Fri Aug 15 20:39:54 UTC 2025 cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR /usr/local/freesurfer/8.1.0/bin/recon-all -i /mnt/hpcdata/TANDEM/FSL_SIENAX/sub-9203_ses-01/struct_bias_head.nii.gz -all -hires -expert /mnt/hpcdata/TANDEM/FS_DIR/expert.opts -subjid sub-9203_ses-01 subjid sub-9203_ses-01 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR FREESURFER_HOME /usr/local/freesurfer/8.1.0 Actual FREESURFER_HOME /usr/local/freesurfer/8.1.0 build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 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 32985088 kbytes maxproc 1030330 maxlocks unlimited maxsignal 1030330 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 1.4Gi 13Gi 8.0Mi 236Gi 248Gi Swap: 8.0Gi 47Mi 8.0Gi ######################################## program versions used 8.1.0 (freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed) 8.1.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 8.1.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 8.1.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:54-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 mris_convert -all-info ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 8.1.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.1.0 TimeStamp: 2025/08/15-20:39:55-GMT BuildTime: Jul 19 2025 00:24:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed User: wsu Machine: bcmhari-hpc11 Platform: Linux PlatformVersion: 5.15.0-105-generic CompilerName: GCC CompilerVersion: 8.4.0 ####################################### GCADIR /usr/local/freesurfer/8.1.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/8.1.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 mri_convert /mnt/hpcdata/TANDEM/FSL_SIENAX/sub-9203_ses-01/struct_bias_head.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig/001.mgz mri_convert /mnt/hpcdata/TANDEM/FSL_SIENAX/sub-9203_ses-01/struct_bias_head.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=1) reading from /mnt/hpcdata/TANDEM/FSL_SIENAX/sub-9203_ses-01/struct_bias_head.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.994439, -0.0644242, -0.0833162) j_ras = (-0.0646489, 0.997908, -4.04058e-11) k_ras = (-0.0831419, -0.00538631, 0.996523) writing to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig/001.mgz... @#@FSTIME 2025:08:15:20:39:55 mri_convert N 2 e 3.35 S 0.06 U 3.23 P 98% M 73028 F 0 R 16855 W 0 c 10 w 573 I 0 O 34208 L 0.00 0.00 0.13 @#@FSLOADPOST 2025:08:15:20:39:58 mri_convert N 2 0.08 0.02 0.13 #-------------------------------------------- #@# MotionCor Fri Aug 15 20:39:59 UTC 2025 Found 1 runs /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig/001.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz mri_info /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 256 x 256 x 256 voxel sizes: 0.800000, 0.800000, 0.800000 type: FLOAT (3) fov: 204.800 dof: 1 xstart: -102.4, xend: 102.4 ystart: -102.4, yend: 102.4 zstart: -102.4, zend: 102.4 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 = -0.9944, y_r = -0.0646, z_r = -0.0831, c_r = -15.1054 : x_a = -0.0644, y_a = 0.9979, z_a = -0.0054, c_a = 6.2787 : x_s = -0.0833, y_s = -0.0000, z_s = 0.9965, c_s = 14.8583 talairach xfm : Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -0.7956 -0.0517 -0.0665 101.8589 -0.0515 0.7983 -0.0043 -88.7584 -0.0667 -0.0000 0.7972 -78.6541 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.512 ras to voxel transform: -1.2430 -0.0805 -0.1041 111.2763 -0.0808 1.2474 -0.0000 118.9473 -0.1039 -0.0067 1.2457 107.9642 -0.0000 -0.0000 -0.0000 1.0000 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 mri_convert /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --conform_min mri_convert /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --conform_min reading from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.994439, -0.0644242, -0.0833162) j_ras = (-0.0646489, 0.997908, -4.04058e-11) k_ras = (-0.0831419, -0.00538631, 0.996523) volume geometry: valid : 2090804288 extent : (256, 256, 256) voxel : ( 0.8000, 0.8000, 0.8000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : (-15.1054, 6.2787, 14.8583) shears : ( 0.0000, 0.0000, 0.0000) file : /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 271852 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz... @#@FSTIME 2025:08:15:20:40:03 mri_convert N 3 e 7.68 S 0.05 U 7.58 P 99% M 89560 F 0 R 29278 W 0 c 25 w 381 I 0 O 11944 L 0.07 0.02 0.13 @#@FSLOADPOST 2025:08:15:20:40:11 mri_convert N 3 0.22 0.05 0.14 mri_add_xform_to_header -c /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/talairach.xfm /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2025:08:15:20:40:11 mri_add_xform_to_header N 4 e 0.69 S 0.01 U 0.64 P 94% M 23256 F 0 R 4552 W 0 c 8 w 361 I 0 O 11944 L 0.22 0.05 0.14 @#@FSLOADPOST 2025:08:15:20:40:11 mri_add_xform_to_header N 4 0.22 0.05 0.14 mri_info /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz orig.mgz ======================================== Volume information for /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz type: MGH intent: MRI (0) dimensions: 256 x 256 x 256 voxel sizes: 0.800000, 0.800000, 0.800000 type: UCHAR (0) fov: 204.800 dof: 1 xstart: -102.4, xend: 102.4 ystart: -102.4, yend: 102.4 zstart: -102.4, zend: 102.4 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 = -15.1054 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 6.2787 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 14.8583 talairach xfm : /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -0.8000 0.0000 0.0000 87.2946 0.0000 0.0000 0.8000 -96.1213 0.0000 -0.8000 0.0000 117.2583 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.512 ras to voxel transform: -1.2500 0.0000 -0.0000 109.1182 -0.0000 0.0000 -1.2500 146.5728 0.0000 1.2500 -0.0000 120.1516 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz --trg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --outlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg2orig.lta --subject sub-9203_ses-01 8.1.0 --inlta: identity.nofile input LTA transform. --src: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg.mgz src image (geometry). --trg: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz trg image (geometry). --outlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg2orig.lta output LTA. --s: sub-9203_ses-01 subject name LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; setting subject to sub-9203_ses-01 Writing LTA to file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/rawavg2orig.lta... lta_convert successful. @#@FSTIME 2025:08:15:20:40:12 lta_convert N 10 e 0.36 S 0.00 U 0.35 P 98% M 6104 F 0 R 238 W 0 c 6 w 7 I 0 O 8 L 0.22 0.05 0.14 @#@FSLOADPOST 2025:08:15:20:40:12 lta_convert N 10 0.22 0.05 0.14 mri_synthstrip --threads 1 -i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz -o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthstrip.mgz If you use SynthStrip in your analysis, please cite: ---------------------------------------------------- SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://doi.org/10.1016/j.neuroimage.2022.119474 Website: https://synthstrip.io @#@FSTIME 2025:08:15:20:40:12 mri_synthstrip N 6 e 40.38 S 9.12 U 31.21 P 99% M 4550952 F 30 R 4728214 W 0 c 171 w 282 I 0 O 5504 L 0.22 0.05 0.14 @#@FSLOADPOST 2025:08:15:20:40:52 mri_synthstrip N 6 0.60 0.17 0.18 mri_synthseg --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthseg.rca.mgz --threads 1 --vol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/stats/synthseg.vol.csv --keepgeom --addctab --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread addctab True predicting 1/1 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 503s 503s/step Reslicing to have same geom as the input [0.80000001 0.80000001 0.80000001] segmentation saved in: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthseg.rca.mgz volumes saved in: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/stats/synthseg.vol.csv #@# mri_synthseg vmpeak 14673968 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 2025:08:15:20:40:52 mri_synthseg N 11 e 526.80 S 30.19 U 496.78 P 100% M 9606104 F 0 R 18834690 W 0 c 1989 w 1430 I 0 O 2912 L 0.60 0.17 0.18 @#@FSLOADPOST 2025:08:15:20:49:39 mri_synthseg N 11 1.00 0.87 0.56 Fri Aug 15 20:49:39 UTC 2025 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthstrip.mgz --t /usr/local/freesurfer/8.1.0/average/mni305.cor.stripped.mgz --affine-only --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305 --threads 1 -rwxr-xr-x 1 root root 30890 Jul 19 00:36 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3082160 Fri Aug 15 20:49:40 UTC 2025 mri_synthmorph -m affine -t /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/aff.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthstrip.mgz /usr/local/freesurfer/8.1.0/average/mni305.cor.stripped.mgz -j 1 #@# mri_synthmorph: affine, threads: 1, VmPeak: 6679928 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 2025:08:15:20:49:40 mri_synthmorph N 8 e 79.05 S 18.01 U 61.01 P 99% M 5453104 F 0 R 10579049 W 0 c 323 w 164 I 0 O 432 L 1.00 0.87 0.56 @#@FSLOADPOST 2025:08:15:20:50:59 mri_synthmorph N 8 1.00 0.91 0.60 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 lta_convert --invert --inlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/aff.lta --outlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta 8.1.0 --invert: will invert transform. --inlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/aff.lta input LTA transform. --outlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta output LTA. LTA read, type : 1 1.07033 0.05644 0.07166 2.70296; -0.07378 0.97625 0.28745 -30.15022; -0.09293 -0.19973 1.08932 -8.61784; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta... lta_convert successful. @#@FSTIME 2025:08:15:20:50:59 lta_convert N 5 e 0.01 S 0.00 U 0.00 P 50% M 5492 F 0 R 208 W 0 c 1 w 5 I 0 O 8 L 1.00 0.91 0.60 @#@FSLOADPOST 2025:08:15:20:50:59 lta_convert N 5 1.00 0.91 0.60 To check affine registration tkregisterfv --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthstrip.mgz --targ /usr/local/freesurfer/8.1.0/average/mni305.cor.stripped.mgz --reg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.mni305/aff.lta AffineOnly specified, so exiting now Started at Fri Aug 15 20:49:39 UTC 2025 Ended at Fri Aug 15 20:50:59 UTC 2025 Fs-Synthmorph-Reg-Run-Time-Sec 80 Fs-Synthmorph-Reg-Run-Time-Min 1.33 Fs-Synthmorph-Reg-Run-Time-Hours 0.02 fs-synthmorph-reg Done @#@FSTIME 2025:08:15:20:49:39 fs-synthmorph-reg N 9 e 79.40 S 18.20 U 61.14 P 99% M 5453104 F 0 R 10596988 W 0 c 334 w 575 I 0 O 696 L 1.00 0.87 0.56 @#@FSLOADPOST 2025:08:15:20:50:59 fs-synthmorph-reg N 9 1.00 0.91 0.60 8.1.0 --ltavox2vox: output LTA as VOX_TO_VOX transform. --inlta: synthmorph.mni305/aff.lta input LTA transform. --outlta: talairach.xfm.lta output LTA. LTA read, type : 1 1.07033 0.05644 0.07166 2.70296; -0.07378 0.97625 0.28745 -30.15022; -0.09293 -0.19973 1.08932 -8.61784; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file talairach.xfm.lta... lta_convert successful. 8.1.0 --inlta: talairach.xfm.lta input LTA transform. --outmni: talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.07033 0.05644 0.07166 2.70297; -0.07378 0.97625 0.28745 -30.15024; -0.09293 -0.19973 1.08932 -8.61784; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. fs-synthmorph-reg --s sub-9203_ses-01 --threads 1 --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --test Fri Aug 15 20:50:59 UTC 2025 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg --s sub-9203_ses-01 --threads 1 --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --test -rwxr-xr-x 1 root root 30890 Jul 19 00:36 /usr/local/freesurfer/8.1.0/bin/fs-synthmorph-reg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3082334 mri_mask -bb 3 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz cropping npad = 3 DoAbs = 0 Computing bounding box, npad = 3, 3, 3, 3, 3, 3 4 16 0 216 235 256 maskval=0, outval=0 Writing masked volume to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done. lta_convert --inlta identity.nofile --src /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --trg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --outlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta 8.1.0 --inlta: identity.nofile input LTA transform. --src: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz src image (geometry). --trg: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz trg image (geometry). --outlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta... lta_convert successful. Fri Aug 15 20:51:00 UTC 2025 mri_synthmorph -m affine -t /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 #@# mri_synthmorph: affine, threads: 1, VmPeak: 6697256 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 2025:08:15:20:51:01 mri_synthmorph N 8 e 79.88 S 17.93 U 61.91 P 99% M 5466628 F 0 R 10443827 W 0 c 301 w 157 I 0 O 432 L 1.00 0.91 0.60 @#@FSLOADPOST 2025:08:15:20:52:20 mri_synthmorph N 8 1.00 0.93 0.64 Fri Aug 15 20:52:20 UTC 2025 mri_concatenate_lta -invert1 -invertout /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta invert the first LTA before applying it invert the output LTA Read individual LTAs Warning: dst volume of lta1 doesn't match src volume of lta2 Volume geometry for lta1-dst: volume geometry: extent : (216, 235, 256) voxel : ( 0.8000, 0.8000, 0.8000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : (-0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, -0.0000) c_(ras) : (-2.3054, 6.2787, 10.4583) shears : ( 0.0000, 0.0000, 0.0000) file : none Volume geometry for lta2-src: volume geometry: extent : (216, 235, 256) voxel : ( 0.8000, 0.8000, 0.8000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : (-2.3054, 6.2787, 10.4583) shears : ( 0.0000, 0.0000, 0.0000) file : /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Inverting output LTA Writing combined LTA to file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta... mri_concatenate_lta successful. @#@FSTIME 2025:08:15:20:52:20 mri_concatenate_lta N 5 e 0.01 S 0.00 U 0.00 P 50% M 5268 F 0 R 207 W 0 c 0 w 7 I 0 O 8 L 1.00 0.93 0.64 @#@FSLOADPOST 2025:08:15:20:52:20 mri_concatenate_lta N 5 1.00 0.93 0.64 mri_concatenate_lta -invert2 /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert the second LTA before applying it Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta... mri_concatenate_lta successful. @#@FSTIME 2025:08:15:20:52:21 mri_concatenate_lta N 4 e 0.00 S 0.00 U 0.00 P 44% M 5236 F 0 R 206 W 0 c 0 w 5 I 0 O 8 L 1.00 0.93 0.64 @#@FSLOADPOST 2025:08:15:20:52:21 mri_concatenate_lta N 4 1.00 0.93 0.64 lta_convert --invert --inlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --outlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta 8.1.0 --invert: will invert transform. --inlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta input LTA transform. --outlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta output LTA. LTA read, type : 1 0.88047 -0.05804 -0.05057 -4.32201; 0.02661 0.93993 -0.19215 25.46313; 0.08493 0.17180 0.81779 12.71384; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta... lta_convert successful. @#@FSTIME 2025:08:15:20:52:21 lta_convert N 5 e 0.00 S 0.00 U 0.00 P 55% M 5724 F 0 R 212 W 0 c 0 w 5 I 0 O 8 L 1.00 0.93 0.64 @#@FSLOADPOST 2025:08:15:20:52:21 lta_convert N 5 1.00 0.93 0.64 lta_convert --inlta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta --outmni /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm 8.1.0 --inlta: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta input LTA transform. --outmni: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm output MNI/XFM matrix. LTA read, type : 1 1.12616 0.05447 0.08243 2.43230; -0.05350 1.01751 0.23577 -29.13782; -0.10571 -0.21942 1.16472 -9.67779; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. To check affine registration tkregisterfv --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz --targ /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --reg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta mri_synthmorph -m deform -t /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz -i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 -o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz #@# mri_synthmorph: deform, threads: 1, VmPeak: 15393588 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 2025:08:15:20:52:21 mri_synthmorph N 12 e 1370.31 S 93.37 U 1276.54 P 99% M 14169496 F 0 R 80933905 W 0 c 5785 w 3047 I 0 O 119368 L 1.00 0.93 0.64 @#@FSLOADPOST 2025:08:15:21:15:11 mri_synthmorph N 12 1.00 1.00 0.95 mri_warp_convert --inras /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz --insrcgeom /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --outm3z /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz --vg-thresh 1e-5 --lta1-inv /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta --lta2 /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta 8.1.0 --inras: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz input RAS warp. --insrcgeom: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz atlas/source image (used for geometry). --outm3z: /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz output M3Z. Setting vg_isEqual_Threshold to 0.000010 Applying LTAs to the GCAM GCAMwrite(/mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [193 x 229 x 193] [INFO] Warpfield::convert(): gcam image [256 x 256 x 256] [INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193] [INFO] Warpfield::convert(): total out of range voxel count: 0 [INFO] niiWrite(): MGZ_INTENT_WARPMAP => NIFTI_INTENT_DISPVECT, intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [INFO] niiWrite(): convert displacement from 0 to 3 mri_warp_convert successful. @#@FSTIME 2025:08:15:21:15:11 mri_warp_convert N 12 e 22.52 S 2.06 U 20.21 P 98% M 3406736 F 0 R 867165 W 0 c 57 w 1891 I 0 O 92440 L 1.00 1.00 0.95 @#@FSLOADPOST 2025:08:15:21:15:34 mri_warp_convert N 12 1.00 1.00 0.95 mri_ca_register -invert-and-save /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading gcam [INFO] niiRead(): intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 Computing inverse of GCAM Filling inverse of GCAM Allocating inv_gcam...(256, 256, 256) Saving inverse to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz GCAMwrite(/mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [256 x 256 x 256] [INFO] Warpfield::convert(): gcam image [193 x 229 x 193] [INFO] Warpfield::convert(): gcam atlas [256 x 256 x 256] [INFO] Warpfield::convert(): total out of range voxel count: 0 [INFO] niiWrite(): MGZ_INTENT_WARPMAP => NIFTI_INTENT_DISPVECT, intent_code = 1006, dimensions = {5, 256, 256, 256, 1, 3, 1, 1} [INFO] niiWrite(): convert displacement from 0 to 3 @#@FSTIME 2025:08:15:21:15:34 mri_ca_register N 3 e 152.52 S 5.08 U 147.21 P 99% M 7132608 F 0 R 1900765 W 0 c 462 w 883 I 0 O 289352 L 1.00 1.00 0.95 @#@FSLOADPOST 2025:08:15:21:18:06 mri_ca_register N 3 1.18 1.04 0.98 mri_vol2vol --regheader --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz --targ /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz movvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz targvol /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1755985145 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 2025:08:15:21:18:06 mri_vol2vol N 7 e 1.69 S 0.04 U 1.52 P 92% M 49040 F 0 R 13347 W 0 c 8 w 909 I 0 O 29296 L 1.18 1.04 0.98 @#@FSLOADPOST 2025:08:15:21:18:08 mri_vol2vol N 7 1.16 1.04 0.98 mri_convert -rt nearest /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz -at /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz mri_convert -rt nearest /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz -at /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.96717e-09, 9.31323e-09) j_ras = (0, 0, -1) k_ras = (1.45519e-09, 1, 0) INFO: Reading transformation from file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... INFO: Applying transformation from file /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... Applying morph_3d ... [INFO] niiRead(): intent_code = 1006, dimensions = {5, 193, 229, 193, 1, 3, 1, 1} [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 morphing to atlas with resample type 0 writing to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz... @#@FSTIME 2025:08:15:21:18:08 mri_convert N 6 e 9.57 S 1.26 U 8.27 P 99% M 2367284 F 0 R 590440 W 0 c 35 w 249 I 0 O 7256 L 1.16 1.04 0.98 @#@FSLOADPOST 2025:08:15:21:18:18 mri_convert N 6 1.14 1.04 0.98 mri_diff --po /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz mri_diff --po /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz diffcount 4137100 Volumes differ in pixel data maxdiff 119.15151978 at 60 26 9 0 tkmeditfv -f /usr/local/freesurfer/8.1.0/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -aux /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz Started at Fri Aug 15 20:50:59 UTC 2025 Ended at Fri Aug 15 21:18:18 UTC 2025 Fs-Synthmorph-Reg-Run-Time-Sec 1639 Fs-Synthmorph-Reg-Run-Time-Min 27.32 Fs-Synthmorph-Reg-Run-Time-Hours 0.46 fs-synthmorph-reg Done @#@FSTIME 2025:08:15:20:50:59 fs-synthmorph-reg N 7 e 1639.44 S 120.27 U 1518.02 P 99% M 14169496 F 1 R 94820453 W 0 c 6693 w 8438 I 0 O 550592 L 1.00 0.91 0.60 @#@FSLOADPOST 2025:08:15:21:18:18 fs-synthmorph-reg N 7 1.14 1.04 0.98 #-------------------------------------------- #@# Nu Intensity Correction Fri Aug 15 21:18:18 UTC 2025 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 /usr/bin/bc /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri /usr/local/freesurfer/8.1.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 8.1.0 Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Fri Aug 15 21:18:18 UTC 2025 tmpdir is ./tmp.mri_nu_correct.mni.3082701 cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.3082701/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.3082701/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.3082701/ones.mgz 8.1.0 cwd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.3082701/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.3082701/ones.mgz sysname Linux hostname bcmhari-hpc11 machine x86_64 user wsu input ./tmp.mri_nu_correct.mni.3082701/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.3082701/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.3082701/ones.mgz Count: 16777216 8589935.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3082701/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3082701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3082701/input.mean.dat 8.1.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3082701/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3082701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3082701/input.mean.dat sysname Linux hostname bcmhari-hpc11 machine x86_64 user wsu whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3082701/ones.mgz Loading orig.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.3082701/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3082701/ones.mgz --i ./tmp.mri_nu_correct.mni.3082701/nu0.mgz --sum ./tmp.mri_nu_correct.mni.3082701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3082701/output.mean.dat 8.1.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3082701/ones.mgz --i ./tmp.mri_nu_correct.mni.3082701/nu0.mgz --sum ./tmp.mri_nu_correct.mni.3082701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3082701/output.mean.dat sysname Linux hostname bcmhari-hpc11 machine x86_64 user wsu whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3082701/ones.mgz Loading ./tmp.mri_nu_correct.mni.3082701/nu0.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.3082701/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.3082701/nu0.mgz ./tmp.mri_nu_correct.mni.3082701/nu0.mgz mul .93966287353578548381 Packing Done packing Unpacking Saving result to './tmp.mri_nu_correct.mni.3082701/nu0.mgz' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 217048 mri_convert ./tmp.mri_nu_correct.mni.3082701/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.3082701/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.3082701/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.96717e-09, 9.31323e-09) j_ras = (0, 0, -1) k_ras = (1.45519e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 4, i2 = 63 #mri_make_uchar# mapping 10 153 to 3 110 : b -4.73475 m 0.751239 : thresh 6.30258 maxsat 345.742 : nzero 10752130 nsat 0 Fri Aug 15 21:22:32 UTC 2025 mri_nu_correct.mni done @#@FSTIME 2025:08:15:21:18:18 mri_nu_correct.mni N 10 e 254.12 S 1.10 U 252.69 P 99% M 613896 F 1 R 516065 W 0 c 751 w 2653 I 0 O 81192 L 1.14 1.04 0.98 @#@FSLOADPOST 2025:08:15:21:22:32 mri_nu_correct.mni N 10 1.00 1.01 1.00 mri_add_xform_to_header -c /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2025:08:15:21:22:33 mri_add_xform_to_header N 4 e 0.62 S 0.02 U 0.56 P 94% M 23452 F 0 R 4556 W 0 c 7 w 325 I 0 O 10152 L 1.00 1.01 1.00 @#@FSLOADPOST 2025:08:15:21:22:33 mri_add_xform_to_header N 4 1.00 1.01 1.00 #-------------------------------------------- #@# Intensity Normalization Fri Aug 15 21:22:33 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.07033 0.05644 0.07166 2.70297; -0.07378 0.97625 0.28745 -30.15024; -0.09293 -0.19973 1.08932 -8.61784; 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 = 19 Starting OpenSpline(): npoints = 19 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 56 (56), valley at 28 (28) csf peak at 10, setting threshold to 40 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 41 (41) csf peak at 10, setting threshold to 44 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 27 seconds. @#@FSTIME 2025:08:15:21:22:33 mri_normalize N 8 e 147.33 S 0.95 U 146.33 P 99% M 583612 F 0 R 263253 W 0 c 491 w 341 I 0 O 9752 L 1.00 1.01 1.00 @#@FSLOADPOST 2025:08:15:21:25:01 mri_normalize N 8 1.04 1.03 1.00 #-------------------------------------- #@# MCADura Segmentation Fri Aug 15 21:25:01 UTC 2025 mri_mcadura_seg --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/mca-dura.mgz --threads 1 --synthmorphdir /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm Fri Aug 15 21:25:01 UTC 2025 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri /usr/local/freesurfer/8.1.0/bin/mri_mcadura_seg --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/mca-dura.mgz --threads 1 --synthmorphdir /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root root 13384 Jul 19 00:36 /usr/local/freesurfer/8.1.0/bin/mri_mcadura_seg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3082858 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_vol2vol --reg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/mcadura.prior.lh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.12616 -0.05447 -0.08243 13.51209; -0.10571 -0.21942 1.16472 -10.65303; 0.05350 -1.01751 -0.23577 0.93784; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/mcadura.prior.lh.nii.gz regfile /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1755579561 Final tkRAS-to-tkRAS Matrix is: -1.12616 -0.05447 -0.08243 13.51209; -0.10571 -0.21942 1.16472 -10.65303; 0.05350 -1.01751 -0.23577 0.93784; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.90093 -0.06595 0.04358 201.17053; 0.04280 -0.18862 0.81401 28.03389; 0.08457 -0.93177 -0.17554 216.75757; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/mcadura.prior.lh.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/lh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 12337 voxels in mask (pct= 0.07) MRIcropToFoV(): thresh=0.001 FoV = (100,100,100) nhits=12337 centroid = (159.055,152.352,182.721) min = (125,127,160) max = (184,172,203) delta = (60,46,44) Region 109 102 133 100 100 100 109 102 133 100 100 100 maskval=0, outval=0 Writing masked volume to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/lh.crop.nii.gz...done. mri_vol2vol --regheader --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --targ /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/lh.crop.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.lh.crop.nii.gz movvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz targvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/lh.crop.nii.gz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/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 1756108789 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -24.79999; 0.00000 1.00000 0.00000 43.99999; -0.00000 0.00000 1.00000 -19.19999; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 108.99998; -0.00000 1.00000 0.00000 101.99998; 0.00000 0.00000 1.00000 132.99998; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.lh.crop.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.mgz /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.lh.crop.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 Loaded input image from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.lh.crop.nii.gz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 3s 3s/step Wrote segmentation to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.mgz vmpcma: 5715340 done mri_vol2vol --regheader --interp nearest --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.mgz --targ /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.uncropped.mgz movvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.mgz targvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/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 1756123870 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 -0.00000 -0.00000 24.80000; -0.00000 1.00000 -0.00000 -44.00001; -0.00000 -0.00000 1.00000 19.20000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 -0.00000 0.00000 -109.00001; -0.00000 1.00000 0.00000 -101.99998; 0.00000 0.00000 1.00000 -133.00002; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --reg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/mcadura.prior.rh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.12616 -0.05447 -0.08243 13.51209; -0.10571 -0.21942 1.16472 -10.65303; 0.05350 -1.01751 -0.23577 0.93784; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /usr/local/freesurfer/8.1.0/average/mca-dura.prior.warp.mni152.1.0mm.rh.nii.gz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/mcadura.prior.rh.nii.gz regfile /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1756272011 Final tkRAS-to-tkRAS Matrix is: -1.12616 -0.05447 -0.08243 13.51209; -0.10571 -0.21942 1.16472 -10.65303; 0.05350 -1.01751 -0.23577 0.93784; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.90093 -0.06595 0.04358 201.17053; 0.04280 -0.18862 0.81401 28.03389; 0.08457 -0.93177 -0.17554 216.75757; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/mcadura.prior.rh.nii.gz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/rh.crop.nii.gz CropToFoVmm 80 80 80 DoAbs = 0 Found 12991 voxels in mask (pct= 0.08) MRIcropToFoV(): thresh=0.001 FoV = (100,100,100) nhits=12991 centroid = (72.4609,143.912,186.904) min = (49,114,165) max = (101,168,211) delta = (53,55,47) Region 22 94 137 100 100 100 22 94 137 100 100 100 maskval=0, outval=0 Writing masked volume to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/rh.crop.nii.gz...done. mri_vol2vol --regheader --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --targ /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/rh.crop.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.nii.gz movvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz targvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/rh.crop.nii.gz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/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 1755804561 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 44.80001; 0.00000 1.00000 0.00000 47.19999; -0.00000 0.00000 1.00000 -12.80000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 22.00000; -0.00000 1.00000 0.00000 94.00000; 0.00000 0.00000 1.00000 136.99998; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.nii.gz --left-right-reverse-pix /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.lrrev.nii.gz mri_convert /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.nii.gz --left-right-reverse-pix /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.lrrev.nii.gz reading from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/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, 7.96717e-09, 9.31323e-09) j_ras = (0, 0, -1) k_ras = (1.45519e-09, 1, 0) writing to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.lrrev.nii.gz... mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.lrrev.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.lrrev.mgz /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.lrrev.nii.gz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.lrrev.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 Loaded input image from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/invol.rh.crop.lrrev.nii.gz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 3s 3s/step Wrote segmentation to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.lrrev.mgz vmpcma: 5715220 done mri_convert /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.lrrev.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.mgz --left-right-swap-label-table /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.index /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.rh.index --left-right-reverse-pix mri_convert /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.lrrev.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.mgz --left-right-swap-label-table /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.lh.index /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/dumca.rh.index --left-right-reverse-pix reading from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.lrrev.mgz... Performing left-right swap of labels MRIlrswapSeg(): nswaps 1511 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, 7.96717e-09, 9.31323e-09) j_ras = (-9.31323e-09, 3.71e-17, -1) k_ras = (7.96717e-09, 1, -3.71e-17) writing to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.mgz... mri_vol2vol --regheader --interp nearest --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.mgz --targ /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.uncropped.mgz movvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.mgz targvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/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 1755436292 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 -0.00000 -0.00000 -44.80000; -0.00000 1.00000 -0.00000 -47.20000; -0.00000 -0.00000 1.00000 12.80000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 -0.00000 0.00000 -22.00000; -0.00000 1.00000 0.00000 -94.00000; 0.00000 0.00000 1.00000 -137.00002; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_concat /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.lh.uncropped.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.mri_mcadura_seg.3082858/seg.rh.uncropped.mgz --sum --ctab /usr/local/freesurfer/8.1.0/models/mca-dura.ctab --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/mca-dura.mgz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing sum across frames Writing to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/mca-dura.mgz fsvglrun freeview -neuro-view --hide-3d-slices --view coronal /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/mca-dura.mgz:isosurface=1:outline=1 Started at Fri Aug 15 21:25:01 UTC 2025 Ended at Fri Aug 15 21:25:33 UTC 2025 mri_mcadura_seg-Run-Time-Sec 32 mri_mcadura_seg Done #-------------------------------------- #@# VSinus Segmentation Fri Aug 15 21:25:33 UTC 2025 mri_vsinus_seg --s sub-9203_ses-01 --rca-synthseg --threads 1 --synthmorphdir /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm Fri Aug 15 21:25:33 UTC 2025 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri /usr/local/freesurfer/8.1.0/bin/mri_vsinus_seg --s sub-9203_ses-01 --rca-synthseg --threads 1 --synthmorphdir /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root root 20960 Jul 19 00:36 /usr/local/freesurfer/8.1.0/bin/mri_vsinus_seg freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 3083139 mri_vol2vol --mov /usr/local/freesurfer/8.1.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz --lta /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --targ /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mgz Matrix from LTA: -1.12616 -0.05447 -0.08243 13.51208; -0.10571 -0.21942 1.16472 -10.65302; 0.05350 -1.01751 -0.23577 0.93784; 0.00000 0.00000 0.00000 1.00000; /usr/local/freesurfer/8.1.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz movvol /usr/local/freesurfer/8.1.0/average/vsinus.no-sp.prior.mni152.1.0mm.mgz targvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mgz regfile /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1756271794 Final tkRAS-to-tkRAS Matrix is: -1.12616 -0.05447 -0.08243 13.51208; -0.10571 -0.21942 1.16472 -10.65300; 0.05350 -1.01751 -0.23577 0.93784; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.90093 -0.06595 0.04358 201.17053; 0.04280 -0.18862 0.81401 28.03392; 0.08457 -0.93177 -0.17554 216.75760; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop 0 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz threshold mask volume at 0.001 cropping npad = 0 DoAbs = 0 Found 167768 voxels in mask (pct= 1.00) Computing bounding box, npad = 0, 0, 0, 0, 0, 0 32 34 19 152 158 107 maskval=0, outval=0 Writing masked volume to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz...done. mri_binarize --crop-around-ras /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz nolta cras /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz 0 144 144 144 Getting cras from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/native.avg12567.prior.mincrop.mgz final ras2vox matrix -1.25000 0.00000 -0.00000 109.11823; -0.00000 0.00000 -1.25000 146.57281; 0.00000 1.25000 -0.00000 120.15155; -0.00000 -0.00000 -0.00000 1.00000; -------------------------- ostr LIA (144 144 144) (144 144 144) rasCenter 0.894592 -38.1213 26.8583 crsCenter 108 113 72.5 MRIcropAroundCRS() vol size 256 256 256 center 108 113 72.5 fov 144 144 144 limits 37 180 42 185 1 144 using MRIextractRegion() mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.no-sp.ctab --keep_ac --conform --percentile 99.9 --vmp --output-base vsinus --logfile mri_vsinus_seg.log --fov 144 --threads 1 --no-cite-sclimbic --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 --ctab /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.no-sp.ctab --keep_ac --conform --percentile 99.9 --vmp --output-base vsinus --logfile mri_vsinus_seg.log --fov 144 --threads 1 --no-cite-sclimbic --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.no-sp.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 6 inshape (144, 144, 144) features 24 (None, 144, 144, 144, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/vsinus.no-sp.m.all.nstd10-070.h5 Segmenting image 1/1 Loaded input image from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/invol.crop-to-prior.norev.mgz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 23s 23s/step Wrote segmentation to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz vmpcma: 7460680 done mri_binarize --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthseg.rca.mgz --match 3 42 --inv --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/ctxsegmask.mgz 8.1.0 cwd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri cmdline mri_binarize --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthseg.rca.mgz --match 3 42 --inv --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/ctxsegmask.mgz sysname Linux hostname bcmhari-hpc11 machine x86_64 user wsu input /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthseg.rca.mgz frame 0 nErode3d 0 nErode2d 0 output /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/ctxsegmask.mgz Binarizing based on matching values nMatch 2 0 3 1 42 binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 936416 values in range Counting number of voxels in first frame Found 936416 voxels in final mask Writing output to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/ctxsegmask.mgz Count: 936416 479445.014772 16777216 5.581474 mri_binarize done mri_vol2vol --mov /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz --targ /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --interp nearest --o /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz --regheader movvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/vsinus.crop-to-prior.norev.mgz targvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz outvol /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1755338525 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -15.20000; 0.00000 1.00000 0.00000 44.00000; -0.00000 0.00000 1.00000 -11.20000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -36.99999; -0.00000 1.00000 0.00000 -41.99999; 0.00000 0.00000 1.00000 -0.99999; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/tmp.vsinus/ctxsegmask.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz...done. mri_segstats --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --seg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz --sum /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/stats/vsinus.stats --subject sub-9203_ses-01 --etiv 8.1.0 cwd cmdline mri_segstats --i /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz --seg /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz --sum /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/stats/vsinus.stats --subject sub-9203_ses-01 --etiv sysname Linux hostname bcmhari-hpc11 machine x86_64 user wsu whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1609647 mm^3 (det: 1.210268 ) Loading /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz Using embedded color table (and excluding seg 0) Loading /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 6 segmentations Computing statistics for each segmentation Reporting on 5 segmentations Using PrintSegStat mri_segstats done fsvglrun freeview --hide-3d-slices --view coronal -neuro-view /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz:lock=1 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz:isosurface=1:outline=1 Started at Fri Aug 15 21:25:33 UTC 2025 Ended at Fri Aug 15 21:26:22 UTC 2025 Mri_Vsinus_Seg-Run-Time-Sec 49 Mri_Vsinus_Seg-Run-Time-Min 0.82 Mri_Vsinus_Seg-Run-Time-Hours 0.01 mri_vsinus_seg Done mri_mask /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/T1.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/synthstrip.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/brainmask.mgz DoAbs = 0 maskval=0, outval=0 Writing masked volume to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/brainmask.mgz...done. #------------------------------------- #@# EM Registration Fri Aug 15 21:26:23 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/8.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/8.1.0/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (32, 44, 21) --> (193, 217, 240) finding center of left hemi white matter using (86, 102, 131) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (66,81,104) --> (105, 123,158) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 4.9 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.688 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.022116 @ (31.579, 10.526, 10.526) max log p = -3.874262 @ (5.263, 5.263, -5.263) max log p = -3.774228 @ (-2.632, 2.632, -2.632) max log p = -3.737427 @ (-1.316, 3.947, 1.316) max log p = -3.732623 @ (0.658, -1.974, 1.974) max log p = -3.697188 @ (0.987, 2.303, -0.329) max log p = -3.697188 @ (0.000, 0.000, 0.000) max log p = -3.697188 @ (0.000, 0.000, 0.000) Found translation: (34.5, 22.7, 5.6): log p = -3.697 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.527, old_max_log_p =-3.697 (thresh=-3.7) 0.85264 0.11129 0.01465 13.52123; -0.11225 0.84535 0.11129 9.60368; 0.00000 -0.10442 0.79316 18.78706; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 19 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.483, old_max_log_p =-3.527 (thresh=-3.5) 0.85264 0.11129 0.01465 13.52123; -0.12909 0.97215 0.12799 -6.59198; 0.00000 -0.10442 0.79316 18.78706; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 19 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.483, old_max_log_p =-3.483 (thresh=-3.5) 0.85264 0.11129 0.01465 13.52123; -0.12909 0.97215 0.12799 -6.59198; 0.00000 -0.10442 0.79316 18.78706; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 19 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.297, old_max_log_p =-3.483 (thresh=-3.5) 0.87291 0.05502 -0.04637 25.65655; -0.06734 0.91998 0.14274 -6.98434; 0.05700 -0.12635 0.77257 17.39225; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 19 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.293, old_max_log_p =-3.297 (thresh=-3.3) 0.87291 0.05502 -0.04637 25.65655; -0.06347 0.90974 0.19296 -12.14563; 0.06243 -0.18974 0.77586 26.19147; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 19 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.293, old_max_log_p =-3.293 (thresh=-3.3) 0.87291 0.05502 -0.04637 25.65655; -0.06347 0.90974 0.19296 -12.14563; 0.06243 -0.18974 0.77586 26.19147; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.280, old_max_log_p =-3.293 (thresh=-3.3) 0.87019 0.07129 -0.04971 24.78312; -0.07865 0.91060 0.18090 -8.63493; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.280, old_max_log_p =-3.280 (thresh=-3.3) 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 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 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.280 (old=-4.688) transform before final EM align: 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 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 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 777232 FSRUNTIME@ mri_em_register 0.1909 hours 1 threads registration took 11 minutes and 27 seconds. @#@FSTIME 2025:08:15:21:26:23 mri_em_register N 7 e 687.38 S 1.76 U 685.57 P 99% M 616300 F 0 R 364279 W 0 c 2210 w 32 I 0 O 32 L 1.05 1.03 1.00 @#@FSLOADPOST 2025:08:15:21:37:51 mri_em_register N 7 1.00 1.00 1.00 #-------------------------------------- #@# CA Normalize Fri Aug 15 21:37:51 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/8.1.0/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/8.1.0/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (32, 44, 21) --> (193, 216, 240) finding center of left hemi white matter using (86, 101, 131) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (66,80,104) --> (105, 122,158) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 4.2 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246437 sample points... INFO: compute sample coordinates transform 0.87019 0.07129 -0.04971 24.78312; -0.07856 0.90954 0.18069 -8.48702; 0.06838 -0.17393 0.77669 23.89513; 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 (105, 55, 26) --> (189, 180, 234) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 2 of 7253 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (38, 54, 27) --> (120, 173, 237) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 6956 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (109, 149, 61) --> (164, 203, 129) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 246 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (56, 148, 60) --> (109, 194, 132) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 186 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (91, 137, 107) --> (132, 213, 145) Brain_Stem: limiting intensities to 90.0 --> 132.0 0 of 302 (0.0%) samples deleted using 14943 total control points for intensity normalization... bias field = 0.987 +- 0.057 101 of 14941 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (105, 55, 26) --> (189, 180, 234) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 7 of 7398 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (38, 54, 27) --> (120, 173, 237) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 1 of 7179 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (109, 149, 61) --> (164, 203, 129) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 292 (3.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (56, 148, 60) --> (109, 194, 132) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 229 (4.4%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (91, 137, 107) --> (132, 213, 145) Brain_Stem: limiting intensities to 88.0 --> 132.0 40 of 431 (9.3%) samples deleted using 15529 total control points for intensity normalization... bias field = 1.035 +- 0.046 72 of 15371 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (105, 55, 26) --> (189, 180, 234) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 7 of 7277 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (38, 54, 27) --> (120, 173, 237) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 6 of 7153 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (109, 149, 61) --> (164, 203, 129) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 120 of 337 (35.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (56, 148, 60) --> (109, 194, 132) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 102 of 241 (42.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (91, 137, 107) --> (132, 213, 145) Brain_Stem: limiting intensities to 88.0 --> 132.0 272 of 527 (51.6%) samples deleted using 15535 total control points for intensity normalization... bias field = 1.028 +- 0.037 32 of 14909 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 5 seconds. @#@FSTIME 2025:08:15:21:37:51 mri_ca_normalize N 8 e 64.82 S 1.09 U 63.61 P 99% M 741984 F 0 R 409310 W 0 c 211 w 205 I 0 O 6416 L 1.00 1.00 1.00 @#@FSLOADPOST 2025:08:15:21:38:56 mri_ca_normalize N 8 1.00 1.00 1.00 #-------------------------------------- #@# EntoWM Segmentation Fri Aug 15 21:38:56 UTC 2025 mri_entowm_seg --s sub-9203_ses-01 --conform --threads 1 mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer/8.1.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-9203_ses-01 --conform --threads 1 /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --no-cite-sclimbic --model /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 --keep_ac --ctab /usr/local/freesurfer/8.1.0/models/entowm.ctab --percentile 99.9 --vmp --output-base entowm --s sub-9203_ses-01 --conform --threads 1 Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/8.1.0/models/entowm.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 5 inshape (160, 160, 160) features 24 (None, 160, 160, 160, 1) Loading weights from /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /usr/local/freesurfer/8.1.0/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5 Using subject directory /mnt/hpcdata/TANDEM/FS_DIR Computed eTIV from talairach Segmenting subject sub-9203_ses-01 1/1 Loaded input image from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/nu.mgz The input image has resolution ['0.80', '0.80', '0.80'] mm, but 1mm-isotropic input is required. However, --conform has been specified, so the volume will be resliced to 1mm iso. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 31s 31s/step Wrote segmentation to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/entowm.mgz Wrote volume stats to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/stats/entowm.stats vmpcma: 8260456 done Started at Fri Aug 15 21:38:56 UTC 2025 Started at Fri Aug 15 21:38:56 UTC 2025 Ended at Fri Aug 15 21:39:32 UTC 2025 Ended at Fri Aug 15 21:39:32 UTC 2025 mri_entowm_seg-Run-Time-Sec 36 mri_entowm_seg-Run-Time-Sec 36 mri_entowm_seg-Run-Time-Min 0.72 mri_entowm_seg-Run-Time-Min 0.72 mri_entowm_seg-Run-Time-Hours 0.01 mri_entowm_seg-Run-Time-Hours 0.01 mri_entowm_seg Done mri_entowm_seg Done 1 3006 1454 808.0407 wm-lh-entorhinal 2 3201 442 254.1672 wm-lh-gyrus-ambiens 3 4006 1689 927.0277 wm-rh-entorhinal 4 4201 476 268.0179 wm-rh-gyrus-ambiens #-------------------------------------- #@# CC Seg Fri Aug 15 21:39:32 UTC 2025 seg2cc --s sub-9203_ses-01 Fri Aug 15 21:39:32 UTC 2025 setenv SUBJECTS_DIR /mnt/hpcdata/TANDEM/FS_DIR cd /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri /usr/local/freesurfer/8.1.0/bin/seg2cc --s sub-9203_ses-01 freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed seg2cc 8.1.0 Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri IsConformed yes Fri Aug 15 21:39:32 UTC 2025 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta sub-9203_ses-01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as transforms/cc_up.lta reading aseg from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/aseg.auto_noCCseg.mgz reading norm from /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/norm.mgz 63749 voxels in left wm, 161133 in right wm, xrange [103, 120] searching rotation angles z=[-11 3], y=[-10 4] searching scale 1 Z rot -11.4 searching scale 1 Z rot -11.1 searching scale 1 Z rot -10.9 searching scale 1 Z rot -10.6 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 global minimum found at slice 114.0, rotations (-3.22, -4.65) final transformation (x=114.0, yr=-3.225, zr=-4.648): 0.99513 0.08103 -0.05607 12.23259; -0.08091 0.99671 0.00456 26.04586; 0.05626 0.00000 0.99842 2.77515; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 min_x_fornix = 130 min_x_fornix = 129 min_x_fornix = 127 min_x_fornix = 126 min_x_fornix = 128 cc center is found at 128 111 119 eigenvectors: -0.00016 -0.00037 1.00000; -0.05695 -0.99838 -0.00038; 0.99838 -0.05695 0.00014; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/aseg.auto.mgz... corpus callosum segmentation took 1.1 minutes #VMPC# mri_cc VmPeak 453220 mri_cc done @#@FSTIME 2025:08:15:21:39:32 mri_cc N 7 e 68.39 S 0.37 U 67.99 P 99% M 356260 F 0 R 287335 W 0 c 221 w 52 I 0 O 1160 L 1.00 1.00 1.00 @#@FSLOADPOST 2025:08:15:21:40:41 mri_cc N 7 1.00 1.00 1.00 Fri Aug 15 21:40:41 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri Started at Fri Aug 15 21:39:32 UTC 2025 Ended at Fri Aug 15 21:40:41 UTC 2025 Seg2cc-Run-Time-Sec 69 Seg2cc-Run-Time-Hours 0.02 seg2cc Done @#@FSTIME 2025:08:15:21:39:32 seg2cc N 2 e 68.83 S 0.50 U 68.27 P 99% M 356260 F 0 R 299986 W 0 c 229 w 417 I 0 O 1424 L 1.00 1.00 1.00 @#@FSLOADPOST 2025:08:15:21:40:41 seg2cc N 2 1.00 1.00 1.00 #-------------------------------------- #@# Merge ASeg Fri Aug 15 21:40:41 UTC 2025 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Aug 15 21:40:41 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_normalize -seed 1234 -mprage -noconform -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 256 (src width 256) normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 1553 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 109 gm peak at 63 (63), valley at 33 (33) 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 63 (63), valley at 33 (33) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 17 seconds. @#@FSTIME 2025:08:15:21:40:41 mri_normalize N 10 e 199.08 S 1.72 U 197.32 P 99% M 1133324 F 0 R 676184 W 0 c 345 w 169 I 0 O 4632 L 1.00 1.00 1.00 @#@FSLOADPOST 2025:08:15:21:44:00 mri_normalize N 10 1.97 1.50 1.20 #-------------------------------------------- #@# Mask BFS Fri Aug 15 21:44:00 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2963264 voxels in mask (pct= 17.66) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2025:08:15:21:44:00 mri_mask N 5 e 1.34 S 0.04 U 1.26 P 97% M 74300 F 0 R 17244 W 0 c 10 w 158 I 0 O 4592 L 1.97 1.50 1.20 @#@FSLOADPOST 2025:08:15:21:44:02 mri_mask N 5 1.97 1.50 1.20 mri_mask -oval 1 -invert brain.finalsurfs.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/mca-dura.mgz brain.finalsurfs.mgz setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 16774334 Resetting threshold to 0.5 DoAbs = 0 Found 16774334 voxels in mask (pct= 99.98) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2025:08:15:21:44:02 mri_mask N 6 e 2.90 S 0.09 U 2.78 P 99% M 172432 F 0 R 41912 W 0 c 14 w 156 I 0 O 4592 L 1.97 1.50 1.20 @#@FSLOADPOST 2025:08:15:21:44:05 mri_mask N 6 1.97 1.50 1.21 mri_mask -oval 1 -invert brain.finalsurfs.mgz /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri/vsinus.mgz brain.finalsurfs.mgz setting masked output voxels to 1.0 instead of 0 Inverting and binarizing mask thresh = 0.5 count 16755195 Resetting threshold to 0.5 DoAbs = 0 Found 16755195 voxels in mask (pct= 99.87) maskval=0, outval=1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2025:08:15:21:44:05 mri_mask N 6 e 2.91 S 0.07 U 2.81 P 99% M 172428 F 0 R 41913 W 0 c 15 w 152 I 0 O 4568 L 1.97 1.50 1.21 @#@FSLOADPOST 2025:08:15:21:44:07 mri_mask N 6 1.97 1.50 1.21 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 = 918 @#@FSTIME 2025:08:15:21:44:08 mri_edit_wm_with_aseg N 7 e 1.81 S 0.02 U 1.76 P 98% M 90100 F 0 R 21166 W 0 c 13 w 142 I 0 O 4568 L 1.97 1.50 1.21 @#@FSLOADPOST 2025:08:15:21:44:09 mri_edit_wm_with_aseg N 7 1.97 1.51 1.21 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 = 6212 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 993 @#@FSTIME 2025:08:15:21:44:09 mri_edit_wm_with_aseg N 6 e 2.05 S 0.05 U 1.94 P 96% M 84620 F 0 R 40307 W 0 c 14 w 149 I 0 O 4568 L 1.97 1.51 1.21 @#@FSLOADPOST 2025:08:15:21:44:11 mri_edit_wm_with_aseg N 6 1.97 1.51 1.21 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Fri Aug 15 21:44:12 UTC 2025 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2025:08:15:21:44:12 AntsDenoiseImageFs N 4 e 66.29 S 0.13 U 66.12 P 99% M 351160 F 0 R 86489 W 0 c 129 w 98 I 0 O 4672 L 1.97 1.51 1.21 @#@FSLOADPOST 2025:08:15:21:45:18 AntsDenoiseImageFs N 4 1.99 1.61 1.27 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 0.8, wsize = 16 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 16 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 771847, nonwhite = 15570791, ambig = 434578, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (103.0): 103.9 +- 5.6 [79.0 --> 125.0] CCS GM (72.0) : 69.6 +- 11.6 [30.0 --> 95.0] white_mean 103.861 white_sigma 5.55212 gray_mean 69.6272 gray_sigma 11.6135 setting bottom of white matter range wm_low to 81.2 setting top of gray matter range gray_hi to 92.9 wm_low 81.2406 wm_hi 125 gray_low 30 gray_hi 92.8541 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=81.2406, wm_hi=125, gray_hi=92.8541 white = 912417, nonwhite = 15641952, ambig = 222847, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 81.2406 wm_hi 125 gray_low 30 gray_hi 92.8541 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 92.8541, wm_low = 81.2406 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=92.8541, wmlow=81.2406 210345 voxels processed (1.25%) 97743 voxels white (0.58%) 112602 voxels non-white (0.67%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=76.2406, gray_hi=92.8541, wsize=16 346037 voxels tested (2.06%) 84372 voxels changed (0.50%) 70863 multi-scale searches (0.42%) Recovering bright white MRIrecoverBrightWhite() wm_low 81.2406 wm_hi 125 slack 5.55212 pct_thresh 0.33 intensity_thresh 130.552 nvox_thresh 8.58 847 voxels tested (0.01%) 626 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=76.2406, hithr=92.8541 smoothing input volume with sigma = 0.250 153088 voxels tested (0.91%) 26516 voxels changed (0.16%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 9214 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2835 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 13763 filled MRIfindBrightNonWM(): 1906 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.9 minutes writing output to wm.seg.mgz... @#@FSTIME 2025:08:15:21:45:18 mri_segment N 5 e 112.16 S 0.37 U 111.76 P 99% M 146904 F 0 R 286876 W 0 c 127 w 59 I 0 O 1408 L 1.99 1.61 1.27 @#@FSLOADPOST 2025:08:15:21:47:10 mri_segment N 5 2.00 1.74 1.36 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 0.79 minutes Fixing entowm 3 255 255 LabelAmygalaCortalJunction((): nhits = 6212 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 45569 additional wm voxels added 0 additional wm voxels added SEG EDIT: 674290 voxels turned on, 68837 voxels turned off. Dilating 1 voxels in 3d propagating editing to output volume from wm.seg.mgz MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 4061 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 993 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2025:08:15:21:47:10 mri_edit_wm_with_aseg N 17 e 47.70 S 0.61 U 47.06 P 99% M 654064 F 0 R 407519 W 0 c 103 w 66 I 0 O 1240 L 2.00 1.74 1.36 @#@FSLOADPOST 2025:08:15:21:47:58 mri_edit_wm_with_aseg N 17 2.00 1.78 1.39 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 45 found - 45 modified | TOTAL: 45 pass 2 (xy+): 0 found - 45 modified | TOTAL: 45 pass 1 (xy-): 36 found - 36 modified | TOTAL: 81 pass 2 (xy-): 0 found - 36 modified | TOTAL: 81 pass 1 (yz+): 38 found - 38 modified | TOTAL: 119 pass 2 (yz+): 0 found - 38 modified | TOTAL: 119 pass 1 (yz-): 45 found - 45 modified | TOTAL: 164 pass 2 (yz-): 0 found - 45 modified | TOTAL: 164 pass 1 (xz+): 34 found - 34 modified | TOTAL: 198 pass 2 (xz+): 0 found - 34 modified | TOTAL: 198 pass 1 (xz-): 34 found - 34 modified | TOTAL: 232 pass 2 (xz-): 0 found - 34 modified | TOTAL: 232 Iteration Number : 1 pass 1 (+++): 33 found - 33 modified | TOTAL: 33 pass 2 (+++): 0 found - 33 modified | TOTAL: 33 pass 1 (+++): 8 found - 8 modified | TOTAL: 41 pass 2 (+++): 0 found - 8 modified | TOTAL: 41 pass 1 (+++): 30 found - 30 modified | TOTAL: 71 pass 2 (+++): 0 found - 30 modified | TOTAL: 71 pass 1 (+++): 22 found - 22 modified | TOTAL: 93 pass 2 (+++): 0 found - 22 modified | TOTAL: 93 Iteration Number : 1 pass 1 (++): 84 found - 84 modified | TOTAL: 84 pass 2 (++): 0 found - 84 modified | TOTAL: 84 pass 1 (+-): 293 found - 293 modified | TOTAL: 377 pass 2 (+-): 1 found - 294 modified | TOTAL: 378 pass 3 (+-): 0 found - 294 modified | TOTAL: 378 pass 1 (--): 131 found - 131 modified | TOTAL: 509 pass 2 (--): 0 found - 131 modified | TOTAL: 509 pass 1 (-+): 78 found - 78 modified | TOTAL: 587 pass 2 (-+): 0 found - 78 modified | TOTAL: 587 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 11 found - 11 modified | TOTAL: 16 pass 2 (xy-): 0 found - 11 modified | TOTAL: 16 pass 1 (yz+): 10 found - 10 modified | TOTAL: 26 pass 2 (yz+): 0 found - 10 modified | TOTAL: 26 pass 1 (yz-): 3 found - 3 modified | TOTAL: 29 pass 2 (yz-): 0 found - 3 modified | TOTAL: 29 pass 1 (xz+): 4 found - 4 modified | TOTAL: 33 pass 2 (xz+): 0 found - 4 modified | TOTAL: 33 pass 1 (xz-): 6 found - 6 modified | TOTAL: 39 pass 2 (xz-): 0 found - 6 modified | TOTAL: 39 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 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 6 found - 6 modified | TOTAL: 9 pass 2 (+-): 0 found - 6 modified | TOTAL: 9 pass 1 (--): 2 found - 2 modified | TOTAL: 11 pass 2 (--): 0 found - 2 modified | TOTAL: 11 pass 1 (-+): 3 found - 3 modified | TOTAL: 14 pass 2 (-+): 0 found - 3 modified | TOTAL: 14 Iteration Number : 3 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 : 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 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 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 = 974 (out of 1133890: 0.085899) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2025:08:15:21:47:58 mri_pretess N 4 e 4.62 S 0.01 U 4.58 P 99% M 56988 F 0 R 12938 W 0 c 13 w 57 I 0 O 1248 L 2.00 1.78 1.39 @#@FSLOADPOST 2025:08:15:21:48:03 mri_pretess N 4 2.00 1.78 1.39 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 = 4061 @#@FSTIME 2025:08:15:21:48:03 mri_edit_wm_with_aseg N 7 e 1.70 S 0.03 U 1.65 P 99% M 89932 F 0 R 21162 W 0 c 14 w 37 I 0 O 1248 L 2.00 1.78 1.39 @#@FSLOADPOST 2025:08:15:21:48:04 mri_edit_wm_with_aseg N 7 2.00 1.79 1.40 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 = 6212 Fixing ACJ 255 255 MRIfixEntoWM(): 255 255 Level=3 MRIfixEntoWM(): nchanged = 993 @#@FSTIME 2025:08:15:21:48:04 mri_edit_wm_with_aseg N 6 e 2.30 S 0.05 U 2.23 P 99% M 84500 F 0 R 40305 W 0 c 14 w 51 I 0 O 1248 L 2.00 1.79 1.40 @#@FSLOADPOST 2025:08:15:21:48:07 mri_edit_wm_with_aseg N 6 2.00 1.79 1.40 #-------------------------------------------- #@# Fill Fri Aug 15 21:48:07 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/8.1.0/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... done. searching for cutting planes...voxel to talairach voxel transform 1.08774 0.08912 -0.06214 -1.02110; -0.09820 1.13692 0.22586 -42.60876; 0.08547 -0.21741 0.97086 -2.13109; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.08774 0.08912 -0.06214 -1.02110; -0.09820 1.13692 0.22586 -42.60876; 0.08547 -0.21741 0.97086 -2.13109; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (546, 2188) area[0] = 2205 (min = 546, max = 2188), aspect = 0.48 (min = 0.10, max = 0.75) need search nearby using seed (125, 113, 80), TAL = (2.4, -38.4, 12.0) talairach voxel to voxel transform 0.90853 -0.05753 0.07153 -1.37131; 0.09035 0.83638 -0.18879 35.32716; -0.05975 0.19237 0.98144 10.22699; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 113, 80) --> (2.4, -38.4, 12.0) done. filling took 1.2 minutes talairach cc position changed to (2.40, -38.40, 12.00) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(20.40, -38.40, 12.00) SRC: (90.97, 124.00, 104.36) search lh wm seed point around talairach space (-15.60, -38.40, 12.00), SRC: (131.86, 128.06, 101.67) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2025:08:15:21:48:07 mri_fill N 10 e 70.05 S 1.48 U 68.54 P 99% M 932368 F 0 R 513951 W 0 c 127 w 33 I 0 O 400 L 2.00 1.79 1.40 @#@FSLOADPOST 2025:08:15:21:49:17 mri_fill N 10 2.00 1.83 1.44 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Fri Aug 15 21:49:17 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 11 found - 11 modified | TOTAL: 17 pass 2 (xy-): 0 found - 11 modified | TOTAL: 17 pass 1 (yz+): 26 found - 26 modified | TOTAL: 43 pass 2 (yz+): 0 found - 26 modified | TOTAL: 43 pass 1 (yz-): 8 found - 8 modified | TOTAL: 51 pass 2 (yz-): 0 found - 8 modified | TOTAL: 51 pass 1 (xz+): 4 found - 4 modified | TOTAL: 55 pass 2 (xz+): 0 found - 4 modified | TOTAL: 55 pass 1 (xz-): 6 found - 6 modified | TOTAL: 61 pass 2 (xz-): 0 found - 6 modified | TOTAL: 61 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 5 found - 5 modified | TOTAL: 10 pass 2 (+-): 0 found - 5 modified | TOTAL: 10 pass 1 (--): 2 found - 2 modified | TOTAL: 12 pass 2 (--): 0 found - 2 modified | TOTAL: 12 pass 1 (-+): 1 found - 1 modified | TOTAL: 13 pass 2 (-+): 0 found - 1 modified | TOTAL: 13 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 78 (out of 549786: 0.014187) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2025:08:15:21:49:17 mri_pretess N 4 e 2.78 S 0.02 U 2.74 P 99% M 40264 F 0 R 8780 W 0 c 11 w 37 I 0 O 392 L 2.00 1.83 1.44 @#@FSLOADPOST 2025:08:15:21:49:20 mri_pretess N 4 2.00 1.84 1.45 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix.predec 8.1.0 8.1.0 slice 30: 2430 vertices, 2601 faces slice 40: 9332 vertices, 9595 faces slice 50: 17953 vertices, 18291 faces slice 60: 28568 vertices, 28972 faces slice 70: 41022 vertices, 41467 faces slice 80: 54194 vertices, 54717 faces slice 90: 67739 vertices, 68220 faces slice 100: 80414 vertices, 80925 faces slice 110: 94499 vertices, 95090 faces slice 120: 109762 vertices, 110310 faces slice 130: 123697 vertices, 124300 faces slice 140: 137921 vertices, 138474 faces slice 150: 151635 vertices, 152181 faces slice 160: 165288 vertices, 165790 faces slice 170: 176395 vertices, 176840 faces slice 180: 187037 vertices, 187476 faces slice 190: 196708 vertices, 197091 faces slice 200: 204994 vertices, 205345 faces slice 210: 212103 vertices, 212437 faces slice 220: 218052 vertices, 218288 faces slice 230: 221733 vertices, 221868 faces slice 240: 222438 vertices, 222516 faces slice 250: 222438 vertices, 222516 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix.predec using vox2ras matrix: -0.80000 0.00000 0.00000 102.40000; 0.00000 0.00000 0.80000 -102.40000; 0.00000 -0.80000 0.00000 102.40000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2025:08:15:21:49:20 mri_tessellate N 3 e 1.72 S 0.01 U 1.65 P 97% M 45164 F 0 R 10271 W 0 c 6 w 354 I 0 O 10432 L 2.00 1.84 1.45 @#@FSLOADPOST 2025:08:15:21:49:21 mri_tessellate N 3 2.00 1.84 1.45 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... 222438 voxel in cpt #1: X=-78 [v=222438,e=667548,f=445032] located at (-15.192953, -5.197600, 8.836092) For the whole surface: X=-78 [v=222438,e=667548,f=445032] One single component has been found nothing to do done @#@FSTIME 2025:08:15:21:49:22 mris_extract_main_component N 2 e 1.72 S 0.25 U 1.41 P 96% M 436600 F 0 R 116251 W 0 c 13 w 552 I 0 O 15648 L 2.00 1.84 1.45 @#@FSLOADPOST 2025:08:15:21:49:23 mris_extract_main_component N 2 2.00 1.84 1.45 mris_remesh --desired-face-area 0.5 --input ../surf/lh.orig.nofix.predec --output ../surf/lh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.32 decimation level = 0.64 target vertices = 142360 Remesher::remeshBKV( 5 , 142360 ) vcount = 222438 vnum: 142360 area = 142410 avel: 0.910457 s0 = 0.859807 st: 1.07476 Targetn: 206422 points: 222438 Targetl: 0.943317 avg l: 0.910457 points: 222438 Maxndown:17617 Points: 222438 avg edge: 0.863855 Targetn: 190406 points: 222438 Targetl: 0.976178 avg l: 0.863855 points: 222466 Maxndown:35266 Points: 187200 avg edge: 0.911891 Targetn: 174391 points: 187200 Targetl: 1.00904 avg l: 0.911891 points: 187333 Maxndown:14236 Points: 173097 avg edge: 0.934401 Targetn: 158375 points: 173097 Targetl: 1.0419 avg l: 0.934401 points: 173132 Maxndown:16232 Points: 156900 avg edge: 0.967538 Targetn: 142360 points: 156900 Targetl: 1.07476 avg l: 0.967538 points: 156952 Maxndown:14592 Points: 142360 avg edge: 1.00332 Final Points: 142360 final avg edge: 1.00332 avg qual before : 0.866025 after: 0.964794 Removing intersections removing intersecting faces 000: 8 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 222438 nv = 142360 0.639999 Area 284876 0.42801 0.05290 0.028517 0.9824 Corner 854628 60.00000 8.58423 12.296747 155.1186 Edge 427314 1.00329 0.10442 0.158856 1.7540 Hinge 427314 33.50282 29.61493 0.000000 175.4256 mris_remesh done @#@FSTIME 2025:08:15:21:49:23 mris_remesh N 6 e 17.60 S 0.73 U 16.82 P 99% M 819860 F 0 R 328444 W 0 c 47 w 205 I 0 O 10016 L 2.00 1.84 1.45 @#@FSLOADPOST 2025:08:15:21:49:41 mris_remesh N 6 2.00 1.85 1.46 #-------------------------------------------- #@# Tessellate rh Fri Aug 15 21:49:41 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/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-): 0 found - 0 modified | TOTAL: 4 pass 1 (yz+): 8 found - 8 modified | TOTAL: 12 pass 2 (yz+): 0 found - 8 modified | TOTAL: 12 pass 1 (yz-): 10 found - 10 modified | TOTAL: 22 pass 2 (yz-): 0 found - 10 modified | TOTAL: 22 pass 1 (xz+): 1 found - 1 modified | TOTAL: 23 pass 2 (xz+): 0 found - 1 modified | TOTAL: 23 pass 1 (xz-): 0 found - 0 modified | TOTAL: 23 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 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 28 (out of 532160: 0.005262) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2025:08:15:21:49:41 mri_pretess N 4 e 2.05 S 0.01 U 2.01 P 99% M 40236 F 0 R 8781 W 0 c 11 w 29 I 0 O 392 L 2.00 1.85 1.46 @#@FSLOADPOST 2025:08:15:21:49:43 mri_pretess N 4 2.00 1.85 1.46 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix.predec 8.1.0 8.1.0 slice 30: 831 vertices, 909 faces slice 40: 5513 vertices, 5748 faces slice 50: 13029 vertices, 13321 faces slice 60: 23370 vertices, 23790 faces slice 70: 35180 vertices, 35604 faces slice 80: 47311 vertices, 47730 faces slice 90: 59153 vertices, 59570 faces slice 100: 71337 vertices, 71821 faces slice 110: 83911 vertices, 84380 faces slice 120: 97601 vertices, 98106 faces slice 130: 111275 vertices, 111783 faces slice 140: 123975 vertices, 124513 faces slice 150: 136620 vertices, 137130 faces slice 160: 148946 vertices, 149466 faces slice 170: 160501 vertices, 160911 faces slice 180: 170747 vertices, 171173 faces slice 190: 180656 vertices, 181060 faces slice 200: 188856 vertices, 189162 faces slice 210: 195470 vertices, 195759 faces slice 220: 201041 vertices, 201275 faces slice 230: 204754 vertices, 204914 faces slice 240: 205648 vertices, 205714 faces slice 250: 205648 vertices, 205714 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix.predec using vox2ras matrix: -0.80000 0.00000 0.00000 102.40000; 0.00000 0.00000 0.80000 -102.40000; 0.00000 -0.80000 0.00000 102.40000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2025:08:15:21:49:43 mri_tessellate N 3 e 1.68 S 0.04 U 1.61 P 97% M 43648 F 0 R 9899 W 0 c 5 w 318 I 0 O 9648 L 2.00 1.85 1.46 @#@FSLOADPOST 2025:08:15:21:49:45 mri_tessellate N 3 2.00 1.85 1.46 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... 205648 voxel in cpt #1: X=-66 [v=205648,e=617142,f=411428] located at (37.544468, -3.134409, 11.610660) For the whole surface: X=-66 [v=205648,e=617142,f=411428] One single component has been found nothing to do done @#@FSTIME 2025:08:15:21:49:45 mris_extract_main_component N 2 e 1.80 S 0.24 U 1.46 P 94% M 404420 F 0 R 106565 W 0 c 10 w 441 I 0 O 14472 L 2.00 1.85 1.46 @#@FSLOADPOST 2025:08:15:21:49:47 mris_extract_main_component N 2 2.00 1.85 1.46 mris_remesh --desired-face-area 0.5 --input ../surf/rh.orig.nofix.predec --output ../surf/rh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.32 decimation level = 0.64 target vertices = 131615 Remesher::remeshBKV( 5 , 131615 ) vcount = 205648 vnum: 131615 area = 131657 avel: 0.910457 s0 = 0.859794 st: 1.07474 Targetn: 190841 points: 205648 Targetl: 0.943314 avg l: 0.910457 points: 205648 Maxndown:16287 Points: 205648 avg edge: 0.864064 Targetn: 176034 points: 205648 Targetl: 0.976171 avg l: 0.864064 points: 205670 Maxndown:32599 Points: 173071 avg edge: 0.912571 Targetn: 161228 points: 173071 Targetl: 1.00903 avg l: 0.912571 points: 173205 Maxndown:13174 Points: 160031 avg edge: 0.935146 Targetn: 146421 points: 160031 Targetl: 1.04188 avg l: 0.935146 points: 160051 Maxndown:14993 Points: 145058 avg edge: 0.968131 Targetn: 131615 points: 145058 Targetl: 1.07474 avg l: 0.968131 points: 145094 Maxndown:13479 Points: 131615 avg edge: 1.00391 Final Points: 131615 final avg edge: 1.00391 avg qual before : 0.866025 after: 0.964868 Removing intersections removing intersecting faces 000: 14 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 205648 nv = 131615 0.640001 Area 263362 0.42850 0.05263 0.009803 1.0522 Corner 790086 60.00000 8.57465 11.514405 155.2633 Edge 395043 1.00383 0.10414 0.133956 1.7051 Hinge 395043 33.66143 29.65605 0.000000 173.4797 mris_remesh done @#@FSTIME 2025:08:15:21:49:47 mris_remesh N 6 e 16.70 S 0.82 U 15.80 P 99% M 749788 F 0 R 467611 W 0 c 36 w 321 I 0 O 9264 L 2.00 1.85 1.46 @#@FSLOADPOST 2025:08:15:21:50:03 mris_remesh N 6 2.00 1.86 1.47 #-------------------------------------------- #@# Smooth1 lh Fri Aug 15 21:50:03 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2025:08:15:21:50:03 mris_smooth N 5 e 3.56 S 0.17 U 3.35 P 98% M 221236 F 0 R 66038 W 0 c 10 w 319 I 0 O 10016 L 2.00 1.86 1.47 @#@FSLOADPOST 2025:08:15:21:50:07 mris_smooth N 5 2.00 1.86 1.48 #-------------------------------------------- #@# Smooth1 rh Fri Aug 15 21:50:07 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2025:08:15:21:50:07 mris_smooth N 5 e 3.26 S 0.14 U 3.09 P 98% M 205220 F 0 R 61093 W 0 c 15 w 296 I 0 O 9264 L 2.00 1.86 1.48 @#@FSLOADPOST 2025:08:15:21:50:10 mris_smooth N 5 2.00 1.86 1.48 #-------------------------------------------- #@# Inflation1 lh Fri Aug 15 21:50:10 UTC 2025 /mnt/hpcdata/TANDEM/FS_DIR/sub-9203_ses-01/scripts mris_inflate -no-save-sulc 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 50 ** failed to open GIFTI XML file '50.gii' mrisReadGIFTIdanum: ERROR reading gifti 50.gii [INFO] read, cannot find 50, trying 50.gii ... error: No such file or directory error: mris_inflate: could not read surface file 50 Command exited with non-zero status 255 @#@FSTIME 2025:08:15:21:50:10 mris_inflate N 4 e 0.00 S 0.00 U 0.00 P 80% M 6260 F 0 R 233 W 0 c 0 w 3 I 0 O 0 L 2.00 1.86 1.48 @#@FSLOADPOST 2025:08:15:21:50:10 mris_inflate N 4 2.00 1.86 1.48 Linux bcmhari-hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-9203_ses-01 exited with ERRORS at Fri Aug 15 21:50:11 UTC 2025 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting