7 (112372,336953,224574) : difference with theory (-6) = 1 CORRECTING DEFECT 23 (vertices=24, convex hull=37, v0=84203) After retessellation of defect 23 (v0=84203), euler #=-6 (112372,336967,224589) : difference with theory (-5) = 1 CORRECTING DEFECT 24 (vertices=45, convex hull=97, v0=88483) After retessellation of defect 24 (v0=88483), euler #=-4 (112390,337065,224671) : difference with theory (-4) = 0 CORRECTING DEFECT 25 (vertices=31, convex hull=30, v0=88972) After retessellation of defect 25 (v0=88972), euler #=-3 (112396,337092,224693) : difference with theory (-3) = 0 CORRECTING DEFECT 26 (vertices=9, convex hull=18, v0=89498) After retessellation of defect 26 (v0=89498), euler #=-2 (112396,337097,224699) : difference with theory (-2) = 0 CORRECTING DEFECT 27 (vertices=99, convex hull=33, v0=103836) After retessellation of defect 27 (v0=103836), euler #=-1 (112408,337146,224737) : difference with theory (-1) = 0 CORRECTING DEFECT 28 (vertices=179, convex hull=80, v0=107363) After retessellation of defect 28 (v0=107363), euler #=0 (112432,337254,224822) : difference with theory (0) = 0 CORRECTING DEFECT 29 (vertices=47, convex hull=65, v0=108345) After retessellation of defect 29 (v0=108345), euler #=1 (112450,337335,224886) : difference with theory (1) = 0 CORRECTING DEFECT 30 (vertices=14, convex hull=26, v0=110973) After retessellation of defect 30 (v0=110973), euler #=2 (112451,337347,224898) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.20 (0.09-->12.81) (max @ vno 1895 --> 1934) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.20 (0.09-->12.81) (max @ vno 1895 --> 1934) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 90 mutations (32.5%), 187 crossovers (67.5%), 149 vertices were eliminated building final representation... 2553 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=112451, nf=224898, ne=337347, g=0) writing corrected surface to /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 114 intersecting 001: 11 intersecting 002: 3 intersecting terminating search with 0 intersecting topology fixing took 1.6 minutes FSRUNTIME@ mris_fix_topology lh 0.0265 hours 1 threads #VMPC# mris_fix_topology VmPeak 920884 @#@FSTIME 2024:12:29:11:59:01 mris_fix_topology N 20 e 95.45 S 0.33 U 95.10 P 99% M 903256 F 0 R 257655 W 0 c 290 w 2 I 0 O 10624 L 11.88 5.39 3.73 @#@FSLOADPOST 2024:12:29:12:00:36 mris_fix_topology N 20 3.25 4.20 3.46 #@# Fix Topology rh Sun 29 Dec 2024 12:00:36 PM GMT mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 -threads 1 sub-31 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 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=-98 (nv=130690, nf=261576, ne=392364, g=50) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 32063 ambiguous faces found in tessellation segmenting defects... 31 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 10 -merging segment 15 into 17 -merging segment 28 into 25 28 defects to be corrected 0 vertices coincident reading input surface /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.8718 (-4.9359) -vertex loglikelihood: -7.1758 (-3.5879) -normal dot loglikelihood: -3.4677 (-3.4677) -quad curv loglikelihood: -5.7018 (-2.8509) Total Loglikelihood : -26.2171 CORRECTING DEFECT 0 (vertices=624, convex hull=260, v0=323) After retessellation of defect 0 (v0=323), euler #=-24 (113774,339501,225703) : difference with theory (-25) = -1 CORRECTING DEFECT 1 (vertices=249, convex hull=151, v0=1109) After retessellation of defect 1 (v0=1109), euler #=-23 (113825,339725,225877) : difference with theory (-24) = -1 CORRECTING DEFECT 2 (vertices=14313, convex hull=1752, v0=4423) *** stack smashing detected ***: terminated Command terminated by signal 6 @#@FSTIME 2024:12:29:12:00:36 mris_fix_topology N 20 e 1163.34 S 0.43 U 1162.87 P 99% M 1187552 F 0 R 358352 W 0 c 4399 w 2 I 0 O 3072 L 3.25 4.20 3.46 @#@FSLOADPOST 2024:12:29:12:20:00 mris_fix_topology N 20 1.00 1.05 1.67 Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7 13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-31 exited with ERRORS at Sun 29 Dec 2024 12:20:00 PM GMT To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting