Sat Feb 18 11:31:02 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139 setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii /usr/local/freesurfer/7.2.0/bin/recon-all -s Sub-139 -i 139.nii -all -parallel -qcache -openmp 4 subjid Sub-139 setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0 build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 15528 maxlocks unlimited maxsignal 15528 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3.8G 1.1G 1.8G 19M 953M 2.5G Swap: 0B 0B 0B ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) 7.2.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.2.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/18-16:31:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-139-generic CompilerName: GCC CompilerVersion: 4.8.5 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/7.2.0/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/7.2.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/developer/Desktop/1st_scan_nii/Sub-139 mri_convert /home/developer/Desktop/1st_scan_nii/139.nii /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig/001.mgz mri_convert /home/developer/Desktop/1st_scan_nii/139.nii /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig/001.mgz reading from /home/developer/Desktop/1st_scan_nii/139.nii... TR=6.76, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99948, 0.029898, -0.012086) j_ras = (-0.03112, 0.992481, -0.118375) k_ras = (0.00845591, 0.11869, 0.992895) writing to /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig/001.mgz... @#@FSTIME 2023:02:18:11:31:03 mri_convert N 2 e 2.76 S 0.09 U 2.85 P 106% M 51120 F 2 R 11401 W 0 c 24 w 13 I 44232 O 23168 L 0.26 0.31 0.13 @#@FSLOADPOST 2023:02:18:11:31:05 mri_convert N 2 0.32 0.32 0.14 #-------------------------------------------- #@# MotionCor Sat Feb 18 11:31:06 EST 2023 Found 1 runs /home/developer/Desktop/1st_scan_nii/Sub-139/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 /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig/001.mgz /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz /home/developer/Desktop/1st_scan_nii/Sub-139 mri_convert /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz --conform mri_convert /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz --conform reading from /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz... TR=6.76, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99948, 0.029898, -0.012086) j_ras = (-0.03112, 0.992481, -0.118375) k_ras = (0.00845591, 0.11869, 0.992895) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 6.86163e+06 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz... @#@FSTIME 2023:02:18:11:31:09 mri_convert N 3 e 3.75 S 0.03 U 3.91 P 105% M 62264 F 0 R 22429 W 0 c 19 w 4 I 0 O 10112 L 0.32 0.32 0.14 @#@FSLOADPOST 2023:02:18:11:31:13 mri_convert N 3 0.46 0.35 0.15 mri_add_xform_to_header -c /home/developer/Desktop/1st_scan_nii/Sub-139/mri/transforms/talairach.xfm /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2023:02:18:11:31:13 mri_add_xform_to_header N 4 e 0.69 S 0.02 U 1.18 P 174% M 23428 F 14 R 4588 W 0 c 16 w 30 I 3184 O 10112 L 0.46 0.35 0.15 @#@FSLOADPOST 2023:02:18:11:31:14 mri_add_xform_to_header N 4 0.46 0.35 0.15 #-------------------------------------------- #@# Talairach Sat Feb 18 11:31:14 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /home/developer/Desktop/1st_scan_nii/Sub-139/mri /usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.2.0 Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Sat Feb 18 11:31:14 EST 2023 tmpdir is ./tmp.mri_nu_correct.mni.2306 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2306/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2306/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2306/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2306/nu0.mgz... TR=6.76, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.56114e-09, -9.31323e-10) j_ras = (0, 0, -1) k_ras = (-5.82077e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Sat Feb 18 11:35:32 EST 2023 mri_nu_correct.mni done @#@FSTIME 2023:02:18:11:31:14 mri_nu_correct.mni N 12 e 258.84 S 0.19 U 259.02 P 100% M 507444 F 19 R 149336 W 0 c 916 w 115 I 4352 O 19280 L 0.46 0.35 0.15 @#@FSLOADPOST 2023:02:18:11:35:32 mri_nu_correct.mni N 12 1.00 0.75 0.37 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Feb 18 11:35:32 EST 2023 Ended at Sat Feb 18 11:36:35 EST 2023 talairach_avi done @#@FSTIME 2023:02:18:11:35:32 talairach_avi N 4 e 63.06 S 0.79 U 56.56 P 90% M 255640 F 13 R 395702 W 0 c 251 w 224 I 272328 O 295272 L 1.00 0.75 0.37 @#@FSLOADPOST 2023:02:18:11:36:35 talairach_avi N 4 0.94 0.78 0.41 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/7.2.0/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.2.0 --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/7.2.0/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.16323 0.08258 -0.01141 8.49524; -0.05107 1.23832 0.00542 -9.30769; 0.03252 -0.15704 1.27839 -61.87592; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Sat Feb 18 11:36:38 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7085, pval=0.4932 >= threshold=0.0050) @#@FSTIME 2023:02:18:11:36:38 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 38% M 5632 F 10 R 199 W 0 c 2 w 17 I 2512 O 0 L 0.86 0.77 0.41 @#@FSLOADPOST 2023:02:18:11:36:38 talairach_afd N 4 0.86 0.77 0.41 awk -f /usr/local/freesurfer/7.2.0/bin/extract_talairach_avi_QA.awk /home/developer/Desktop/1st_scan_nii/Sub-139/mri/transforms/talairach_avi.log tal_QC_AZS /home/developer/Desktop/1st_scan_nii/Sub-139/mri/transforms/talairach_avi.log TalAviQA: 0.97308 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Sat Feb 18 11:36:38 EST 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /home/developer/Desktop/1st_scan_nii/Sub-139/mri /usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.2.0 Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Sat Feb 18 11:36:38 EST 2023 tmpdir is ./tmp.mri_nu_correct.mni.2555 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2555/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.2555/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2555/ones.mgz 7.2.0 cwd /home/developer/Desktop/1st_scan_nii/Sub-139/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2555/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2555/ones.mgz sysname Linux hostname developer-VirtualBox machine x86_64 user developer input ./tmp.mri_nu_correct.mni.2555/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2555/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.2555/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2555/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2555/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2555/input.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2555/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2555/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2555/input.mean.dat sysname Linux hostname developer-VirtualBox machine x86_64 user developer whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2555/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2555/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2555/ones.mgz --i ./tmp.mri_nu_correct.mni.2555/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2555/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2555/output.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2555/ones.mgz --i ./tmp.mri_nu_correct.mni.2555/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2555/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2555/output.mean.dat sysname Linux hostname developer-VirtualBox machine x86_64 user developer whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2555/ones.mgz Loading ./tmp.mri_nu_correct.mni.2555/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2555/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2555/nu0.mgz ./tmp.mri_nu_correct.mni.2555/nu0.mgz mul 1.19206401949382510937 Saving result to './tmp.mri_nu_correct.mni.2555/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2555/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2555/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.2555/nu0.mgz... TR=6.76, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.56114e-09, -9.31323e-10) j_ras = (0, 0, -1) k_ras = (-5.82077e-10, 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. mapping ( 5, 173) to ( 3, 110) Sat Feb 18 11:41:11 EST 2023 mri_nu_correct.mni done @#@FSTIME 2023:02:18:11:36:38 mri_nu_correct.mni N 9 e 273.71 S 0.90 U 277.68 P 101% M 614484 F 27 R 555741 W 0 c 1157 w 241 I 7560 O 47104 L 0.86 0.77 0.41 @#@FSLOADPOST 2023:02:18:11:41:11 mri_nu_correct.mni N 9 1.17 1.02 0.61 mri_add_xform_to_header -c /home/developer/Desktop/1st_scan_nii/Sub-139/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2023:02:18:11:41:11 mri_add_xform_to_header N 4 e 0.46 S 0.04 U 0.77 P 177% M 23464 F 1 R 4594 W 0 c 11 w 7 I 512 O 7736 L 1.17 1.02 0.61 @#@FSLOADPOST 2023:02:18:11:41:12 mri_add_xform_to_header N 4 1.17 1.02 0.61 #-------------------------------------------- #@# Intensity Normalization Sat Feb 18 11:41:12 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.16323 0.08258 -0.01141 8.49524; -0.05107 1.23832 0.00542 -9.30769; 0.03252 -0.15704 1.27839 -61.87592; 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 = 18 Starting OpenSpline(): npoints = 18 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 48 (48), valley at 24 (24) csf peak at 24, 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 48 (48), valley at 24 (24) csf peak at 25, setting threshold to 40 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 11 seconds. @#@FSTIME 2023:02:18:11:41:12 mri_normalize N 7 e 192.03 S 0.20 U 204.74 P 106% M 583680 F 5 R 263313 W 0 c 810 w 24 I 1480 O 7368 L 1.17 1.02 0.61 @#@FSLOADPOST 2023:02:18:11:44:24 mri_normalize N 7 1.25 1.06 0.71 #-------------------------------------------- #@# Skull Stripping Sat Feb 18 11:44:24 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/7.2.0/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/7.2.0/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (49, 15, 33) --> (207, 242, 213) finding center of left hemi white matter using (102, 91, 123) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (83,63,101) --> (121, 119,145) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.6 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.549 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.406571 @ (-10.526, 10.526, -10.526) max log p = -4.274020 @ (5.263, 5.263, -5.263) max log p = -4.227491 @ (2.632, -2.632, 2.632) max log p = -4.207557 @ (1.316, 3.947, -9.211) max log p = -4.178119 @ (0.658, -1.974, 4.605) max log p = -4.178119 @ (0.000, 0.000, 0.000) max log p = -4.178119 @ (0.000, 0.000, 0.000) max log p = -4.178119 @ (0.000, 0.000, 0.000) Found translation: (-0.7, 15.1, -17.8): log p = -4.178 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.900, old_max_log_p =-4.178 (thresh=-4.2) 1.14016 0.00000 -0.13053 -1.45585; 0.00000 1.23625 0.00000 1.25789; 0.16136 0.00000 1.06580 -39.04029; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.847, old_max_log_p =-3.900 (thresh=-3.9) 1.05465 0.00000 -0.12074 8.03602; 0.00000 1.23625 0.00000 1.25789; 0.17347 0.00000 1.14574 -50.30588; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 22 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.847, old_max_log_p =-3.847 (thresh=-3.8) 1.05465 0.00000 -0.12074 8.03602; 0.00000 1.23625 0.00000 1.25789; 0.17347 0.00000 1.14574 -50.30588; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.800, old_max_log_p =-3.847 (thresh=-3.8) 1.07469 0.00259 -0.12008 3.46116; 0.00328 1.18925 0.03625 -0.21637; 0.17269 -0.03958 1.12273 -44.95357; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.797, old_max_log_p =-3.800 (thresh=-3.8) 1.09484 0.00264 -0.12234 1.18039; 0.00328 1.18925 0.03625 -0.21637; 0.17269 -0.03958 1.12273 -44.95357; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.779, old_max_log_p =-3.797 (thresh=-3.8) 1.09849 -0.01688 -0.12335 3.09793; 0.01843 1.19381 0.01597 0.31381; 0.17302 -0.02007 1.12314 -47.28443; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.773, old_max_log_p =-3.779 (thresh=-3.8) 1.09965 -0.02698 -0.11443 2.54409; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11614; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.768, old_max_log_p =-3.773 (thresh=-3.8) 1.10352 -0.02708 -0.11484 2.11289; 0.03030 1.19594 0.03345 -4.06451; 0.16408 -0.03960 1.12634 -44.29811; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.766, old_max_log_p =-3.768 (thresh=-3.8) 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.766 (old=-4.549) transform before final EM align: 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 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: 013: -log(p) = 4.1 tol 0.000000 final transform: 1.10481 -0.02711 -0.11497 1.96910; 0.03030 1.19594 0.03345 -4.06451; 0.16389 -0.03955 1.12502 -44.11592; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 827744 FSRUNTIME@ mri_em_register 0.0675 hours 4 threads registration took 4 minutes and 3 seconds. @#@FSTIME 2023:02:18:11:44:24 mri_em_register N 4 e 243.06 S 2.69 U 826.63 P 341% M 629156 F 5 R 166655 W 0 c 16769 w 320 I 151112 O 16 L 1.25 1.06 0.71 @#@FSLOADPOST 2023:02:18:11:48:27 mri_em_register N 4 2.94 2.30 1.31 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/7.2.0/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=95 z=123 r=90 first estimation of the main basin volume: 3064398 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=149, y=92, z=79, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=8967403193 voxels, voxel volume =1.000 = 8967403193 mmm3 = 8967403.520 cm3 done. PostAnalyze...Basin Prior 16 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=98, z=117, r=9049 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=35 , nb = 44424 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=50 , nb = 3132 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=70 , nb = 2826 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=34 , nb = 18684 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=33 , nb = 19314 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 468 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 35, 38, 41, 67 after analyzing : 35, 40, 41, 46 RIGHT_CER before analyzing : 50, 46, 44, 73 after analyzing : 27, 46, 46, 52 LEFT_CER before analyzing : 70, 51, 42, 77 after analyzing : 29, 51, 51, 57 RIGHT_BRAIN before analyzing : 34, 38, 42, 67 after analyzing : 34, 40, 42, 46 LEFT_BRAIN before analyzing : 33, 36, 39, 67 after analyzing : 33, 38, 39, 45 OTHER before analyzing : 9, 15, 22, 30 after analyzing : 9, 21, 25, 23 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 65.246, std = 5.754 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.28, sigma = 5.80 after rotation: sse = 4.28, sigma = 5.80 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.92, its var is 6.44 before Erosion-Dilatation 2.03% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...44 iterations mri_strip_skull: done peeling brain Brain Size = 1410542 voxels, voxel volume = 1.000 mm3 = 1410542 mmm3 = 1410.542 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 17.959757 mri_watershed stimesec 1.810757 mri_watershed ru_maxrss 816908 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 207046 mri_watershed ru_majflt 10 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9864 mri_watershed ru_oublock 2120 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 573 mri_watershed ru_nivcsw 166 mri_watershed done @#@FSTIME 2023:02:18:11:48:27 mri_watershed N 6 e 15.44 S 1.82 U 17.95 P 128% M 816908 F 10 R 207048 W 0 c 166 w 574 I 9864 O 2120 L 2.94 2.30 1.31 @#@FSLOADPOST 2023:02:18:11:48:43 mri_watershed N 6 2.51 2.24 1.31 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Feb 18 11:48:44 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/7.2.0/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 = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/7.2.0/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=24.9 skull bounding box = (61, 41, 46) --> (193, 150, 201) finding center of left hemi white matter using (105, 77, 124) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (89,64,105) --> (121, 90,143) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.3 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.494 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.122766 @ (-10.526, 10.526, -10.526) max log p = -3.898929 @ (5.263, 5.263, -5.263) max log p = -3.842057 @ (2.632, 2.632, -2.632) max log p = -3.813061 @ (3.947, -1.316, 6.579) max log p = -3.804461 @ (-0.658, -0.658, -0.658) max log p = -3.798985 @ (-1.645, 0.329, 1.645) max log p = -3.798985 @ (0.000, 0.000, 0.000) max log p = -3.798985 @ (0.000, 0.000, 0.000) Found translation: (-1.0, 16.8, -10.9): log p = -3.799 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.537, old_max_log_p =-3.799 (thresh=-3.8) 1.04563 -0.12074 -0.13766 21.56625; 0.15998 1.06580 -0.02106 -0.46442; 0.15011 0.00000 1.14016 -46.33450; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 19 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.489, old_max_log_p =-3.537 (thresh=-3.5) 1.05994 0.01822 -0.11978 4.38369; 0.04322 1.14316 0.15567 -13.59800; 0.12794 -0.13912 1.13316 -29.40509; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.427, old_max_log_p =-3.489 (thresh=-3.5) 1.05994 0.01822 -0.11978 4.38369; 0.02811 1.23790 0.00692 -3.42429; 0.12255 0.01044 1.05800 -34.27070; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.427, old_max_log_p =-3.427 (thresh=-3.4) 1.05994 0.01822 -0.11978 4.38369; 0.02811 1.23790 0.00692 -3.42429; 0.12255 0.01044 1.05800 -34.27070; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.319, old_max_log_p =-3.427 (thresh=-3.4) 1.09896 -0.05605 -0.09317 3.43072; 0.10076 1.16615 0.07151 -13.30936; 0.09088 -0.06897 1.11895 -31.62624; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 18 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.319, old_max_log_p =-3.319 (thresh=-3.3) 1.09896 -0.05605 -0.09317 3.43072; 0.10076 1.16615 0.07151 -13.30936; 0.09088 -0.06897 1.11895 -31.62624; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 18 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.277, old_max_log_p =-3.319 (thresh=-3.3) 1.09658 -0.04692 -0.08317 1.21310; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 18 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.274, old_max_log_p =-3.277 (thresh=-3.3) 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 18 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.274, old_max_log_p =-3.274 (thresh=-3.3) 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.274 (old=-4.494) transform before final EM align: 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 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: 013: -log(p) = 3.8 tol 0.000000 final transform: 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 815196 FSRUNTIME@ mri_em_register 0.0595 hours 4 threads registration took 3 minutes and 34 seconds. @#@FSTIME 2023:02:18:11:48:44 mri_em_register N 7 e 214.11 S 3.17 U 732.36 P 343% M 616608 F 0 R 166708 W 0 c 16122 w 400 I 139952 O 16 L 2.51 2.24 1.31 @#@FSLOADPOST 2023:02:18:11:52:18 mri_em_register N 7 3.50 2.91 1.76 #-------------------------------------- #@# CA Normalize Sat Feb 18 11:52:18 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/7.2.0/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/7.2.0/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=24.9 skull bounding box = (61, 41, 46) --> (193, 150, 201) finding center of left hemi white matter using (105, 77, 124) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (89,64,105) --> (121, 90,143) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.3 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 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58043; 0.08215 -0.06859 1.12363 -31.10372; 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 (122, 37, 47) --> (188, 136, 196) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 4 of 9270 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 40, 49) --> (131, 142, 198) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 5 of 8791 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 110, 68) --> (173, 149, 116) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 581 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 110, 69) --> (127, 151, 120) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 2 of 218 (0.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 105, 101) --> (145, 164, 128) Brain_Stem: limiting intensities to 92.0 --> 132.0 0 of 691 (0.0%) samples deleted using 19551 total control points for intensity normalization... bias field = 0.981 +- 0.062 165 of 19540 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (122, 37, 47) --> (188, 136, 196) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 2 of 9360 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 40, 49) --> (131, 142, 198) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 5 of 8904 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 110, 68) --> (173, 149, 116) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 592 (0.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 110, 69) --> (127, 151, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 281 (4.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 105, 101) --> (145, 164, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 3 of 778 (0.4%) samples deleted using 19915 total control points for intensity normalization... bias field = 1.013 +- 0.048 143 of 19809 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (122, 37, 47) --> (188, 136, 196) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 4 of 9358 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 40, 49) --> (131, 142, 198) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 6 of 8842 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 110, 68) --> (173, 149, 116) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 83 of 586 (14.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 110, 69) --> (127, 151, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 278 (8.6%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 105, 101) --> (145, 164, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 82 of 788 (10.4%) samples deleted using 19852 total control points for intensity normalization... bias field = 1.010 +- 0.039 119 of 19500 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 28 seconds. @#@FSTIME 2023:02:18:11:52:18 mri_ca_normalize N 8 e 87.56 S 0.32 U 89.14 P 102% M 719292 F 5 R 409693 W 0 c 484 w 137 I 1352 O 3736 L 3.50 2.91 1.76 @#@FSLOADPOST 2023:02:18:11:53:45 mri_ca_normalize N 8 1.60 2.43 1.69 #-------------------------------------- #@# CA Reg Sat Feb 18 11:53:45 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/7.2.0/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/7.2.0/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.804059 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.726192) vs oldopt=(dt=369.92,rms=0.748937) #GCMRL# 0 dt 221.952000 rms 0.726 9.684% neg 0 invalid 762 tFOTS 6.0540 tGradient 7.7360 tsec 14.2640 #FOTS# QuadFit found better minimum quadopt=(dt=190.824,rms=0.707337) vs oldopt=(dt=92.48,rms=0.712563) #GCMRL# 1 dt 190.823529 rms 0.707 2.596% neg 0 invalid 762 tFOTS 6.5410 tGradient 8.1990 tsec 15.2400 #FOTS# QuadFit found better minimum quadopt=(dt=161.251,rms=0.697896) vs oldopt=(dt=92.48,rms=0.699853) #GCMRL# 2 dt 161.251397 rms 0.698 1.335% neg 0 invalid 762 tFOTS 6.4490 tGradient 10.2570 tsec 17.1970 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.690658) vs oldopt=(dt=369.92,rms=0.693085) #GCMRL# 3 dt 221.952000 rms 0.691 1.037% neg 0 invalid 762 tFOTS 6.1010 tGradient 9.2810 tsec 16.0560 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.68663) vs oldopt=(dt=92.48,rms=0.687101) #GCMRL# 4 dt 129.472000 rms 0.687 0.583% neg 0 invalid 762 tFOTS 6.6450 tGradient 9.6370 tsec 16.8020 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.680988) vs oldopt=(dt=369.92,rms=0.681095) #GCMRL# 5 dt 443.904000 rms 0.681 0.822% neg 0 invalid 762 tFOTS 6.1690 tGradient 9.0550 tsec 15.6940 #FOTS# QuadFit found better minimum quadopt=(dt=95.3263,rms=0.677519) vs oldopt=(dt=92.48,rms=0.677534) #GCMRL# 6 dt 95.326316 rms 0.678 0.510% neg 0 invalid 762 tFOTS 6.5200 tGradient 8.7190 tsec 15.7130 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.665211) vs oldopt=(dt=1479.68,rms=0.666614) #GCMRL# 7 dt 2071.552000 rms 0.665 1.817% neg 0 invalid 762 tFOTS 6.1460 tGradient 8.7710 tsec 15.3840 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.664127) vs oldopt=(dt=92.48,rms=0.664272) #GCMRL# 8 dt 129.472000 rms 0.664 0.000% neg 0 invalid 762 tFOTS 6.0730 tGradient 8.3950 tsec 14.9530 #GCMRL# 9 dt 129.472000 rms 0.664 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4220 tsec 8.9220 #GCMRL# 10 dt 129.472000 rms 0.663 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8050 tsec 9.2720 #GCMRL# 11 dt 129.472000 rms 0.663 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4940 tsec 8.9690 #GCMRL# 12 dt 129.472000 rms 0.663 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7940 tsec 9.2600 #GCMRL# 13 dt 129.472000 rms 0.663 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8020 tsec 9.2770 #GCMRL# 14 dt 129.472000 rms 0.662 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4310 tsec 8.8920 #GCMRL# 15 dt 129.472000 rms 0.661 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1380 tsec 9.6150 #GCMRL# 16 dt 129.472000 rms 0.660 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4710 tsec 8.9340 #GCMRL# 17 dt 129.472000 rms 0.659 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6540 tsec 9.1300 #GCMRL# 18 dt 129.472000 rms 0.657 0.207% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.2060 tsec 8.6710 #GCMRL# 19 dt 129.472000 rms 0.656 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3570 tsec 8.8190 #GCMRL# 20 dt 129.472000 rms 0.655 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5630 tsec 9.0260 #GCMRL# 21 dt 129.472000 rms 0.654 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7070 tsec 9.1970 #GCMRL# 22 dt 129.472000 rms 0.653 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3830 tsec 8.8430 #GCMRL# 23 dt 129.472000 rms 0.652 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3530 tsec 8.8200 #GCMRL# 24 dt 129.472000 rms 0.651 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4980 tsec 8.9600 #GCMRL# 25 dt 129.472000 rms 0.650 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7130 tsec 9.1730 #GCMRL# 26 dt 129.472000 rms 0.650 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3790 tsec 8.8650 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.64955) vs oldopt=(dt=92.48,rms=0.649561) #GCMRL# 27 dt 129.472000 rms 0.650 0.000% neg 0 invalid 762 tFOTS 6.4120 tGradient 8.5350 tsec 15.4330 #GCMRL# 28 dt 129.472000 rms 0.650 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5270 tsec 9.0040 #GCMRL# 29 dt 129.472000 rms 0.650 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8150 tsec 9.2790 #GCAMreg# pass 0 level1 5 level2 1 tsec 357.731 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.650104 #GCMRL# 31 dt 369.920000 rms 0.648 0.384% neg 0 invalid 762 tFOTS 6.0300 tGradient 8.2850 tsec 14.7730 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.647194) vs oldopt=(dt=92.48,rms=0.647224) #GCMRL# 32 dt 129.472000 rms 0.647 0.000% neg 0 invalid 762 tFOTS 6.0620 tGradient 8.5510 tsec 15.1000 #GCMRL# 33 dt 129.472000 rms 0.647 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4030 tsec 8.8650 #GCMRL# 34 dt 129.472000 rms 0.647 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5470 tsec 9.0130 #GCMRL# 35 dt 129.472000 rms 0.647 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5990 tsec 9.0640 #GCMRL# 36 dt 129.472000 rms 0.646 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.8160 tsec 9.2780 #GCMRL# 37 dt 129.472000 rms 0.646 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5330 tsec 9.0000 #GCMRL# 38 dt 129.472000 rms 0.646 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6080 tsec 9.0780 #GCMRL# 39 dt 129.472000 rms 0.646 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6370 tsec 9.1180 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.657656 #GCMRL# 41 dt 25.920000 rms 0.657 0.172% neg 0 invalid 762 tFOTS 6.0050 tGradient 5.5710 tsec 12.0310 #GCMRL# 42 dt 25.920000 rms 0.656 0.000% neg 0 invalid 762 tFOTS 5.7010 tGradient 5.7590 tsec 11.9410 #GCMRL# 43 dt 25.920000 rms 0.656 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3750 tsec 5.8390 #GCMRL# 44 dt 25.920000 rms 0.656 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6430 tsec 6.1040 #GCMRL# 45 dt 25.920000 rms 0.655 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6960 tsec 6.1580 #GCMRL# 46 dt 25.920000 rms 0.655 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5170 tsec 5.9780 #GCMRL# 47 dt 25.920000 rms 0.653 0.236% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5710 tsec 6.0330 #GCMRL# 48 dt 25.920000 rms 0.651 0.405% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4740 tsec 5.9360 #GCMRL# 49 dt 25.920000 rms 0.647 0.494% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7480 tsec 6.2090 #GCMRL# 50 dt 25.920000 rms 0.644 0.532% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7690 tsec 6.2460 #GCMRL# 51 dt 25.920000 rms 0.641 0.484% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3030 tsec 5.7680 #GCMRL# 52 dt 25.920000 rms 0.638 0.397% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6820 tsec 6.1510 #GCMRL# 53 dt 25.920000 rms 0.636 0.285% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1080 tsec 6.5740 #GCMRL# 54 dt 25.920000 rms 0.635 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7230 tsec 6.1840 #GCMRL# 55 dt 25.920000 rms 0.635 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6860 tsec 6.1480 #GCMRL# 56 dt 25.920000 rms 0.634 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8650 tsec 6.3520 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.633575) vs oldopt=(dt=103.68,rms=0.633634) #GCMRL# 57 dt 145.152000 rms 0.634 0.129% neg 0 invalid 762 tFOTS 6.0260 tGradient 5.8570 tsec 12.3720 #GCMRL# 58 dt 0.450000 rms 0.634 0.000% neg 0 invalid 762 tFOTS 5.6730 tGradient 5.4560 tsec 11.6100 #GCAMreg# pass 0 level1 4 level2 1 tsec 151.022 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.634207 #GCMRL# 60 dt 25.920000 rms 0.633 0.122% neg 0 invalid 762 tFOTS 5.6420 tGradient 5.4670 tsec 11.5640 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.665271 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.664612) vs oldopt=(dt=0.5,rms=0.664619) #GCMRL# 62 dt 0.700000 rms 0.665 0.099% neg 0 invalid 762 tFOTS 5.6400 tGradient 4.0350 tsec 10.1280 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.664591) vs oldopt=(dt=0.125,rms=0.664591) #GCMRL# 63 dt 0.175000 rms 0.665 0.000% neg 0 invalid 762 tFOTS 5.6470 tGradient 4.2220 tsec 10.3750 #GCAMreg# pass 0 level1 3 level2 1 tsec 36.087 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.665217 #GCMRL# 65 dt 0.500000 rms 0.665 0.097% neg 0 invalid 762 tFOTS 5.6970 tGradient 3.8910 tsec 10.0380 #FOTS# QuadFit found better minimum quadopt=(dt=0.04375,rms=0.664563) vs oldopt=(dt=0.03125,rms=0.664563) #GCMRL# 66 dt 0.043750 rms 0.665 0.000% neg 0 invalid 762 tFOTS 5.7140 tGradient 4.2770 tsec 10.4780 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.751694 #FOTS# QuadFit found better minimum quadopt=(dt=2.67702,rms=0.724679) vs oldopt=(dt=2.88,rms=0.724837) #GCMRL# 68 dt 2.677019 rms 0.725 3.594% neg 0 invalid 762 tFOTS 5.5940 tGradient 3.2560 tsec 9.3340 #FOTS# QuadFit found better minimum quadopt=(dt=1.78855,rms=0.721785) vs oldopt=(dt=2.88,rms=0.722802) #GCMRL# 69 dt 1.788546 rms 0.722 0.399% neg 0 invalid 762 tFOTS 5.6830 tGradient 3.0930 tsec 9.2360 #FOTS# QuadFit found better minimum quadopt=(dt=1.36364,rms=0.721192) vs oldopt=(dt=0.72,rms=0.721289) #GCMRL# 70 dt 1.363636 rms 0.721 0.000% neg 0 invalid 762 tFOTS 5.6460 tGradient 3.1560 tsec 9.2880 #GCAMreg# pass 0 level1 2 level2 1 tsec 42.753 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.721789 #FOTS# QuadFit found better minimum quadopt=(dt=0.01575,rms=0.721193) vs oldopt=(dt=0.01125,rms=0.721193) #GCMRL# 72 dt 0.015750 rms 0.721 0.083% neg 0 invalid 762 tFOTS 5.3220 tGradient 3.1590 tsec 8.9340 #FOTS# QuadFit found better minimum quadopt=(dt=0.00225,rms=0.721193) vs oldopt=(dt=0.0028125,rms=0.721193) #GCMRL# 73 dt 0.002250 rms 0.721 0.000% neg 0 invalid 762 tFOTS 5.6780 tGradient 3.1880 tsec 9.3550 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.788801 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.786702) vs oldopt=(dt=0.32,rms=0.786773) #GCMRL# 75 dt 0.384000 rms 0.787 0.266% neg 0 invalid 762 tFOTS 5.6440 tGradient 2.4330 tsec 8.5330 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.77994) vs oldopt=(dt=1.28,rms=0.780273) #GCMRL# 76 dt 1.024000 rms 0.780 0.860% neg 0 invalid 762 tFOTS 5.6740 tGradient 2.4800 tsec 8.6140 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.77835) vs oldopt=(dt=0.32,rms=0.778821) #GCMRL# 77 dt 0.192000 rms 0.778 0.000% neg 0 invalid 762 tFOTS 5.6760 tGradient 2.5730 tsec 8.7320 #GCMRL# 78 dt 0.192000 rms 0.778 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6690 tsec 3.1330 #GCMRL# 79 dt 0.192000 rms 0.777 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7980 tsec 3.2620 #GCMRL# 80 dt 0.192000 rms 0.775 0.234% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4960 tsec 2.9580 #GCMRL# 81 dt 0.192000 rms 0.773 0.354% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6740 tsec 3.1260 #GCMRL# 82 dt 0.192000 rms 0.771 0.267% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5410 tsec 2.9970 #GCMRL# 83 dt 0.192000 rms 0.770 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6550 tsec 3.1190 #GCMRL# 84 dt 0.192000 rms 0.770 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8660 tsec 3.3260 #GCMRL# 85 dt 0.192000 rms 0.770 -0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6250 tsec 3.4720 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.768662) vs oldopt=(dt=0.32,rms=0.768846) #GCMRL# 86 dt 0.448000 rms 0.769 0.119% neg 0 invalid 762 tFOTS 5.6670 tGradient 2.6350 tsec 8.7670 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.768105) vs oldopt=(dt=0.32,rms=0.768138) #GCAMreg# pass 0 level1 1 level2 1 tsec 79.412 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.768703 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.766966) vs oldopt=(dt=0.32,rms=0.767014) #GCMRL# 88 dt 0.384000 rms 0.767 0.226% neg 0 invalid 762 tFOTS 5.6870 tGradient 2.7530 tsec 8.9070 #FOTS# QuadFit found better minimum quadopt=(dt=0.096,rms=0.76689) vs oldopt=(dt=0.08,rms=0.76689) #GCMRL# 89 dt 0.096000 rms 0.767 0.000% neg 0 invalid 762 tFOTS 5.6850 tGradient 2.4750 tsec 8.6430 #GCMRL# 90 dt 0.096000 rms 0.767 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5930 tsec 3.0600 #GCMRL# 91 dt 0.096000 rms 0.767 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6220 tsec 3.0820 #GCMRL# 92 dt 0.096000 rms 0.767 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4470 tsec 2.9170 #GCMRL# 93 dt 0.096000 rms 0.766 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6060 tsec 3.0800 #GCMRL# 94 dt 0.096000 rms 0.766 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5770 tsec 3.0440 #GCMRL# 95 dt 0.096000 rms 0.766 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6760 tsec 3.1350 #GCMRL# 96 dt 0.096000 rms 0.765 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7350 tsec 3.1970 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.728772 #FOTS# QuadFit found better minimum quadopt=(dt=0.220568,rms=0.723563) vs oldopt=(dt=0.32,rms=0.724258) #GCMRL# 98 dt 0.220568 rms 0.724 0.715% neg 0 invalid 762 tFOTS 5.6240 tGradient 2.0080 tsec 8.0800 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.723334) vs oldopt=(dt=0.02,rms=0.723335) #GCMRL# 99 dt 0.024000 rms 0.723 0.000% neg 0 invalid 762 tFOTS 5.6750 tGradient 1.9580 tsec 8.1170 #GCAMreg# pass 0 level1 0 level2 1 tsec 29.768 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.723937 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.723331) vs oldopt=(dt=0.005,rms=0.723335) #GCMRL# 101 dt 0.007000 rms 0.723 0.084% neg 0 invalid 762 tFOTS 5.6570 tGradient 1.9520 tsec 8.0650 #FOTS# QuadFit found better minimum quadopt=(dt=0.00175,rms=0.723318) vs oldopt=(dt=0.00125,rms=0.723318) #GCMRL# 102 dt 0.001750 rms 0.723 0.000% neg 0 invalid 762 tFOTS 5.6770 tGradient 1.8650 tsec 8.0290 GCAMregister done in 15.828 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.30013 (23) Left_Lateral_Ventricle (4): linear fit = 1.25 x + 0.0 (893 voxels, overlap=0.462) Left_Lateral_Ventricle (4): linear fit = 1.25 x + 0.0 (893 voxels, peak = 20), gca=19.9 gca peak = 0.17690 (16) mri peak = 0.24118 (23) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (679 voxels, overlap=0.355) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (679 voxels, peak = 22), gca=22.5 gca peak = 0.28275 (96) mri peak = 0.16220 (101) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (743 voxels, overlap=0.550) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (743 voxels, peak = 102), gca=102.2 gca peak = 0.18948 (93) mri peak = 0.14687 (103) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (683 voxels, overlap=0.640) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (683 voxels, peak = 100), gca=100.0 gca peak = 0.20755 (55) mri peak = 0.07526 (75) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (765 voxels, overlap=0.018) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (765 voxels, peak = 70), gca=69.6 gca peak = 0.31831 (58) mri peak = 0.09594 (70) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (686 voxels, overlap=0.010) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (686 voxels, peak = 70), gca=70.5 gca peak = 0.11957 (102) mri peak = 0.20429 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (50608 voxels, overlap=0.505) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (50608 voxels, peak = 106), gca=105.6 gca peak = 0.11429 (102) mri peak = 0.19211 (107) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (53526 voxels, overlap=0.366) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (53526 voxels, peak = 107), gca=106.6 gca peak = 0.14521 (59) mri peak = 0.03336 (66) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (20149 voxels, overlap=0.441) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (20149 voxels, peak = 68), gca=67.6 gca peak = 0.14336 (58) mri peak = 0.03794 (66) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (18465 voxels, overlap=0.788) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (18465 voxels, peak = 66), gca=66.4 gca peak = 0.13305 (70) mri peak = 0.18345 (74) Right_Caudate (50): linear fit = 1.11 x + 0.0 (508 voxels, overlap=0.124) Right_Caudate (50): linear fit = 1.11 x + 0.0 (508 voxels, peak = 77), gca=77.3 gca peak = 0.15761 (71) mri peak = 0.19708 (79) Left_Caudate (11): linear fit = 1.07 x + 0.0 (774 voxels, overlap=0.469) Left_Caudate (11): linear fit = 1.07 x + 0.0 (774 voxels, peak = 76), gca=75.6 gca peak = 0.13537 (57) mri peak = 0.04038 (64) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21324 voxels, overlap=0.721) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21324 voxels, peak = 64), gca=63.6 gca peak = 0.13487 (56) mri peak = 0.03305 (62) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (20366 voxels, overlap=0.175) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (20366 voxels, peak = 67), gca=67.5 gca peak = 0.19040 (84) mri peak = 0.08559 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7432 voxels, overlap=0.542) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7432 voxels, peak = 89), gca=89.5 gca peak = 0.18871 (83) mri peak = 0.08175 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5793 voxels, overlap=0.016) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5793 voxels, peak = 92), gca=91.7 gca peak = 0.24248 (57) mri peak = 0.10788 (71) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (359 voxels, overlap=0.047) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (359 voxels, peak = 70), gca=69.8 gca peak = 0.35833 (56) mri peak = 0.11247 (71) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (413 voxels, overlap=0.040) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (413 voxels, peak = 70), gca=69.7 gca peak = 0.12897 (85) mri peak = 0.07070 (91) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4443 voxels, overlap=0.851) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4443 voxels, peak = 91), gca=90.5 gca peak = 0.13127 (83) mri peak = 0.07833 (88) Right_Thalamus (49): linear fit = 1.08 x + 0.0 (3686 voxels, overlap=0.655) Right_Thalamus (49): linear fit = 1.08 x + 0.0 (3686 voxels, peak = 89), gca=89.2 gca peak = 0.12974 (78) mri peak = 0.08651 (85) Left_Putamen (12): linear fit = 1.11 x + 0.0 (1969 voxels, overlap=0.519) Left_Putamen (12): linear fit = 1.11 x + 0.0 (1969 voxels, peak = 86), gca=86.2 gca peak = 0.17796 (79) mri peak = 0.12725 (84) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1965 voxels, overlap=0.594) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1965 voxels, peak = 87), gca=86.5 gca peak = 0.10999 (80) mri peak = 0.09567 (93) Brain_Stem (16): linear fit = 1.14 x + 0.0 (8804 voxels, overlap=0.128) Brain_Stem (16): linear fit = 1.14 x + 0.0 (8804 voxels, peak = 92), gca=91.6 gca peak = 0.13215 (88) mri peak = 0.11331 (97) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (726 voxels, overlap=0.131) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (726 voxels, peak = 98), gca=98.1 gca peak = 0.11941 (89) mri peak = 0.12461 (99) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1009 voxels, overlap=0.164) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1009 voxels, peak = 98), gca=98.3 gca peak = 0.20775 (25) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13297 (21) mri peak = 0.27817 (23) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (483 voxels, overlap=0.389) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (483 voxels, peak = 26), gca=26.1 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.21 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.30 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 3.05402 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.736118 #FOTS# QuadFit found better minimum quadopt=(dt=191.693,rms=0.692412) vs oldopt=(dt=92.48,rms=0.70445) #GCMRL# 104 dt 191.692800 rms 0.692 5.937% neg 0 invalid 762 tFOTS 5.9100 tGradient 2.9300 tsec 9.3030 #FOTS# QuadFit found better minimum quadopt=(dt=324.485,rms=0.675035) vs oldopt=(dt=369.92,rms=0.675378) #GCMRL# 105 dt 324.485175 rms 0.675 2.510% neg 0 invalid 762 tFOTS 6.0010 tGradient 2.9480 tsec 9.4090 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.670308) vs oldopt=(dt=92.48,rms=0.670837) #GCMRL# 106 dt 129.472000 rms 0.670 0.700% neg 0 invalid 762 tFOTS 6.0130 tGradient 2.9610 tsec 9.4390 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.661741) vs oldopt=(dt=369.92,rms=0.663123) #GCMRL# 107 dt 517.888000 rms 0.662 1.278% neg 0 invalid 762 tFOTS 6.0760 tGradient 3.0070 tsec 9.5440 #GCMRL# 108 dt 92.480000 rms 0.659 0.356% neg 0 invalid 762 tFOTS 6.3670 tGradient 3.1260 tsec 9.9600 #GCMRL# 109 dt 1479.680000 rms 0.651 1.329% neg 0 invalid 762 tFOTS 6.0520 tGradient 2.9910 tsec 9.5110 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.648101) vs oldopt=(dt=92.48,rms=0.648389) #GCMRL# 110 dt 129.472000 rms 0.648 0.388% neg 0 invalid 762 tFOTS 6.0420 tGradient 2.9010 tsec 9.4140 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.646911) vs oldopt=(dt=369.92,rms=0.646933) #GCMRL# 111 dt 295.936000 rms 0.647 0.184% neg 0 invalid 762 tFOTS 6.0750 tGradient 2.9360 tsec 9.4830 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.646412) vs oldopt=(dt=92.48,rms=0.646417) #GCMRL# 112 dt 110.976000 rms 0.646 0.077% neg 0 invalid 762 tFOTS 6.0550 tGradient 3.2230 tsec 9.7360 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.645189) vs oldopt=(dt=369.92,rms=0.645336) #GCMRL# 113 dt 517.888000 rms 0.645 0.189% neg 0 invalid 762 tFOTS 6.4350 tGradient 3.1280 tsec 10.0220 #GCMRL# 114 dt 92.480000 rms 0.644 0.116% neg 0 invalid 762 tFOTS 6.0400 tGradient 2.9190 tsec 9.4240 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.640272) vs oldopt=(dt=1479.68,rms=0.640901) #GCMRL# 115 dt 2071.552000 rms 0.640 0.647% neg 0 invalid 762 tFOTS 6.4490 tGradient 3.1080 tsec 10.0270 #GCMRL# 116 dt 92.480000 rms 0.639 0.206% neg 0 invalid 762 tFOTS 6.4140 tGradient 3.2920 tsec 10.1700 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.638502) vs oldopt=(dt=369.92,rms=0.638523) #GCMRL# 117 dt 295.936000 rms 0.639 0.071% neg 0 invalid 762 tFOTS 6.1110 tGradient 3.0920 tsec 9.6710 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.638051) vs oldopt=(dt=369.92,rms=0.63811) #GCMRL# 118 dt 295.936000 rms 0.638 0.071% neg 0 invalid 762 tFOTS 6.3800 tGradient 3.1350 tsec 9.9920 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.637593) vs oldopt=(dt=92.48,rms=0.637651) #GCMRL# 119 dt 129.472000 rms 0.638 0.072% neg 0 invalid 762 tFOTS 6.0580 tGradient 3.0890 tsec 9.6170 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.637424) vs oldopt=(dt=92.48,rms=0.637458) #GCMRL# 120 dt 129.472000 rms 0.637 0.000% neg 0 invalid 762 tFOTS 6.3960 tGradient 3.1800 tsec 10.0640 #GCMRL# 121 dt 129.472000 rms 0.637 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1630 tsec 3.6250 #GCMRL# 122 dt 129.472000 rms 0.637 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1160 tsec 3.5840 #GCMRL# 123 dt 129.472000 rms 0.636 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1730 tsec 3.6340 #GCMRL# 124 dt 129.472000 rms 0.635 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1360 tsec 3.6000 #GCMRL# 125 dt 129.472000 rms 0.635 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0930 tsec 3.5550 #GCMRL# 126 dt 129.472000 rms 0.634 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0430 tsec 3.5080 #GCMRL# 127 dt 129.472000 rms 0.633 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0620 tsec 3.5260 #GCMRL# 128 dt 129.472000 rms 0.632 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0590 tsec 3.5190 #GCMRL# 129 dt 129.472000 rms 0.631 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9170 tsec 3.3860 #GCMRL# 130 dt 129.472000 rms 0.630 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0860 tsec 3.5530 #GCMRL# 131 dt 129.472000 rms 0.629 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0720 tsec 3.5340 #GCMRL# 132 dt 129.472000 rms 0.628 0.153% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9420 tsec 3.4040 #GCMRL# 133 dt 129.472000 rms 0.627 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9490 tsec 3.4150 #GCMRL# 134 dt 129.472000 rms 0.626 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0400 tsec 3.5010 #GCMRL# 135 dt 129.472000 rms 0.625 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1000 tsec 3.5700 #GCMRL# 136 dt 129.472000 rms 0.624 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8870 tsec 3.3460 #GCMRL# 137 dt 129.472000 rms 0.623 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0780 tsec 3.5320 #GCMRL# 138 dt 129.472000 rms 0.623 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9900 tsec 3.4560 #GCMRL# 139 dt 129.472000 rms 0.622 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9860 tsec 3.4570 #GCMRL# 140 dt 129.472000 rms 0.621 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1400 tsec 3.5990 #GCMRL# 141 dt 129.472000 rms 0.620 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0020 tsec 3.4700 #GCMRL# 142 dt 129.472000 rms 0.620 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9660 tsec 3.4330 #GCMRL# 143 dt 129.472000 rms 0.619 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0070 tsec 3.4710 #GCMRL# 144 dt 129.472000 rms 0.618 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1590 tsec 3.6230 #GCMRL# 145 dt 129.472000 rms 0.618 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1240 tsec 3.5870 #GCMRL# 146 dt 129.472000 rms 0.617 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9670 tsec 3.4340 #GCMRL# 147 dt 129.472000 rms 0.617 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8930 tsec 3.3530 #GCMRL# 148 dt 129.472000 rms 0.616 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9700 tsec 3.4310 #GCMRL# 149 dt 129.472000 rms 0.616 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9650 tsec 3.4340 #GCMRL# 150 dt 129.472000 rms 0.615 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8970 tsec 3.3480 #GCMRL# 151 dt 129.472000 rms 0.615 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0780 tsec 3.5330 #GCMRL# 152 dt 129.472000 rms 0.614 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9830 tsec 3.4500 #GCMRL# 153 dt 129.472000 rms 0.614 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9390 tsec 3.3960 #GCMRL# 154 dt 129.472000 rms 0.614 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7950 tsec 3.2560 #GCMRL# 155 dt 129.472000 rms 0.613 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0890 tsec 3.5640 #GCMRL# 156 dt 129.472000 rms 0.613 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 3.5020 #GCMRL# 157 dt 129.472000 rms 0.612 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7800 tsec 3.2480 #GCMRL# 158 dt 129.472000 rms 0.612 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1560 tsec 3.6260 #GCMRL# 159 dt 129.472000 rms 0.612 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0780 tsec 3.5390 #GCMRL# 160 dt 129.472000 rms 0.611 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9620 tsec 3.4150 #GCMRL# 161 dt 129.472000 rms 0.611 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0050 tsec 3.4660 #GCMRL# 162 dt 129.472000 rms 0.611 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0460 tsec 3.5080 #GCMRL# 163 dt 129.472000 rms 0.610 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 3.5020 #GCMRL# 164 dt 129.472000 rms 0.610 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1020 tsec 3.5640 #GCMRL# 165 dt 129.472000 rms 0.610 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0450 tsec 3.5200 #GCMRL# 166 dt 129.472000 rms 0.610 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0990 tsec 3.5630 #GCMRL# 167 dt 129.472000 rms 0.609 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9760 tsec 3.4410 #GCMRL# 168 dt 129.472000 rms 0.609 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8490 tsec 3.3140 #GCMRL# 169 dt 129.472000 rms 0.609 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9280 tsec 3.3910 #GCMRL# 170 dt 129.472000 rms 0.609 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1770 tsec 3.6360 #GCMRL# 171 dt 129.472000 rms 0.609 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2040 tsec 3.6640 #GCMRL# 172 dt 129.472000 rms 0.608 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9940 tsec 3.4570 #GCMRL# 173 dt 129.472000 rms 0.608 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2560 tsec 3.7170 #GCMRL# 174 dt 129.472000 rms 0.608 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2020 tsec 3.6680 #GCMRL# 175 dt 129.472000 rms 0.608 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1520 tsec 3.6140 #GCMRL# 176 dt 129.472000 rms 0.608 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1990 tsec 3.6690 #GCMRL# 177 dt 129.472000 rms 0.607 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1980 tsec 3.6600 #GCMRL# 178 dt 129.472000 rms 0.607 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0370 tsec 3.5040 #GCMRL# 179 dt 129.472000 rms 0.607 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8790 tsec 3.3400 #GCMRL# 180 dt 129.472000 rms 0.607 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8750 tsec 3.3350 #GCMRL# 181 dt 129.472000 rms 0.607 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0080 tsec 3.4680 #GCMRL# 182 dt 129.472000 rms 0.607 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0870 tsec 3.5720 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.60628) vs oldopt=(dt=1479.68,rms=0.606298) #GCMRL# 183 dt 1183.744000 rms 0.606 0.040% neg 0 invalid 762 tFOTS 6.3800 tGradient 3.0640 tsec 9.9110 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.606263) vs oldopt=(dt=23.12,rms=0.606271) #GCMRL# 184 dt 32.368000 rms 0.606 0.000% neg 0 invalid 762 tFOTS 6.4110 tGradient 2.9750 tsec 9.8750 #GCMRL# 185 dt 32.368000 rms 0.606 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9860 tsec 3.4500 #GCAMreg# pass 0 level1 5 level2 1 tsec 416.621 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.606575 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.604901) vs oldopt=(dt=369.92,rms=0.604961) #GCMRL# 187 dt 295.936000 rms 0.605 0.276% neg 0 invalid 762 tFOTS 6.0330 tGradient 2.8530 tsec 9.3650 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.604496) vs oldopt=(dt=92.48,rms=0.604559) #GCMRL# 188 dt 129.472000 rms 0.604 0.067% neg 0 invalid 762 tFOTS 6.0580 tGradient 3.2740 tsec 9.7990 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.60421) vs oldopt=(dt=369.92,rms=0.604234) #GCMRL# 189 dt 517.888000 rms 0.604 0.000% neg 0 invalid 762 tFOTS 6.5090 tGradient 3.1280 tsec 10.1460 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.606579 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.602882) vs oldopt=(dt=103.68,rms=0.60311) #GCMRL# 191 dt 145.152000 rms 0.603 0.609% neg 0 invalid 762 tFOTS 6.7770 tGradient 3.1340 tsec 10.4220 #FOTS# QuadFit found better minimum quadopt=(dt=154.318,rms=0.595776) vs oldopt=(dt=103.68,rms=0.59649) #GCMRL# 192 dt 154.317757 rms 0.596 1.179% neg 0 invalid 762 tFOTS 7.2300 tGradient 2.9190 tsec 10.6840 #FOTS# QuadFit found better minimum quadopt=(dt=66.3273,rms=0.592551) vs oldopt=(dt=25.92,rms=0.593309) #GCMRL# 193 dt 66.327273 rms 0.593 0.541% neg 0 invalid 762 tFOTS 6.8850 tGradient 3.1260 tsec 10.5160 #FOTS# QuadFit found better minimum quadopt=(dt=140.642,rms=0.589493) vs oldopt=(dt=103.68,rms=0.589656) #GCMRL# 194 dt 140.641975 rms 0.589 0.516% neg 0 invalid 762 tFOTS 6.7870 tGradient 3.0110 tsec 10.3680 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.587204) vs oldopt=(dt=25.92,rms=0.587676) #GCMRL# 195 dt 36.288000 rms 0.587 0.388% neg 0 invalid 762 tFOTS 6.8190 tGradient 3.2080 tsec 10.5420 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.582305) vs oldopt=(dt=414.72,rms=0.582496) #GCMRL# 196 dt 331.776000 rms 0.582 0.834% neg 0 invalid 762 tFOTS 6.8370 tGradient 3.1320 tsec 10.5100 #FOTS# QuadFit found better minimum quadopt=(dt=60.5867,rms=0.578596) vs oldopt=(dt=25.92,rms=0.579552) #GCMRL# 197 dt 60.586667 rms 0.579 0.637% neg 0 invalid 762 tFOTS 6.8860 tGradient 2.8120 tsec 10.1990 #FOTS# QuadFit found better minimum quadopt=(dt=95.2195,rms=0.576945) vs oldopt=(dt=103.68,rms=0.576958) #GCMRL# 198 dt 95.219512 rms 0.577 0.285% neg 0 invalid 762 tFOTS 7.2450 tGradient 3.1340 tsec 10.9310 #FOTS# QuadFit found better minimum quadopt=(dt=70.5306,rms=0.575711) vs oldopt=(dt=103.68,rms=0.575975) #GCMRL# 199 dt 70.530612 rms 0.576 0.214% neg 0 invalid 762 tFOTS 6.7980 tGradient 2.8960 tsec 10.2300 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.574162) vs oldopt=(dt=103.68,rms=0.574174) #GCMRL# 200 dt 124.416000 rms 0.574 0.269% neg 0 invalid 762 tFOTS 6.7770 tGradient 3.0730 tsec 10.4190 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.573067) vs oldopt=(dt=25.92,rms=0.573287) #GCMRL# 201 dt 36.288000 rms 0.573 0.191% neg 0 invalid 762 tFOTS 6.9730 tGradient 3.0700 tsec 10.5680 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.569379) vs oldopt=(dt=414.72,rms=0.569511) #GCMRL# 202 dt 497.664000 rms 0.569 0.644% neg 0 invalid 762 tFOTS 6.8740 tGradient 3.0020 tsec 10.4020 #FOTS# QuadFit found better minimum quadopt=(dt=57.1429,rms=0.566296) vs oldopt=(dt=25.92,rms=0.566971) #GCMRL# 203 dt 57.142857 rms 0.566 0.541% neg 0 invalid 762 tFOTS 6.8380 tGradient 2.8910 tsec 10.2830 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.565525) vs oldopt=(dt=103.68,rms=0.565611) #GCMRL# 204 dt 82.944000 rms 0.566 0.136% neg 0 invalid 762 tFOTS 6.7970 tGradient 2.7260 tsec 10.0620 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.564665) vs oldopt=(dt=103.68,rms=0.564731) #GCMRL# 205 dt 82.944000 rms 0.565 0.152% neg 0 invalid 762 tFOTS 7.0180 tGradient 3.1850 tsec 10.7270 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.564011) vs oldopt=(dt=103.68,rms=0.564105) #GCMRL# 206 dt 82.944000 rms 0.564 0.116% neg 0 invalid 762 tFOTS 6.4070 tGradient 2.9090 tsec 9.8390 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.563226) vs oldopt=(dt=103.68,rms=0.563312) #GCMRL# 207 dt 82.944000 rms 0.563 0.139% neg 0 invalid 762 tFOTS 6.4400 tGradient 2.9250 tsec 9.8690 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.562591) vs oldopt=(dt=103.68,rms=0.562741) #GCMRL# 208 dt 62.208000 rms 0.563 0.113% neg 0 invalid 762 tFOTS 6.4250 tGradient 2.7750 tsec 9.6910 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.561696) vs oldopt=(dt=103.68,rms=0.561808) #GCMRL# 209 dt 145.152000 rms 0.562 0.159% neg 0 invalid 762 tFOTS 6.8880 tGradient 2.8320 tsec 10.2680 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.561109) vs oldopt=(dt=25.92,rms=0.561229) #GCMRL# 210 dt 36.288000 rms 0.561 0.105% neg 0 invalid 762 tFOTS 6.5100 tGradient 2.7850 tsec 9.7960 #FOTS# QuadFit found better minimum quadopt=(dt=995.328,rms=0.556714) vs oldopt=(dt=1658.88,rms=0.5574) #GCMRL# 211 dt 995.328000 rms 0.557 0.783% neg 0 invalid 762 tFOTS 6.9580 tGradient 2.7870 tsec 10.2780 #FOTS# QuadFit found better minimum quadopt=(dt=61.3333,rms=0.554412) vs oldopt=(dt=25.92,rms=0.554879) #GCMRL# 212 dt 61.333333 rms 0.554 0.413% neg 0 invalid 762 tFOTS 6.7860 tGradient 3.0210 tsec 10.3630 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.553819) vs oldopt=(dt=103.68,rms=0.553999) #GCMRL# 213 dt 62.208000 rms 0.554 0.107% neg 0 invalid 762 tFOTS 6.5230 tGradient 2.8210 tsec 9.8910 #GCMRL# 214 dt 103.680000 rms 0.553 0.092% neg 0 invalid 762 tFOTS 6.9030 tGradient 2.7170 tsec 10.1510 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.552924) vs oldopt=(dt=103.68,rms=0.55304) #GCMRL# 215 dt 62.208000 rms 0.553 0.070% neg 0 invalid 762 tFOTS 6.9540 tGradient 2.6960 tsec 10.2340 #GCMRL# 216 dt 103.680000 rms 0.553 0.075% neg 0 invalid 762 tFOTS 6.8220 tGradient 2.7550 tsec 10.0950 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.552232) vs oldopt=(dt=25.92,rms=0.552286) #GCMRL# 217 dt 36.288000 rms 0.552 0.050% neg 0 invalid 762 tFOTS 7.3250 tGradient 2.9720 tsec 10.8090 #FOTS# QuadFit found better minimum quadopt=(dt=2322.43,rms=0.544943) vs oldopt=(dt=1658.88,rms=0.546173) #GCMRL# 218 dt 2322.432000 rms 0.545 1.320% neg 0 invalid 762 tFOTS 6.9490 tGradient 2.6710 tsec 10.1360 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.543331) vs oldopt=(dt=25.92,rms=0.543585) #GCMRL# 219 dt 36.288000 rms 0.543 0.296% neg 0 invalid 762 tFOTS 6.8740 tGradient 2.8190 tsec 10.2590 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.543116) vs oldopt=(dt=25.92,rms=0.543138) #GCMRL# 220 dt 36.288000 rms 0.543 0.000% neg 0 invalid 762 tFOTS 7.3080 tGradient 2.9260 tsec 10.8560 #GCMRL# 221 dt 36.288000 rms 0.543 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9620 tsec 3.4900 #GCMRL# 222 dt 36.288000 rms 0.543 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7300 tsec 3.2560 #GCMRL# 223 dt 36.288000 rms 0.543 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9480 tsec 3.4910 #GCMRL# 224 dt 36.288000 rms 0.542 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6920 tsec 3.2040 #GCMRL# 225 dt 36.288000 rms 0.542 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9220 tsec 3.4500 #GCMRL# 226 dt 36.288000 rms 0.542 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6690 tsec 3.2120 #GCMRL# 227 dt 36.288000 rms 0.541 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7440 tsec 3.2600 #GCMRL# 228 dt 36.288000 rms 0.541 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5460 tsec 3.0670 #GCMRL# 229 dt 36.288000 rms 0.540 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7610 tsec 3.3250 #GCMRL# 230 dt 36.288000 rms 0.540 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7540 tsec 3.3030 #GCMRL# 231 dt 36.288000 rms 0.539 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6670 tsec 3.2420 #GCMRL# 232 dt 36.288000 rms 0.539 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6990 tsec 3.2720 #GCMRL# 233 dt 36.288000 rms 0.538 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8090 tsec 3.3610 #GCMRL# 234 dt 36.288000 rms 0.538 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7180 tsec 3.2180 #GCMRL# 235 dt 36.288000 rms 0.537 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8620 tsec 3.4380 #GCMRL# 236 dt 36.288000 rms 0.537 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8200 tsec 3.3360 #GCMRL# 237 dt 36.288000 rms 0.536 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7300 tsec 3.2690 #GCMRL# 238 dt 36.288000 rms 0.536 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7560 tsec 3.2940 #GCMRL# 239 dt 36.288000 rms 0.535 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7460 tsec 3.2790 #GCMRL# 240 dt 36.288000 rms 0.535 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7780 tsec 3.3010 #GCMRL# 241 dt 36.288000 rms 0.534 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6810 tsec 3.2610 #GCMRL# 242 dt 36.288000 rms 0.534 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7610 tsec 3.3170 #GCMRL# 243 dt 36.288000 rms 0.533 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7440 tsec 3.2950 #GCMRL# 244 dt 36.288000 rms 0.533 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6630 tsec 3.1960 #GCMRL# 245 dt 36.288000 rms 0.533 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6980 tsec 3.2570 #GCMRL# 246 dt 36.288000 rms 0.532 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6440 tsec 3.1730 #GCMRL# 247 dt 36.288000 rms 0.532 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8030 tsec 3.3200 #GCMRL# 248 dt 36.288000 rms 0.531 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7490 tsec 3.3130 #GCMRL# 249 dt 36.288000 rms 0.531 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6250 tsec 3.1590 #GCMRL# 250 dt 36.288000 rms 0.531 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8190 tsec 3.3580 #GCMRL# 251 dt 36.288000 rms 0.530 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8930 tsec 3.4030 #GCMRL# 252 dt 36.288000 rms 0.530 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7620 tsec 3.3000 #GCMRL# 253 dt 36.288000 rms 0.530 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6370 tsec 3.1870 #GCMRL# 254 dt 36.288000 rms 0.529 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7440 tsec 3.2810 #GCMRL# 255 dt 36.288000 rms 0.529 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9510 tsec 3.5250 #GCMRL# 256 dt 36.288000 rms 0.529 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7470 tsec 3.2780 #GCMRL# 257 dt 36.288000 rms 0.528 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6040 tsec 3.1270 #GCMRL# 258 dt 36.288000 rms 0.528 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6630 tsec 3.2450 #GCMRL# 259 dt 36.288000 rms 0.528 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8960 tsec 3.4420 #GCMRL# 260 dt 36.288000 rms 0.528 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7810 tsec 3.3830 #GCMRL# 261 dt 36.288000 rms 0.527 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5810 tsec 3.1560 #GCMRL# 262 dt 36.288000 rms 0.527 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5920 tsec 3.1190 #GCMRL# 263 dt 36.288000 rms 0.527 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7110 tsec 3.2950 #GCMRL# 264 dt 36.288000 rms 0.527 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7010 tsec 3.2410 #GCMRL# 265 dt 36.288000 rms 0.526 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6370 tsec 3.1440 #GCMRL# 266 dt 36.288000 rms 0.526 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6390 tsec 3.1870 #GCMRL# 267 dt 36.288000 rms 0.526 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6740 tsec 3.2110 #GCMRL# 268 dt 36.288000 rms 0.526 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7400 tsec 3.2430 #GCMRL# 269 dt 36.288000 rms 0.525 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5820 tsec 3.1120 #GCMRL# 270 dt 36.288000 rms 0.525 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6290 tsec 3.1790 #GCMRL# 271 dt 36.288000 rms 0.525 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7940 tsec 3.3590 #GCMRL# 272 dt 36.288000 rms 0.525 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6070 tsec 3.1410 #GCMRL# 273 dt 36.288000 rms 0.525 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7970 tsec 3.3070 #GCMRL# 274 dt 36.288000 rms 0.524 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7100 tsec 3.2340 #GCMRL# 275 dt 36.288000 rms 0.524 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7230 tsec 3.2570 #GCMRL# 276 dt 36.288000 rms 0.524 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6700 tsec 3.1830 #GCMRL# 277 dt 36.288000 rms 0.524 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6080 tsec 3.1570 #GCMRL# 278 dt 36.288000 rms 0.524 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5610 tsec 3.1010 #GCMRL# 279 dt 36.288000 rms 0.523 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5280 tsec 3.0650 #GCMRL# 280 dt 36.288000 rms 0.523 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5860 tsec 3.1610 #GCMRL# 281 dt 36.288000 rms 0.523 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5970 tsec 3.1140 #GCMRL# 282 dt 36.288000 rms 0.523 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5410 tsec 3.0620 #GCMRL# 283 dt 36.288000 rms 0.523 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5910 tsec 3.1440 #GCMRL# 284 dt 36.288000 rms 0.522 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5770 tsec 3.1280 #GCMRL# 285 dt 36.288000 rms 0.522 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5330 tsec 3.0590 #GCMRL# 286 dt 36.288000 rms 0.522 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6980 tsec 3.2590 #GCMRL# 287 dt 36.288000 rms 0.522 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7050 tsec 3.2280 #GCMRL# 288 dt 36.288000 rms 0.522 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5360 tsec 3.0780 #GCMRL# 289 dt 36.288000 rms 0.522 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7010 tsec 3.2440 #GCMRL# 290 dt 36.288000 rms 0.522 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6840 tsec 3.2120 #GCMRL# 291 dt 36.288000 rms 0.521 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6460 tsec 3.1640 #GCMRL# 292 dt 36.288000 rms 0.521 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5850 tsec 3.0920 #GCMRL# 293 dt 36.288000 rms 0.521 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6840 tsec 3.2050 #GCMRL# 294 dt 36.288000 rms 0.521 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5790 tsec 3.1270 #GCMRL# 295 dt 36.288000 rms 0.521 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5630 tsec 3.0860 #GCMRL# 296 dt 36.288000 rms 0.521 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6420 tsec 3.2030 #GCMRL# 297 dt 36.288000 rms 0.521 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6680 tsec 3.2300 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.520332) vs oldopt=(dt=414.72,rms=0.520376) #GCMRL# 298 dt 580.608000 rms 0.520 0.047% neg 0 invalid 762 tFOTS 7.4250 tGradient 2.6770 tsec 10.6510 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.520311) vs oldopt=(dt=25.92,rms=0.520313) #GCMRL# 299 dt 36.288000 rms 0.520 0.000% neg 0 invalid 762 tFOTS 7.4280 tGradient 2.5940 tsec 10.5720 #GCMRL# 300 dt 36.288000 rms 0.520 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6730 tsec 3.2040 #GCAMreg# pass 0 level1 4 level2 1 tsec 595.628 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.520792 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.518289) vs oldopt=(dt=103.68,rms=0.518413) #GCMRL# 302 dt 145.152000 rms 0.518 0.481% neg 0 invalid 762 tFOTS 6.4530 tGradient 2.6940 tsec 9.7010 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.517789) vs oldopt=(dt=103.68,rms=0.517925) #GCMRL# 303 dt 62.208000 rms 0.518 0.096% neg 0 invalid 762 tFOTS 6.9300 tGradient 2.5590 tsec 10.0340 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.517321) vs oldopt=(dt=103.68,rms=0.517405) #GCMRL# 304 dt 145.152000 rms 0.517 0.090% neg 0 invalid 762 tFOTS 7.0600 tGradient 2.6310 tsec 10.2650 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.517055) vs oldopt=(dt=103.68,rms=0.51707) #GCMRL# 305 dt 82.944000 rms 0.517 0.051% neg 0 invalid 762 tFOTS 6.8560 tGradient 2.6520 tsec 10.0740 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.5168) vs oldopt=(dt=103.68,rms=0.516811) #GCMRL# 306 dt 82.944000 rms 0.517 0.000% neg 0 invalid 762 tFOTS 6.8680 tGradient 2.5700 tsec 10.0230 #GCMRL# 307 dt 82.944000 rms 0.517 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6530 tsec 3.2070 #GCMRL# 308 dt 82.944000 rms 0.516 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6790 tsec 3.2410 #GCMRL# 309 dt 82.944000 rms 0.516 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6700 tsec 3.1680 #GCMRL# 310 dt 82.944000 rms 0.516 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5620 tsec 3.1010 #GCMRL# 311 dt 82.944000 rms 0.515 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6350 tsec 3.2030 #GCMRL# 312 dt 82.944000 rms 0.515 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6490 tsec 3.1780 #GCMRL# 313 dt 82.944000 rms 0.514 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6750 tsec 3.2070 #GCMRL# 314 dt 82.944000 rms 0.514 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6490 tsec 3.1810 #GCMRL# 315 dt 82.944000 rms 0.514 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6280 tsec 3.1670 #GCMRL# 316 dt 82.944000 rms 0.513 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6550 tsec 3.2220 #GCMRL# 317 dt 82.944000 rms 0.513 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7580 tsec 3.3000 #GCMRL# 318 dt 82.944000 rms 0.513 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5900 tsec 3.1350 #GCMRL# 319 dt 82.944000 rms 0.512 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5980 tsec 3.1600 #GCMRL# 320 dt 82.944000 rms 0.512 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5840 tsec 3.1290 #GCMRL# 321 dt 82.944000 rms 0.512 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5910 tsec 3.1350 #GCMRL# 322 dt 82.944000 rms 0.511 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5840 tsec 3.1740 #GCMRL# 323 dt 82.944000 rms 0.511 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5990 tsec 3.1300 #GCMRL# 324 dt 82.944000 rms 0.511 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5920 tsec 3.1640 #GCMRL# 325 dt 82.944000 rms 0.511 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7250 tsec 3.2420 #GCMRL# 326 dt 82.944000 rms 0.510 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5650 tsec 3.1070 #GCMRL# 327 dt 82.944000 rms 0.510 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5450 tsec 3.0710 #GCMRL# 328 dt 82.944000 rms 0.510 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5720 tsec 3.1060 #GCMRL# 329 dt 82.944000 rms 0.510 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7590 tsec 3.3190 #GCMRL# 330 dt 82.944000 rms 0.509 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7570 tsec 3.2860 #GCMRL# 331 dt 82.944000 rms 0.509 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6920 tsec 3.2120 #GCMRL# 332 dt 82.944000 rms 0.509 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6510 tsec 3.2280 #GCMRL# 333 dt 82.944000 rms 0.509 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6600 tsec 3.2350 #GCMRL# 334 dt 82.944000 rms 0.508 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9550 tsec 3.4510 #GCMRL# 335 dt 82.944000 rms 0.508 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8560 tsec 3.4580 #GCMRL# 336 dt 82.944000 rms 0.508 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8220 tsec 3.3400 #GCMRL# 337 dt 82.944000 rms 0.508 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0590 tsec 3.6500 #GCMRL# 338 dt 82.944000 rms 0.508 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8380 tsec 3.3970 #GCMRL# 339 dt 82.944000 rms 0.507 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7370 tsec 3.2970 #GCMRL# 340 dt 82.944000 rms 0.507 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6050 tsec 3.1360 #GCMRL# 341 dt 82.944000 rms 0.507 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6720 tsec 3.2440 #GCMRL# 342 dt 82.944000 rms 0.507 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7080 tsec 3.2260 #GCMRL# 343 dt 82.944000 rms 0.507 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6150 tsec 3.1370 #GCMRL# 344 dt 82.944000 rms 0.507 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6720 tsec 3.2440 #GCMRL# 345 dt 82.944000 rms 0.506 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6540 tsec 3.1970 #GCMRL# 346 dt 82.944000 rms 0.506 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6290 tsec 3.1630 #GCMRL# 347 dt 82.944000 rms 0.506 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6660 tsec 3.2060 #GCMRL# 348 dt 82.944000 rms 0.506 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7470 tsec 3.3170 #GCMRL# 349 dt 82.944000 rms 0.506 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6870 tsec 3.2330 #GCMRL# 350 dt 82.944000 rms 0.505 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7210 tsec 3.2740 #GCMRL# 351 dt 82.944000 rms 0.505 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6130 tsec 3.1330 #GCMRL# 352 dt 82.944000 rms 0.505 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6750 tsec 3.1920 #GCMRL# 353 dt 82.944000 rms 0.505 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6740 tsec 3.2180 #GCMRL# 354 dt 82.944000 rms 0.505 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7790 tsec 3.3270 #GCMRL# 355 dt 82.944000 rms 0.505 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7430 tsec 3.2660 #GCMRL# 356 dt 82.944000 rms 0.505 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7280 tsec 3.2430 #GCMRL# 357 dt 82.944000 rms 0.504 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6650 tsec 3.2200 #GCMRL# 358 dt 82.944000 rms 0.504 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7450 tsec 3.2970 #GCMRL# 359 dt 82.944000 rms 0.504 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7320 tsec 3.3190 #GCMRL# 360 dt 82.944000 rms 0.504 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7070 tsec 3.2700 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.504037) vs oldopt=(dt=103.68,rms=0.504058) #GCMRL# 361 dt 62.208000 rms 0.504 0.000% neg 0 invalid 762 tFOTS 7.0030 tGradient 2.7140 tsec 10.2990 #GCMRL# 362 dt 62.208000 rms 0.504 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6970 tsec 3.2190 #GCMRL# 363 dt 62.208000 rms 0.504 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6340 tsec 3.1710 #GCMRL# 364 dt 62.208000 rms 0.504 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6880 tsec 3.2420 #GCMRL# 365 dt 62.208000 rms 0.504 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6730 tsec 3.2050 #GCMRL# 366 dt 62.208000 rms 0.504 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7040 tsec 3.2180 #GCMRL# 367 dt 62.208000 rms 0.504 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6160 tsec 3.1640 #GCMRL# 368 dt 62.208000 rms 0.504 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6700 tsec 3.2230 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.516487 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.515774) vs oldopt=(dt=8,rms=0.515783) #GCMRL# 370 dt 9.600000 rms 0.516 0.138% neg 0 invalid 762 tFOTS 7.0350 tGradient 2.3840 tsec 9.9450 #GCMRL# 371 dt 8.000000 rms 0.516 0.000% neg 0 invalid 762 tFOTS 7.0330 tGradient 2.4630 tsec 10.0890 #GCMRL# 372 dt 8.000000 rms 0.516 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4730 tsec 2.9970 #GCAMreg# pass 0 level1 3 level2 1 tsec 35.076 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.516126 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.513779) vs oldopt=(dt=32,rms=0.514024) #GCMRL# 374 dt 44.800000 rms 0.514 0.455% neg 0 invalid 762 tFOTS 6.8960 tGradient 2.5390 tsec 9.9960 #FOTS# QuadFit found better minimum quadopt=(dt=79.4483,rms=0.511376) vs oldopt=(dt=128,rms=0.51216) #GCMRL# 375 dt 79.448276 rms 0.511 0.468% neg 0 invalid 762 tFOTS 6.9380 tGradient 2.4180 tsec 9.9030 #FOTS# QuadFit found better minimum quadopt=(dt=30.303,rms=0.509712) vs oldopt=(dt=32,rms=0.509731) #GCMRL# 376 dt 30.303030 rms 0.510 0.325% neg 0 invalid 762 tFOTS 6.8340 tGradient 2.4950 tsec 9.8690 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.507957) vs oldopt=(dt=32,rms=0.508156) #GCMRL# 377 dt 44.800000 rms 0.508 0.344% neg 0 invalid 762 tFOTS 6.9130 tGradient 2.5480 tsec 9.9880 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.50683) vs oldopt=(dt=32,rms=0.506854) #GCMRL# 378 dt 25.600000 rms 0.507 0.222% neg 0 invalid 762 tFOTS 6.8770 tGradient 2.4350 tsec 9.9090 #FOTS# QuadFit found better minimum quadopt=(dt=80.4065,rms=0.50483) vs oldopt=(dt=128,rms=0.505371) #GCMRL# 379 dt 80.406467 rms 0.505 0.395% neg 0 invalid 762 tFOTS 6.9710 tGradient 2.4380 tsec 9.9280 #FOTS# QuadFit found better minimum quadopt=(dt=21.0173,rms=0.503409) vs oldopt=(dt=32,rms=0.50385) #GCMRL# 380 dt 21.017284 rms 0.503 0.281% neg 0 invalid 762 tFOTS 6.8340 tGradient 2.4070 tsec 9.7780 #FOTS# QuadFit found better minimum quadopt=(dt=117.169,rms=0.501622) vs oldopt=(dt=128,rms=0.501659) #GCMRL# 381 dt 117.169231 rms 0.502 0.355% neg 0 invalid 762 tFOTS 6.9320 tGradient 2.3600 tsec 9.8150 #FOTS# QuadFit found better minimum quadopt=(dt=21.6434,rms=0.499929) vs oldopt=(dt=32,rms=0.500413) #GCMRL# 382 dt 21.643411 rms 0.500 0.338% neg 0 invalid 762 tFOTS 6.8080 tGradient 2.2760 tsec 9.6470 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.498799) vs oldopt=(dt=32,rms=0.498986) #GCMRL# 383 dt 44.800000 rms 0.499 0.226% neg 0 invalid 762 tFOTS 7.0040 tGradient 2.3680 tsec 9.9210 #GCMRL# 384 dt 32.000000 rms 0.498 0.115% neg 0 invalid 762 tFOTS 6.9120 tGradient 2.4410 tsec 9.8740 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.497382) vs oldopt=(dt=32,rms=0.497414) #GCMRL# 385 dt 38.400000 rms 0.497 0.169% neg 0 invalid 762 tFOTS 7.0190 tGradient 2.5540 tsec 10.1450 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.496865) vs oldopt=(dt=32,rms=0.496906) #GCMRL# 386 dt 25.600000 rms 0.497 0.104% neg 0 invalid 762 tFOTS 6.8940 tGradient 2.3470 tsec 9.8000 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.496066) vs oldopt=(dt=32,rms=0.49618) #GCMRL# 387 dt 44.800000 rms 0.496 0.161% neg 0 invalid 762 tFOTS 6.9850 tGradient 2.4810 tsec 10.0300 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.495603) vs oldopt=(dt=32,rms=0.495626) #GCMRL# 388 dt 25.600000 rms 0.496 0.093% neg 0 invalid 762 tFOTS 6.9200 tGradient 2.5030 tsec 9.9350 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.494855) vs oldopt=(dt=32,rms=0.494965) #GCMRL# 389 dt 44.800000 rms 0.495 0.151% neg 0 invalid 762 tFOTS 6.9460 tGradient 2.3330 tsec 9.8220 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.49452) vs oldopt=(dt=32,rms=0.494612) #GCMRL# 390 dt 19.200000 rms 0.495 0.068% neg 0 invalid 762 tFOTS 7.0490 tGradient 2.4060 tsec 9.9600 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.492883) vs oldopt=(dt=128,rms=0.493069) #GCMRL# 391 dt 179.200000 rms 0.493 0.331% neg 0 invalid 762 tFOTS 6.5960 tGradient 2.3630 tsec 9.5290 #FOTS# QuadFit found better minimum quadopt=(dt=23.4872,rms=0.491797) vs oldopt=(dt=32,rms=0.492029) #GCMRL# 392 dt 23.487179 rms 0.492 0.220% neg 0 invalid 762 tFOTS 6.6000 tGradient 2.7970 tsec 9.9320 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.491053) vs oldopt=(dt=32,rms=0.491152) #GCMRL# 393 dt 44.800000 rms 0.491 0.151% neg 0 invalid 762 tFOTS 6.7040 tGradient 2.4230 tsec 9.7040 #GCMRL# 394 dt 32.000000 rms 0.491 0.065% neg 0 invalid 762 tFOTS 6.8180 tGradient 2.3730 tsec 9.7520 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.490221) vs oldopt=(dt=32,rms=0.490291) #GCMRL# 395 dt 44.800000 rms 0.490 0.105% neg 0 invalid 762 tFOTS 6.6380 tGradient 2.4040 tsec 9.6040 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.490005) vs oldopt=(dt=32,rms=0.490072) #GCMRL# 396 dt 19.200000 rms 0.490 0.000% neg 0 invalid 762 tFOTS 6.9710 tGradient 2.4810 tsec 9.9870 #GCMRL# 397 dt 19.200000 rms 0.490 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3600 tsec 2.8900 #GCMRL# 398 dt 19.200000 rms 0.489 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2900 tsec 2.8130 #GCMRL# 399 dt 19.200000 rms 0.489 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3950 tsec 2.9640 #GCMRL# 400 dt 19.200000 rms 0.488 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3300 tsec 2.8320 #GCMRL# 401 dt 19.200000 rms 0.488 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3750 tsec 2.8990 #GCMRL# 402 dt 19.200000 rms 0.487 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3150 tsec 2.8370 #GCMRL# 403 dt 19.200000 rms 0.486 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3900 tsec 2.9300 #GCMRL# 404 dt 19.200000 rms 0.485 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4840 tsec 3.0850 #GCMRL# 405 dt 19.200000 rms 0.484 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2850 tsec 2.7940 #GCMRL# 406 dt 19.200000 rms 0.483 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5090 tsec 3.0410 #GCMRL# 407 dt 19.200000 rms 0.483 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4110 tsec 2.9380 #GCMRL# 408 dt 19.200000 rms 0.482 0.160% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3280 tsec 2.8440 #GCMRL# 409 dt 19.200000 rms 0.481 0.156% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3910 tsec 2.8940 #GCMRL# 410 dt 19.200000 rms 0.480 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3660 tsec 2.9020 #GCMRL# 411 dt 19.200000 rms 0.480 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3520 tsec 2.9140 #GCMRL# 412 dt 19.200000 rms 0.479 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3670 tsec 2.8960 #GCMRL# 413 dt 19.200000 rms 0.478 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3470 tsec 2.8830 #GCMRL# 414 dt 19.200000 rms 0.478 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4490 tsec 2.9990 #GCMRL# 415 dt 19.200000 rms 0.477 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2860 tsec 2.8270 #GCMRL# 416 dt 19.200000 rms 0.477 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2820 tsec 2.8210 #GCMRL# 417 dt 19.200000 rms 0.477 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3610 tsec 2.9080 #GCMRL# 418 dt 19.200000 rms 0.476 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4180 tsec 2.9410 #GCMRL# 419 dt 19.200000 rms 0.476 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3050 tsec 2.8500 #GCMRL# 420 dt 19.200000 rms 0.475 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3730 tsec 2.9140 #GCMRL# 421 dt 19.200000 rms 0.475 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3630 tsec 2.9400 #GCMRL# 422 dt 19.200000 rms 0.475 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2310 tsec 2.7680 #GCMRL# 423 dt 19.200000 rms 0.475 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3100 tsec 2.8950 #GCMRL# 424 dt 19.200000 rms 0.474 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2400 tsec 2.7860 #GCMRL# 425 dt 19.200000 rms 0.474 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2850 tsec 2.8110 #GCMRL# 426 dt 19.200000 rms 0.474 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2960 tsec 2.8420 #GCMRL# 427 dt 19.200000 rms 0.474 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2620 tsec 2.8160 #GCMRL# 428 dt 19.200000 rms 0.473 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3850 tsec 2.9160 #GCMRL# 429 dt 19.200000 rms 0.473 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3840 tsec 2.9030 #GCMRL# 430 dt 19.200000 rms 0.473 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3260 tsec 2.9020 #GCMRL# 431 dt 19.200000 rms 0.473 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3510 tsec 2.9080 #GCMRL# 432 dt 19.200000 rms 0.473 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2840 tsec 2.8480 #GCMRL# 433 dt 19.200000 rms 0.472 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2600 tsec 2.7840 #GCMRL# 434 dt 19.200000 rms 0.472 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2850 tsec 2.8330 #GCMRL# 435 dt 19.200000 rms 0.472 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3710 tsec 2.9180 #GCMRL# 436 dt 19.200000 rms 0.472 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3400 tsec 2.8720 #GCMRL# 437 dt 19.200000 rms 0.472 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3280 tsec 2.8610 #GCMRL# 438 dt 19.200000 rms 0.472 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2820 tsec 2.8250 #GCMRL# 439 dt 19.200000 rms 0.471 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2810 tsec 2.8150 #GCMRL# 440 dt 19.200000 rms 0.471 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2730 tsec 2.8000 #GCMRL# 441 dt 19.200000 rms 0.471 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4550 tsec 3.0000 #GCMRL# 442 dt 19.200000 rms 0.471 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4240 tsec 2.9550 #GCMRL# 443 dt 19.200000 rms 0.471 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3760 tsec 2.9230 #GCMRL# 444 dt 19.200000 rms 0.471 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4150 tsec 2.9850 #GCMRL# 445 dt 19.200000 rms 0.471 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2080 tsec 2.7760 #GCMRL# 446 dt 19.200000 rms 0.471 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2640 tsec 2.8470 #GCMRL# 447 dt 32.000000 rms 0.471 0.000% neg 0 invalid 762 tFOTS 6.9290 tGradient 2.2290 tsec 9.7500 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.496394 #GCMRL# 449 dt 0.000000 rms 0.496 0.068% neg 0 invalid 762 tFOTS 6.4360 tGradient 2.1160 tsec 9.0860 #GCMRL# 450 dt 0.150000 rms 0.496 0.000% neg 0 invalid 762 tFOTS 6.4570 tGradient 2.1920 tsec 9.6230 #GCAMreg# pass 0 level1 2 level2 1 tsec 30.461 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.496394 #GCMRL# 452 dt 0.000000 rms 0.496 0.068% neg 0 invalid 762 tFOTS 6.5960 tGradient 2.1570 tsec 9.2580 #GCMRL# 453 dt 0.150000 rms 0.496 0.000% neg 0 invalid 762 tFOTS 6.5300 tGradient 2.1660 tsec 9.6830 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.546607 #FOTS# QuadFit found better minimum quadopt=(dt=1.08077,rms=0.543588) vs oldopt=(dt=1.28,rms=0.543597) #GCMRL# 455 dt 1.080769 rms 0.544 0.552% neg 0 invalid 762 tFOTS 6.5310 tGradient 2.0750 tsec 9.1460 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.543532) vs oldopt=(dt=0.32,rms=0.543548) #GCMRL# 456 dt 0.192000 rms 0.544 0.000% neg 0 invalid 762 tFOTS 6.5490 tGradient 2.0440 tsec 9.1730 #GCAMreg# pass 0 level1 1 level2 1 tsec 30.079 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.543854 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.543309) vs oldopt=(dt=0.32,rms=0.543328) #GCMRL# 458 dt 0.448000 rms 0.543 0.100% neg 0 invalid 762 tFOTS 6.3920 tGradient 2.2940 tsec 9.2010 #FOTS# QuadFit found better minimum quadopt=(dt=0.048,rms=0.543309) vs oldopt=(dt=0.08,rms=0.54331) #GCMRL# 459 dt 0.048000 rms 0.543 0.000% neg 0 invalid 762 tFOTS 6.5130 tGradient 2.1700 tsec 9.2290 #GCMRL# 460 dt 0.048000 rms 0.543 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1320 tsec 2.6740 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.477908 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.46559) vs oldopt=(dt=0.32,rms=0.468831) #GCMRL# 462 dt 0.448000 rms 0.466 2.577% neg 0 invalid 762 tFOTS 6.1140 tGradient 1.6360 tsec 8.2820 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.463009) vs oldopt=(dt=0.32,rms=0.463719) #GCMRL# 463 dt 0.448000 rms 0.463 0.554% neg 0 invalid 762 tFOTS 6.0760 tGradient 1.5680 tsec 8.1890 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.461709) vs oldopt=(dt=0.32,rms=0.461922) #GCMRL# 464 dt 0.384000 rms 0.462 0.281% neg 0 invalid 762 tFOTS 6.2120 tGradient 1.5850 tsec 8.3180 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.460667) vs oldopt=(dt=0.32,rms=0.460953) #GCMRL# 465 dt 0.448000 rms 0.461 0.226% neg 0 invalid 762 tFOTS 6.0030 tGradient 1.4380 tsec 7.9830 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.459929) vs oldopt=(dt=0.32,rms=0.460133) #GCMRL# 466 dt 0.448000 rms 0.460 0.160% neg 0 invalid 762 tFOTS 6.0350 tGradient 1.4420 tsec 7.9880 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.459404) vs oldopt=(dt=0.32,rms=0.459548) #GCMRL# 467 dt 0.448000 rms 0.459 0.114% neg 0 invalid 762 tFOTS 6.1180 tGradient 1.5360 tsec 8.1950 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.458963) vs oldopt=(dt=0.32,rms=0.45908) #GCMRL# 468 dt 0.448000 rms 0.459 0.096% neg 0 invalid 762 tFOTS 6.0110 tGradient 1.4740 tsec 8.0150 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.45862) vs oldopt=(dt=0.32,rms=0.458707) #GCMRL# 469 dt 0.448000 rms 0.459 0.075% neg 0 invalid 762 tFOTS 6.1070 tGradient 1.4810 tsec 8.1500 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.458342) vs oldopt=(dt=0.32,rms=0.458416) #GCMRL# 470 dt 0.448000 rms 0.458 0.061% neg 0 invalid 762 tFOTS 6.0210 tGradient 1.4810 tsec 8.0230 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.458105) vs oldopt=(dt=0.32,rms=0.45816) #GCMRL# 471 dt 0.448000 rms 0.458 0.052% neg 0 invalid 762 tFOTS 6.0650 tGradient 1.4850 tsec 8.0740 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.457904) vs oldopt=(dt=0.32,rms=0.457954) #GCMRL# 472 dt 0.448000 rms 0.458 0.000% neg 0 invalid 762 tFOTS 6.1130 tGradient 1.5490 tsec 8.2600 #GCMRL# 473 dt 0.448000 rms 0.458 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4560 tsec 2.0280 #GCMRL# 474 dt 0.448000 rms 0.457 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5570 tsec 2.1040 #GCMRL# 475 dt 0.224000 rms 0.457 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6330 tsec 2.7060 #GCMRL# 476 dt 0.224000 rms 0.457 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4560 tsec 2.3230 #GCMRL# 477 dt 0.224000 rms 0.457 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5310 tsec 2.0700 #GCMRL# 478 dt 0.224000 rms 0.457 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6070 tsec 2.1470 #GCMRL# 479 dt 0.224000 rms 0.457 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4560 tsec 2.0040 #GCMRL# 480 dt 0.224000 rms 0.457 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4770 tsec 2.0180 #GCMRL# 481 dt 0.224000 rms 0.457 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5380 tsec 2.0710 #GCMRL# 482 dt 0.224000 rms 0.456 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4720 tsec 2.0130 #GCMRL# 483 dt 0.224000 rms 0.456 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5170 tsec 2.0270 #GCMRL# 484 dt 0.224000 rms 0.456 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4790 tsec 2.0160 #GCMRL# 485 dt 0.224000 rms 0.456 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5980 tsec 2.1520 #GCMRL# 486 dt 0.224000 rms 0.456 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5310 tsec 2.1320 #FOTS# QuadFit found better minimum quadopt=(dt=2.5e-06,rms=0.455963) vs oldopt=(dt=3.125e-06,rms=0.455963) #GCMRL# 487 dt 0.000003 rms 0.456 0.000% neg 0 invalid 762 tFOTS 8.3220 tGradient 1.5330 tsec 10.4680 #GCAMreg# pass 0 level1 0 level2 1 tsec 141.155 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.456391 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.452982) vs oldopt=(dt=0.32,rms=0.453448) #GCMRL# 489 dt 0.384000 rms 0.453 0.747% neg 0 invalid 762 tFOTS 6.0750 tGradient 1.5030 tsec 8.1400 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.452303) vs oldopt=(dt=0.32,rms=0.452411) #GCMRL# 490 dt 0.384000 rms 0.452 0.150% neg 0 invalid 762 tFOTS 6.1180 tGradient 1.5560 tsec 8.2340 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.452071) vs oldopt=(dt=0.32,rms=0.452105) #GCMRL# 491 dt 0.384000 rms 0.452 0.051% neg 0 invalid 762 tFOTS 6.1810 tGradient 1.4400 tsec 8.1690 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.45199) vs oldopt=(dt=0.32,rms=0.451999) #GCMRL# 492 dt 0.384000 rms 0.452 0.000% neg 0 invalid 762 tFOTS 6.2410 tGradient 1.4540 tsec 8.2280 #GCMRL# 493 dt 0.384000 rms 0.452 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4910 tsec 2.0030 #GCMRL# 494 dt 0.384000 rms 0.452 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5010 tsec 2.0970 #GCMRL# 495 dt 0.192000 rms 0.452 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6570 tsec 2.7290 #GCMRL# 496 dt 0.192000 rms 0.452 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4850 tsec 2.0490 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.451836) vs oldopt=(dt=0.32,rms=0.451837) GCAMregister done in 33.9211 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.450245 #GCMRL# 498 dt 0.000000 rms 0.450 0.096% neg 0 invalid 762 tFOTS 7.2790 tGradient 3.0000 tsec 10.8400 #GCAMreg# pass 0 level1 5 level2 1 tsec 30.858 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.450245 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.449057) vs oldopt=(dt=369.92,rms=0.449108) #GCMRL# 500 dt 295.936000 rms 0.449 0.264% neg 0 invalid 762 tFOTS 7.3290 tGradient 2.9810 tsec 10.8460 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.448923) vs oldopt=(dt=92.48,rms=0.448935) #GCMRL# 501 dt 73.984000 rms 0.449 0.000% neg 0 invalid 762 tFOTS 7.4200 tGradient 2.9410 tsec 10.9300 #GCMRL# 502 dt 73.984000 rms 0.449 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8540 tsec 3.3970 #GCMRL# 503 dt 73.984000 rms 0.449 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9180 tsec 3.4650 #GCMRL# 504 dt 73.984000 rms 0.449 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0000 tsec 3.5080 #GCMRL# 505 dt 73.984000 rms 0.449 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0570 tsec 3.5930 #GCMRL# 506 dt 73.984000 rms 0.448 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8820 tsec 3.4010 #GCMRL# 507 dt 73.984000 rms 0.448 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9420 tsec 3.4900 #GCMRL# 508 dt 73.984000 rms 0.448 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9390 tsec 3.5030 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.448214) vs oldopt=(dt=92.48,rms=0.448215) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.448683 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.448222) vs oldopt=(dt=6.48,rms=0.448225) #GCMRL# 510 dt 9.072000 rms 0.448 0.103% neg 0 invalid 762 tFOTS 7.8010 tGradient 2.5680 tsec 10.8750 #GCMRL# 511 dt 6.480000 rms 0.448 0.000% neg 0 invalid 762 tFOTS 7.7950 tGradient 2.5400 tsec 10.8700 #GCMRL# 512 dt 6.480000 rms 0.448 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4660 tsec 3.0090 #GCAMreg# pass 0 level1 4 level2 1 tsec 36.71 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.448653 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.446272) vs oldopt=(dt=103.68,rms=0.446636) #GCMRL# 514 dt 145.152000 rms 0.446 0.531% neg 0 invalid 762 tFOTS 7.3700 tGradient 2.4910 tsec 10.3820 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.445935) vs oldopt=(dt=25.92,rms=0.446002) #GCMRL# 515 dt 36.288000 rms 0.446 0.000% neg 0 invalid 762 tFOTS 7.3760 tGradient 2.4760 tsec 10.4150 #GCMRL# 516 dt 36.288000 rms 0.446 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4750 tsec 3.0160 #GCMRL# 517 dt 36.288000 rms 0.445 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4880 tsec 3.0400 #GCMRL# 518 dt 36.288000 rms 0.445 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4950 tsec 3.0720 #GCMRL# 519 dt 36.288000 rms 0.444 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4570 tsec 2.9820 #GCMRL# 520 dt 36.288000 rms 0.444 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3970 tsec 2.9670 #GCMRL# 521 dt 36.288000 rms 0.443 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5650 tsec 3.0960 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.443178) vs oldopt=(dt=103.68,rms=0.443184) #GCMRL# 522 dt 124.416000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 7.3590 tGradient 2.5650 tsec 10.5270 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.443886 #FOTS# QuadFit found better minimum quadopt=(dt=30.8257,rms=0.44204) vs oldopt=(dt=32,rms=0.442051) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 524 dt 30.825688 rms 0.442 0.416% neg 0 invalid 762 tFOTS 7.7150 tGradient 2.3250 tsec 13.0390 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.440286) vs oldopt=(dt=32,rms=0.440463) iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 525 dt 44.800000 rms 0.440 0.397% neg 0 invalid 762 tFOTS 7.8800 tGradient 2.3120 tsec 13.0640 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.439343) vs oldopt=(dt=32,rms=0.439402) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 526 dt 25.600000 rms 0.439 0.000% neg 0 invalid 762 tFOTS 7.7490 tGradient 2.6240 tsec 13.4090 #GCMRL# 527 dt 25.600000 rms 0.438 0.203% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5420 tsec 3.0920 #GCMRL# 528 dt 25.600000 rms 0.437 0.253% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4730 tsec 3.0040 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 529 dt 25.600000 rms 0.436 0.220% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6710 tsec 10.2340 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 530 dt 25.600000 rms 0.435 0.215% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6370 tsec 7.9290 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 531 dt 25.600000 rms 0.435 0.153% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4560 tsec 17.9640 iter 0, gcam->neg = 12 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 532 dt 25.600000 rms 0.434 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5370 tsec 12.4090 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 533 dt 25.600000 rms 0.434 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4540 tsec 8.8940 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 534 dt 25.600000 rms 0.433 0.160% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4990 tsec 13.5700 iter 0, gcam->neg = 15 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 535 dt 25.600000 rms 0.432 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5400 tsec 23.8950 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 536 dt 25.600000 rms 0.432 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6650 tsec 7.8980 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 537 dt 25.600000 rms 0.431 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5240 tsec 9.9120 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 538 dt 25.600000 rms 0.431 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5300 tsec 13.5610 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 539 dt 25.600000 rms 0.430 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6070 tsec 11.3110 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.430165) vs oldopt=(dt=8,rms=0.4302) #GCMRL# 540 dt 11.200000 rms 0.430 0.000% neg 0 invalid 762 tFOTS 7.6190 tGradient 2.6640 tsec 10.8450 #GCMRL# 541 dt 11.200000 rms 0.430 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5050 tsec 3.0130 #GCMRL# 542 dt 11.200000 rms 0.430 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4520 tsec 3.0450 #GCMRL# 543 dt 11.200000 rms 0.430 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4870 tsec 3.0360 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 544 dt 11.200000 rms 0.430 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4520 tsec 8.9820 #GCMRL# 545 dt 11.200000 rms 0.430 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5210 tsec 3.0740 #GCAMreg# pass 0 level1 3 level2 1 tsec 226.916 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.429798 #FOTS# QuadFit found better minimum quadopt=(dt=66.3226,rms=0.425755) vs oldopt=(dt=32,rms=0.42651) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 547 dt 66.322581 rms 0.426 0.941% neg 0 invalid 762 tFOTS 7.7080 tGradient 2.4450 tsec 14.2970 #FOTS# QuadFit found better minimum quadopt=(dt=24.4148,rms=0.424619) vs oldopt=(dt=32,rms=0.424786) #GCMRL# 548 dt 24.414815 rms 0.425 0.267% neg 0 invalid 762 tFOTS 7.7920 tGradient 2.6150 tsec 10.9430 #GCMRL# 549 dt 32.000000 rms 0.424 0.000% neg 0 invalid 762 tFOTS 7.8750 tGradient 2.5410 tsec 10.9740 #GCMRL# 550 dt 32.000000 rms 0.424 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5930 tsec 3.1290 #GCMRL# 551 dt 32.000000 rms 0.423 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4570 tsec 2.9550 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 552 dt 32.000000 rms 0.423 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5450 tsec 7.8210 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 553 dt 32.000000 rms 0.422 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5460 tsec 12.4160 #GCMRL# 554 dt 32.000000 rms 0.422 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5840 tsec 3.0900 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 555 dt 32.000000 rms 0.422 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5800 tsec 11.2600 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.421357) vs oldopt=(dt=8,rms=0.421425) #GCMRL# 556 dt 11.200000 rms 0.421 0.091% neg 0 invalid 762 tFOTS 7.6810 tGradient 2.5390 tsec 10.7530 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.421203) vs oldopt=(dt=32,rms=0.421217) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 557 dt 25.600000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 7.7360 tGradient 2.4310 tsec 14.2270 #GCMRL# 558 dt 25.600000 rms 0.421 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5250 tsec 3.0570 #GCMRL# 559 dt 25.600000 rms 0.421 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5200 tsec 3.0420 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 560 dt 25.600000 rms 0.421 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4360 tsec 7.6850 #GCMRL# 561 dt 25.600000 rms 0.421 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5310 tsec 3.0750 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.425957 #GCMRL# 563 dt 0.000000 rms 0.425 0.117% neg 0 invalid 762 tFOTS 7.4330 tGradient 2.2640 tsec 10.2340 #GCAMreg# pass 0 level1 2 level2 1 tsec 29.819 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.425957 #FOTS# QuadFit found better minimum quadopt=(dt=1.75,rms=0.425427) vs oldopt=(dt=0.72,rms=0.425436) #GCMRL# 565 dt 1.750000 rms 0.425 0.125% neg 0 invalid 762 tFOTS 7.7150 tGradient 2.2860 tsec 10.5050 #FOTS# QuadFit found better minimum quadopt=(dt=0.576,rms=0.425414) vs oldopt=(dt=0.72,rms=0.425414) #GCMRL# 566 dt 0.576000 rms 0.425 0.000% neg 0 invalid 762 tFOTS 7.7010 tGradient 2.2790 tsec 10.5340 #GCMRL# 567 dt 0.576000 rms 0.425 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3270 tsec 2.8550 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.434958 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.433974) vs oldopt=(dt=1.28,rms=0.434023) #GCMRL# 569 dt 1.024000 rms 0.434 0.226% neg 0 invalid 762 tFOTS 7.7660 tGradient 2.1210 tsec 10.4560 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.433967) vs oldopt=(dt=0.08,rms=0.433969) #GCMRL# 570 dt 0.112000 rms 0.434 0.000% neg 0 invalid 762 tFOTS 7.7560 tGradient 2.1160 tsec 10.4440 #GCMRL# 571 dt 0.112000 rms 0.434 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0640 tsec 2.5910 #GCAMreg# pass 0 level1 1 level2 1 tsec 35.026 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.434408 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.433174) vs oldopt=(dt=1.28,rms=0.433207) #GCMRL# 573 dt 1.536000 rms 0.433 0.284% neg 0 invalid 762 tFOTS 7.8020 tGradient 2.0850 tsec 10.4340 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.43312) vs oldopt=(dt=0.32,rms=0.433131) #GCMRL# 574 dt 0.448000 rms 0.433 0.000% neg 0 invalid 762 tFOTS 7.7010 tGradient 2.1630 tsec 10.4210 #GCMRL# 575 dt 0.448000 rms 0.433 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1370 tsec 2.6610 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.425812 #FOTS# QuadFit found better minimum quadopt=(dt=2.06233,rms=0.401064) vs oldopt=(dt=1.28,rms=0.40474) iter 0, gcam->neg = 587 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 577 dt 2.062334 rms 0.400 5.957% neg 0 invalid 762 tFOTS 7.7710 tGradient 1.4430 tsec 29.5130 #GCMRL# 578 dt 0.020000 rms 0.400 0.000% neg 0 invalid 762 tFOTS 7.7420 tGradient 1.5680 tsec 9.8630 #GCAMreg# pass 0 level1 0 level2 1 tsec 50.574 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.400962 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.400289) vs oldopt=(dt=0.08,rms=0.400296) #GCMRL# 580 dt 0.064000 rms 0.400 0.168% neg 0 invalid 762 tFOTS 7.8520 tGradient 1.4590 tsec 9.8410 #FOTS# QuadFit found better minimum quadopt=(dt=-4.06901e-05,rms=0.400269) vs oldopt=(dt=1.95313e-05,rms=0.400269) #GCMRL# 581 dt -0.000041 rms 0.400 0.000% neg 0 invalid 762 tFOTS 9.8570 tGradient 1.4270 tsec 11.8230 label assignment complete, 0 changed (0.00%) GCAMregister done in 12.1922 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.387888 #GCAMreg# pass 0 level1 5 level2 1 tsec 19.164 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.387888 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.387872) vs oldopt=(dt=23.12,rms=0.387875) #GCMRL# 584 dt 32.368000 rms 0.388 0.004% neg 0 invalid 762 tFOTS 7.6470 tGradient 2.7690 tsec 10.9570 #FOTS# QuadFit found better minimum quadopt=(dt=55.488,rms=0.387864) vs oldopt=(dt=92.48,rms=0.387867) #GCMRL# 585 dt 55.488000 rms 0.388 0.000% neg 0 invalid 762 tFOTS 7.1190 tGradient 2.8220 tsec 10.5230 #GCMRL# 586 dt 55.488000 rms 0.388 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8040 tsec 3.3110 #GCMRL# 587 dt 55.488000 rms 0.388 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8380 tsec 3.3960 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.388009 #GCAMreg# pass 0 level1 4 level2 1 tsec 18.636 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.388009 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.387818) vs oldopt=(dt=103.68,rms=0.387821) #GCMRL# 590 dt 124.416000 rms 0.388 0.049% neg 0 invalid 762 tFOTS 7.1160 tGradient 2.1700 tsec 9.8180 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.387636) vs oldopt=(dt=103.68,rms=0.38765) #GCMRL# 591 dt 145.152000 rms 0.388 0.000% neg 0 invalid 762 tFOTS 6.9540 tGradient 2.1650 tsec 9.6780 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.388215 #GCMRL# 593 dt 8.000000 rms 0.388 0.026% neg 0 invalid 762 tFOTS 7.4900 tGradient 1.7550 tsec 9.7780 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.388098) vs oldopt=(dt=2,rms=0.388101) #GCMRL# 594 dt 2.800000 rms 0.388 0.000% neg 0 invalid 762 tFOTS 7.5270 tGradient 1.6780 tsec 9.7500 #GCMRL# 595 dt 2.800000 rms 0.388 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7320 tsec 2.2480 #GCAMreg# pass 0 level1 3 level2 1 tsec 32.915 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.388092 #FOTS# QuadFit found better minimum quadopt=(dt=76.6897,rms=0.386015) vs oldopt=(dt=32,rms=0.386496) iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 597 dt 76.689655 rms 0.386 0.536% neg 0 invalid 762 tFOTS 7.4680 tGradient 1.7730 tsec 12.1890 #FOTS# QuadFit found better minimum quadopt=(dt=22.5819,rms=0.384909) vs oldopt=(dt=32,rms=0.385161) iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 598 dt 22.581940 rms 0.385 0.283% neg 0 invalid 762 tFOTS 7.5710 tGradient 1.7410 tsec 15.7930 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.384455) vs oldopt=(dt=32,rms=0.384526) #GCMRL# 599 dt 44.800000 rms 0.384 0.000% neg 0 invalid 762 tFOTS 7.1910 tGradient 1.7030 tsec 9.4660 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 600 dt 44.800000 rms 0.384 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7260 tsec 12.7250 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 601 dt 44.800000 rms 0.383 0.251% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7110 tsec 10.4730 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 602 dt 44.800000 rms 0.383 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7030 tsec 4.6940 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 603 dt 44.800000 rms 0.382 0.208% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7090 tsec 4.6920 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 604 dt 44.800000 rms 0.381 0.209% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7770 tsec 5.9120 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 605 dt 44.800000 rms 0.381 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6980 tsec 13.8040 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 606 dt 44.800000 rms 0.380 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6770 tsec 8.0500 iter 0, gcam->neg = 8 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 607 dt 44.800000 rms 0.380 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7370 tsec 10.5110 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 608 dt 44.800000 rms 0.380 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7240 tsec 20.6700 iter 0, gcam->neg = 16 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 609 dt 44.800000 rms 0.379 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6880 tsec 12.7190 iter 0, gcam->neg = 35 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 610 dt 44.800000 rms 0.379 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6820 tsec 12.7960 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.378831) vs oldopt=(dt=32,rms=0.378871) #GCMRL# 611 dt 19.200000 rms 0.379 0.039% neg 0 invalid 762 tFOTS 7.4360 tGradient 1.6640 tsec 9.6740 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.378789) vs oldopt=(dt=32,rms=0.378789) #GCMRL# 612 dt 38.400000 rms 0.379 0.000% neg 0 invalid 762 tFOTS 7.1000 tGradient 1.6900 tsec 9.3550 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 613 dt 38.400000 rms 0.379 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7030 tsec 10.5030 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 614 dt 38.400000 rms 0.379 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7030 tsec 8.1390 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 615 dt 38.400000 rms 0.379 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7240 tsec 8.2080 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.382789 #FOTS# QuadFit found better minimum quadopt=(dt=0.000246094,rms=0.382789) vs oldopt=(dt=0.000175781,rms=0.382789) #GCMRL# 617 dt 0.000246 rms 0.383 0.000% neg 0 invalid 762 tFOTS 9.5060 tGradient 1.5580 tsec 11.6030 #GCAMreg# pass 0 level1 2 level2 1 tsec 29.735 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.382789 #FOTS# QuadFit found better minimum quadopt=(dt=3,rms=0.382728) vs oldopt=(dt=2.88,rms=0.382728) #GCMRL# 619 dt 3.000000 rms 0.383 0.016% neg 0 invalid 762 tFOTS 7.4890 tGradient 1.4860 tsec 9.4750 #FOTS# QuadFit found better minimum quadopt=(dt=1.5,rms=0.382716) vs oldopt=(dt=0.72,rms=0.38272) #GCMRL# 620 dt 1.500000 rms 0.383 0.000% neg 0 invalid 762 tFOTS 7.4590 tGradient 1.5260 tsec 9.5220 #GCMRL# 621 dt 1.500000 rms 0.383 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4980 tsec 2.0020 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.390192 #GCAMreg# pass 0 level1 1 level2 1 tsec 17.934 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.390192 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.377647 #FOTS# QuadFit found better minimum quadopt=(dt=0.990625,rms=0.37071) vs oldopt=(dt=1.28,rms=0.371332) iter 0, gcam->neg = 508 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 625 dt 0.990625 rms 0.371 1.888% neg 0 invalid 762 tFOTS 7.5090 tGradient 0.7770 tsec 27.4630 #FOTS# QuadFit found better minimum quadopt=(dt=2.73438e-05,rms=0.370518) vs oldopt=(dt=1.95313e-05,rms=0.370518) #GCMRL# 626 dt 0.000027 rms 0.371 0.000% neg 0 invalid 762 tFOTS 9.4570 tGradient 0.7820 tsec 10.7990 #GCAMreg# pass 0 level1 0 level2 1 tsec 48.477 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.370518 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.370325) vs oldopt=(dt=0.08,rms=0.370346) #GCMRL# 628 dt 0.112000 rms 0.370 0.052% neg 0 invalid 762 tFOTS 7.5650 tGradient 0.7220 tsec 8.7780 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.370225) vs oldopt=(dt=0.08,rms=0.370238) #GCMRL# 629 dt 0.112000 rms 0.370 0.000% neg 0 invalid 762 tFOTS 7.5130 tGradient 0.6950 tsec 8.7780 #GCMRL# 630 dt 0.112000 rms 0.370 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.7270 tsec 1.2640 #GCMRL# 631 dt 0.112000 rms 0.370 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.6710 tsec 1.1740 GCAMregister done in 8.33345 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4338 tmin = 3.775 Calls to gcamLabelEnergy 3803 tmin = 0.8465 Calls to gcamJacobianEnergy 4338 tmin = 6.12287 Calls to gcamSmoothnessEnergy 4338 tmin = 3.61043 Calls to gcamLogLikelihoodTerm 633 tmin = 1.14587 Calls to gcamLabelTerm 583 tmin = 10.2034 Calls to gcamJacobianTerm 633 tmin = 3.78237 Calls to gcamSmoothnessTerm 633 tmin = 0.993 Calls to gcamComputeGradient 633 tmin = 31.7761 Calls to gcamComputeMetricProperties 6147 tmin = 6.86618 mri_ca_register took 1 hours, 13 minutes and 36 seconds. #VMPC# mri_ca_register VmPeak 2325684 FSRUNTIME@ mri_ca_register 1.2267 hours 4 threads @#@FSTIME 2023:02:18:11:53:45 mri_ca_register N 9 e 4416.12 S 91.22 U 10413.22 P 237% M 1334972 F 7 R 1026623 W 0 c 109281 w 67606 I 1976 O 63408 L 1.60 2.43 1.69 @#@FSLOADPOST 2023:02:18:13:07:21 mri_ca_register N 9 1.83 1.76 1.83 #-------------------------------------- #@# SubCort Seg Sat Feb 18 13:07:21 EST 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/7.2.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname developer-VirtualBox machine x86_64 setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/7.2.0/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/freesurfer/7.2.0/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.51 Atlas used for the 3D morph was /usr/local/freesurfer/7.2.0/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.25374 (23) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (1039 voxels, overlap=0.598) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (1039 voxels, peak = 22), gca=21.9 gca peak = 0.20380 (13) mri peak = 0.27561 (23) Right_Lateral_Ventricle (43): linear fit = 1.67 x + 0.0 (830 voxels, overlap=0.283) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (830 voxels, peak = 22), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.24068 (101) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (641 voxels, overlap=0.574) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (641 voxels, peak = 101), gca=101.3 gca peak = 0.15814 (97) mri peak = 0.23373 (102) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (646 voxels, overlap=0.361) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (646 voxels, peak = 103), gca=103.3 gca peak = 0.27624 (56) mri peak = 0.09561 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (886 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (886 voxels, peak = 69), gca=68.6 gca peak = 0.28723 (59) mri peak = 0.10553 (70) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (807 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (807 voxels, peak = 72), gca=72.3 gca peak = 0.07623 (103) mri peak = 0.23188 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38302 voxels, overlap=0.457) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38302 voxels, peak = 105), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.19998 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (39060 voxels, overlap=0.421) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (39060 voxels, peak = 108), gca=107.6 gca peak = 0.10165 (58) mri peak = 0.04420 (69) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (22494 voxels, overlap=0.645) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (22494 voxels, peak = 68), gca=67.6 gca peak = 0.11113 (58) mri peak = 0.04825 (66) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (20265 voxels, overlap=0.812) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (20265 voxels, peak = 66), gca=66.4 gca peak = 0.27796 (67) mri peak = 0.19766 (76) Right_Caudate (50): linear fit = 1.12 x + 0.0 (803 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.12 x + 0.0 (803 voxels, peak = 75), gca=75.4 gca peak = 0.14473 (69) mri peak = 0.20675 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (680 voxels, overlap=0.418) Left_Caudate (11): linear fit = 1.05 x + 0.0 (680 voxels, peak = 73), gca=72.8 gca peak = 0.14301 (56) mri peak = 0.05962 (64) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (19721 voxels, overlap=0.807) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (19721 voxels, peak = 64), gca=63.6 gca peak = 0.14610 (55) mri peak = 0.05601 (67) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (20768 voxels, overlap=0.637) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (20768 voxels, peak = 64), gca=63.5 gca peak = 0.16309 (85) mri peak = 0.13097 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5480 voxels, overlap=0.562) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5480 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.17289 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4507 voxels, overlap=0.068) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4507 voxels, peak = 91), gca=91.1 gca peak = 0.30461 (58) mri peak = 0.13771 (71) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (471 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (471 voxels, peak = 70), gca=70.5 gca peak = 0.32293 (57) mri peak = 0.15564 (71) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (512 voxels, overlap=0.040) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (512 voxels, peak = 72), gca=71.5 gca peak = 0.11083 (90) mri peak = 0.08767 (91) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (3515 voxels, overlap=0.903) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (3515 voxels, peak = 93), gca=93.1 gca peak = 0.11393 (83) mri peak = 0.09845 (88) Right_Thalamus (49): linear fit = 1.04 x + 0.0 (3435 voxels, overlap=0.785) Right_Thalamus (49): linear fit = 1.04 x + 0.0 (3435 voxels, peak = 87), gca=86.7 gca peak = 0.08575 (81) mri peak = 0.10290 (85) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1516 voxels, overlap=0.439) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1516 voxels, peak = 90), gca=90.3 gca peak = 0.08618 (78) mri peak = 0.13766 (84) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1621 voxels, overlap=0.484) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1621 voxels, peak = 84), gca=83.9 gca peak = 0.08005 (78) mri peak = 0.08775 (88) Brain_Stem (16): linear fit = 1.11 x + 0.0 (11292 voxels, overlap=0.366) Brain_Stem (16): linear fit = 1.11 x + 0.0 (11292 voxels, peak = 86), gca=86.2 gca peak = 0.12854 (88) mri peak = 0.12234 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1143 voxels, overlap=0.214) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1143 voxels, peak = 98), gca=98.1 gca peak = 0.15703 (87) mri peak = 0.11780 (99) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1191 voxels, overlap=0.177) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1191 voxels, peak = 97), gca=97.0 gca peak = 0.17522 (25) mri peak = 0.66667 (26) gca peak = 0.17113 (14) mri peak = 0.26382 (23) Fourth_Ventricle (15): linear fit = 1.48 x + 0.0 (267 voxels, overlap=0.102) Fourth_Ventricle (15): linear fit = 1.48 x + 0.0 (267 voxels, peak = 21), gca=20.6 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.21 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 Left_Pallidum too bright - rescaling by 0.996 (from 1.065) to 102.9 (was 103.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15101 (22) mri peak = 0.25374 (23) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (1039 voxels, overlap=0.731) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (1039 voxels, peak = 24), gca=23.7 gca peak = 0.16085 (19) mri peak = 0.27561 (23) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (830 voxels, overlap=0.594) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (830 voxels, peak = 22), gca=21.6 gca peak = 0.20926 (101) mri peak = 0.24068 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (641 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (641 voxels, peak = 100), gca=100.5 gca peak = 0.14337 (103) mri peak = 0.23373 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (646 voxels, overlap=0.974) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (646 voxels, peak = 103), gca=103.0 gca peak = 0.24478 (68) mri peak = 0.09561 (70) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (886 voxels, overlap=1.004) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (886 voxels, peak = 67), gca=67.0 gca peak = 0.30360 (69) mri peak = 0.10553 (70) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (807 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (807 voxels, peak = 68), gca=68.0 gca peak = 0.07891 (105) mri peak = 0.23188 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38302 voxels, overlap=0.508) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38302 voxels, peak = 105), gca=105.0 gca peak = 0.07733 (107) mri peak = 0.19998 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39060 voxels, overlap=0.546) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39060 voxels, peak = 107), gca=107.0 gca peak = 0.08362 (66) mri peak = 0.04420 (69) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (22494 voxels, overlap=0.975) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (22494 voxels, peak = 65), gca=65.0 gca peak = 0.10030 (67) mri peak = 0.04825 (66) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (20265 voxels, overlap=0.966) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (20265 voxels, peak = 66), gca=66.0 gca peak = 0.22736 (75) mri peak = 0.19766 (76) Right_Caudate (50): linear fit = 1.01 x + 0.0 (803 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.01 x + 0.0 (803 voxels, peak = 76), gca=76.1 gca peak = 0.14836 (82) mri peak = 0.20675 (79) Left_Caudate (11): linear fit = 0.99 x + 0.0 (680 voxels, overlap=0.670) Left_Caudate (11): linear fit = 0.99 x + 0.0 (680 voxels, peak = 81), gca=80.8 gca peak = 0.12143 (64) mri peak = 0.05962 (64) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (19721 voxels, overlap=0.997) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (19721 voxels, peak = 63), gca=63.0 gca peak = 0.13439 (64) mri peak = 0.05601 (67) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20768 voxels, overlap=0.996) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20768 voxels, peak = 66), gca=65.6 gca peak = 0.15248 (90) mri peak = 0.13097 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5480 voxels, overlap=0.916) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5480 voxels, peak = 90), gca=89.6 gca peak = 0.14957 (92) mri peak = 0.17289 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4507 voxels, overlap=0.801) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4507 voxels, peak = 92), gca=92.0 gca peak = 0.26998 (69) mri peak = 0.13771 (71) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (471 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (471 voxels, peak = 70), gca=70.0 gca peak = 0.25869 (72) mri peak = 0.15564 (71) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (512 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (512 voxels, peak = 72), gca=72.0 gca peak = 0.09816 (90) mri peak = 0.08767 (91) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3515 voxels, overlap=0.963) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3515 voxels, peak = 90), gca=89.6 gca peak = 0.09480 (86) mri peak = 0.09845 (88) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3435 voxels, overlap=0.950) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3435 voxels, peak = 86), gca=85.6 gca peak = 0.08944 (84) mri peak = 0.10290 (85) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1516 voxels, overlap=0.746) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1516 voxels, peak = 82), gca=81.9 gca peak = 0.08572 (83) mri peak = 0.13766 (84) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1621 voxels, overlap=0.811) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1621 voxels, peak = 84), gca=84.2 gca peak = 0.07929 (90) mri peak = 0.08775 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11292 voxels, overlap=0.762) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11292 voxels, peak = 90), gca=89.6 gca peak = 0.12036 (98) mri peak = 0.12234 (99) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1143 voxels, overlap=0.747) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1143 voxels, peak = 96), gca=95.6 gca peak = 0.14736 (95) mri peak = 0.11780 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1191 voxels, overlap=0.820) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1191 voxels, peak = 95), gca=95.5 gca peak = 0.16334 (36) mri peak = 0.66667 (26) gca peak = 0.14790 (22) mri peak = 0.26382 (23) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (267 voxels, overlap=0.593) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (267 voxels, peak = 22), gca=22.0 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.17357 (34) gca peak Third_Ventricle = 0.16334 (36) gca peak CSF = 0.13858 (49) gca peak Left_Accumbens_area = 0.67139 (66) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.10623 (35) gca peak Right_Inf_Lat_Vent = 0.22619 (28) gca peak Right_Accumbens_area = 0.31508 (73) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13291 (38) gca peak Fifth_Ventricle = 0.77755 (43) gca peak WM_hypointensities = 0.10897 (78) gca peak non_WM_hypointensities = 0.08220 (42) gca peak Optic_Chiasm = 0.45445 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.07 x + 0.0 Left_Pallidum too bright - rescaling by 0.998 (from 1.000) to 102.8 (was 103.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 32976 voxels changed in iteration 0 of unlikely voxel relabeling 134 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 31008 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 316 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 45245 changed. image ll: -2.050, PF=0.500 pass 2: 10286 changed. image ll: -2.050, PF=0.500 pass 3: 3052 changed. 25448 voxels changed in iteration 0 of unlikely voxel relabeling 184 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4764 voxels changed in iteration 0 of unlikely voxel relabeling 56 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4115 voxels changed in iteration 0 of unlikely voxel relabeling 41 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 3470 voxels changed in iteration 0 of unlikely voxel relabeling 26 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 5168 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 134 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 4805 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 479 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2421.808214 mri_ca_label stimesec 2.034206 mri_ca_label ru_maxrss 2104080 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1091632 mri_ca_label ru_majflt 12 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2480 mri_ca_label ru_oublock 584 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 948 mri_ca_label ru_nivcsw 9585 auto-labeling took 39 minutes and 1 seconds. @#@FSTIME 2023:02:18:13:07:22 mri_ca_label N 10 e 2340.92 S 2.13 U 2421.80 P 103% M 2104080 F 12 R 1091634 W 0 c 9590 w 949 I 2480 O 584 L 1.83 1.76 1.83 @#@FSLOADPOST 2023:02:18:13:46:22 mri_ca_label N 10 1.18 1.12 1.12 #-------------------------------------- #@# CC Seg Sat Feb 18 13:46:22 EST 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/developer/Desktop/1st_scan_nii/Sub-139/mri/transforms/cc_up.lta Sub-139 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/developer/Desktop/1st_scan_nii/Sub-139/mri/transforms/cc_up.lta reading aseg from /home/developer/Desktop/1st_scan_nii/Sub-139/mri/aseg.auto_noCCseg.mgz reading norm from /home/developer/Desktop/1st_scan_nii/Sub-139/mri/norm.mgz MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 29478 voxels in left wm, 66928 in right wm, xrange [119, 132] searching rotation angles z=[-8 6], y=[-12 2] 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 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 global minimum found at slice 127.2, rotations (-4.50, -0.65) final transformation (x=127.2, yr=-4.504, zr=-0.647): 0.99685 0.01130 -0.07853 9.58034; -0.01126 0.99994 0.00089 47.33288; 0.07853 0.00000 0.99691 0.37817; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 140 min_x_fornix = 139 min_x_fornix = 141 min_x_fornix = 141 min_x_fornix = 138 cc center is found at 128 82 118 eigenvectors: 0.00001 -0.00199 1.00000; 0.09947 -0.99504 -0.00199; 0.99504 0.09947 0.00019; MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab writing aseg with callosum to /home/developer/Desktop/1st_scan_nii/Sub-139/mri/aseg.auto.mgz... corpus callosum segmentation took 1.0 minutes #VMPC# mri_cc VmPeak 477864 mri_cc done @#@FSTIME 2023:02:18:13:46:22 mri_cc N 7 e 58.81 S 0.27 U 59.25 P 101% M 344332 F 18 R 277649 W 0 c 220 w 53 I 4624 O 576 L 1.18 1.12 1.12 @#@FSLOADPOST 2023:02:18:13:47:21 mri_cc N 7 1.11 1.11 1.12 #-------------------------------------- #@# Merge ASeg Sat Feb 18 13:47:21 EST 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Feb 18 13:47:21 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... NOT doing gentle normalization with control points/label processing with aseg MRIcopyHeader(): source has ctab removing outliers in the aseg WM... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 266 control points removed MRIcopyHeader(): source has ctab Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 72 (72), valley at 40 (40) csf peak at 37, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 74 (74), valley at 42 (42) csf peak at 24, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 44 seconds. @#@FSTIME 2023:02:18:13:47:21 mri_normalize N 9 e 225.22 S 0.78 U 243.73 P 108% M 1206344 F 16 R 634783 W 0 c 1225 w 80 I 4208 O 2192 L 1.11 1.11 1.12 @#@FSLOADPOST 2023:02:18:13:51:07 mri_normalize N 9 1.02 1.08 1.09 #-------------------------------------------- #@# Mask BFS Sat Feb 18 13:51:07 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1374819 voxels in mask (pct= 8.19) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2023:02:18:13:51:07 mri_mask N 5 e 1.17 S 0.02 U 1.61 P 139% M 74328 F 15 R 17276 W 0 c 21 w 28 I 3600 O 2152 L 1.02 1.08 1.09 @#@FSLOADPOST 2023:02:18:13:51:08 mri_mask N 5 1.10 1.09 1.10 #-------------------------------------------- #@# WM Segmentation Sat Feb 18 13:51:08 EST 2023 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2023:02:18:13:51:08 AntsDenoiseImageFs N 4 e 24.77 S 0.12 U 24.92 P 101% M 350816 F 20 R 86512 W 0 c 112 w 26 I 4504 O 2192 L 1.10 1.09 1.10 @#@FSLOADPOST 2023:02:18:13:51:33 AntsDenoiseImageFs N 4 1.13 1.10 1.10 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (102.0): 101.1 +- 6.9 [79.0 --> 125.0] CCS GM (74.0) : 72.9 +- 10.3 [30.0 --> 95.0] white_mean 101.055 white_sigma 6.8658 gray_mean 72.9422 gray_sigma 10.3 setting bottom of white matter range wm_low to 83.2 setting top of gray matter range gray_hi to 93.5 wm_low 83.2422 wm_hi 125 gray_low 30 gray_hi 93.5422 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 83.2422 wm_hi 125 gray_low 30 gray_hi 93.5422 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 93.5422, wm_low = 83.2422 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=93.5422, wmlow=83.2422 112718 voxels processed (0.67%) 51357 voxels white (0.31%) 61361 voxels non-white (0.37%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=78.2422, gray_hi=93.5422, wsize=13 211787 voxels tested (1.26%) 40207 voxels changed (0.24%) 48569 multi-scale searches (0.29%) Recovering bright white MRIrecoverBrightWhite() wm_low 83.2422 wm_hi 125 slack 6.8658 pct_thresh 0.33 intensity_thresh 131.866 nvox_thresh 8.58 478 voxels tested (0.00%) 341 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=78.2422, hithr=93.5422 smoothing input volume with sigma = 0.250 75678 voxels tested (0.45%) 14402 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1660 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1083 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 2871 filled MRIfindBrightNonWM(): 1457 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 2.0 minutes writing output to wm.seg.mgz... @#@FSTIME 2023:02:18:13:51:33 mri_segment N 5 e 122.30 S 0.15 U 122.82 P 100% M 146380 F 15 R 211702 W 0 c 525 w 29 I 3752 O 704 L 1.13 1.10 1.10 @#@FSLOADPOST 2023:02:18:13:53:35 mri_segment N 5 1.09 1.08 1.09 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.94 minutes reading wm segmentation from wm.seg.mgz... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 0 voxels added to wm to prevent paths from MTL structures to cortex 2553 additional wm voxels added 0 additional wm voxels added SEG EDIT: 31218 voxels turned on, 40933 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2023:02:18:13:53:35 mri_edit_wm_with_aseg N 5 e 56.38 S 0.18 U 57.73 P 102% M 462164 F 15 R 317225 W 0 c 203 w 70 I 3608 O 640 L 1.09 1.08 1.09 @#@FSLOADPOST 2023:02:18:13:54:31 mri_edit_wm_with_aseg N 5 1.10 1.08 1.09 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 10 found - 10 modified | TOTAL: 17 pass 2 (xy-): 0 found - 10 modified | TOTAL: 17 pass 1 (yz+): 20 found - 20 modified | TOTAL: 37 pass 2 (yz+): 0 found - 20 modified | TOTAL: 37 pass 1 (yz-): 27 found - 27 modified | TOTAL: 64 pass 2 (yz-): 0 found - 27 modified | TOTAL: 64 pass 1 (xz+): 8 found - 8 modified | TOTAL: 72 pass 2 (xz+): 0 found - 8 modified | TOTAL: 72 pass 1 (xz-): 3 found - 3 modified | TOTAL: 75 pass 2 (xz-): 0 found - 3 modified | TOTAL: 75 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 8 pass 2 (+++): 0 found - 6 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 9 found - 9 modified | TOTAL: 19 pass 2 (+++): 0 found - 9 modified | TOTAL: 19 Iteration Number : 1 pass 1 (++): 36 found - 36 modified | TOTAL: 36 pass 2 (++): 0 found - 36 modified | TOTAL: 36 pass 1 (+-): 30 found - 30 modified | TOTAL: 66 pass 2 (+-): 0 found - 30 modified | TOTAL: 66 pass 1 (--): 19 found - 19 modified | TOTAL: 85 pass 2 (--): 0 found - 19 modified | TOTAL: 85 pass 1 (-+): 16 found - 16 modified | TOTAL: 101 pass 2 (-+): 0 found - 16 modified | TOTAL: 101 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 3 found - 3 modified | TOTAL: 7 pass 2 (yz-): 0 found - 3 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 1 found - 1 modified | TOTAL: 3 pass 2 (+-): 0 found - 1 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 2 found - 2 modified | TOTAL: 6 pass 2 (-+): 0 found - 2 modified | TOTAL: 6 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 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 = 211 (out of 500136: 0.042189) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:02:18:13:54:31 mri_pretess N 4 e 2.28 S 0.03 U 2.70 P 119% M 56924 F 15 R 12990 W 0 c 15 w 25 I 3568 O 640 L 1.10 1.08 1.09 @#@FSLOADPOST 2023:02:18:13:54:34 mri_pretess N 4 1.09 1.08 1.09 #-------------------------------------------- #@# Fill Sat Feb 18 13:54:34 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/7.2.0/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... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58041; 0.08215 -0.06859 1.12363 -31.10373; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.09401 -0.04681 -0.08298 1.50745; 0.09162 1.16522 0.07196 -12.58041; 0.08215 -0.06859 1.12363 -31.10373; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Looking for area (min, max) = (350, 1400) area[0] = 1275 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) no need to search using seed (126, 122, 150), TAL = (2.0, 22.0, 6.0) talairach voxel to voxel transform 0.90587 0.04018 0.06432 1.14066; -0.06689 0.85202 -0.05951 8.96870; -0.07031 0.04907 0.88164 28.14565; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 122, 150) --> (2.0, 22.0, 6.0) done. filling took 1.6 minutes talairach cc position changed to (2.00, 22.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 22.00, 6.00) SRC: (113.53, 96.77, 158.79) search lh wm seed point around talairach space (-16.00, 22.00, 6.00), SRC: (146.14, 94.36, 156.25) 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 2023:02:18:13:54:34 mri_fill N 10 e 96.50 S 0.64 U 96.56 P 100% M 915912 F 16 R 489339 W 0 c 462 w 28 I 3928 O 232 L 1.09 1.08 1.09 @#@FSLOADPOST 2023:02:18:13:56:10 mri_fill N 10 1.12 1.11 1.09 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Sat Feb 18 13:56:10 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 13 found - 13 modified | TOTAL: 15 pass 2 (yz+): 0 found - 13 modified | TOTAL: 15 pass 1 (yz-): 9 found - 9 modified | TOTAL: 24 pass 2 (yz-): 0 found - 9 modified | TOTAL: 24 pass 1 (xz+): 0 found - 0 modified | TOTAL: 24 pass 1 (xz-): 1 found - 1 modified | TOTAL: 25 pass 2 (xz-): 0 found - 1 modified | TOTAL: 25 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 = 28 (out of 242582: 0.011542) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:02:18:13:56:10 mri_pretess N 4 e 1.25 S 0.02 U 1.67 P 135% M 40584 F 0 R 8858 W 0 c 90 w 9 I 0 O 224 L 1.12 1.11 1.09 @#@FSLOADPOST 2023:02:18:13:56:11 mri_pretess N 4 1.12 1.11 1.09 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.2.0 7.2.0 slice 50: 369 vertices, 427 faces slice 60: 4371 vertices, 4528 faces slice 70: 10146 vertices, 10369 faces slice 80: 18258 vertices, 18538 faces slice 90: 27579 vertices, 27936 faces slice 100: 37680 vertices, 38004 faces slice 110: 49020 vertices, 49403 faces slice 120: 60175 vertices, 60539 faces slice 130: 70724 vertices, 71059 faces slice 140: 80517 vertices, 80865 faces slice 150: 89480 vertices, 89776 faces slice 160: 97642 vertices, 97927 faces slice 170: 103993 vertices, 104218 faces slice 180: 109857 vertices, 110081 faces slice 190: 113624 vertices, 113742 faces slice 200: 114542 vertices, 114566 faces slice 210: 114542 vertices, 114566 faces slice 220: 114542 vertices, 114566 faces slice 230: 114542 vertices, 114566 faces slice 240: 114542 vertices, 114566 faces slice 250: 114542 vertices, 114566 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2023:02:18:13:56:11 mri_tessellate N 3 e 0.89 S 0.02 U 1.11 P 127% M 35856 F 15 R 7937 W 0 c 15 w 25 I 3856 O 5376 L 1.12 1.11 1.09 @#@FSLOADPOST 2023:02:18:13:56:12 mri_tessellate N 3 1.12 1.11 1.09 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 114542 voxel in cpt #1: X=-24 [v=114542,e=343698,f=229132] located at (-26.446735, -10.280386, 37.841003) For the whole surface: X=-24 [v=114542,e=343698,f=229132] One single component has been found nothing to do done @#@FSTIME 2023:02:18:13:56:12 mris_extract_main_component N 2 e 0.50 S 0.12 U 0.55 P 135% M 228648 F 14 R 60416 W 0 c 11 w 26 I 3264 O 8056 L 1.12 1.11 1.09 @#@FSLOADPOST 2023:02:18:13:56:13 mris_extract_main_component N 2 1.11 1.11 1.09 #-------------------------------------------- #@# Tessellate rh Sat Feb 18 13:56:13 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 11 found - 11 modified | TOTAL: 11 pass 2 (yz+): 0 found - 11 modified | TOTAL: 11 pass 1 (yz-): 10 found - 10 modified | TOTAL: 21 pass 2 (yz-): 0 found - 10 modified | TOTAL: 21 pass 1 (xz+): 2 found - 2 modified | TOTAL: 23 pass 2 (xz+): 0 found - 2 modified | TOTAL: 23 pass 1 (xz-): 0 found - 0 modified | TOTAL: 23 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 23 (out of 239451: 0.009605) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:02:18:13:56:13 mri_pretess N 4 e 0.91 S 0.03 U 1.36 P 153% M 40660 F 0 R 8860 W 0 c 65 w 9 I 0 O 224 L 1.11 1.11 1.09 @#@FSLOADPOST 2023:02:18:13:56:14 mri_pretess N 4 1.11 1.11 1.09 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.2.0 7.2.0 slice 50: 53 vertices, 68 faces slice 60: 2256 vertices, 2361 faces slice 70: 7386 vertices, 7594 faces slice 80: 14833 vertices, 15108 faces slice 90: 24044 vertices, 24381 faces slice 100: 33922 vertices, 34251 faces slice 110: 44430 vertices, 44778 faces slice 120: 55895 vertices, 56289 faces slice 130: 66776 vertices, 67148 faces slice 140: 77529 vertices, 77927 faces slice 150: 87190 vertices, 87567 faces slice 160: 95542 vertices, 95840 faces slice 170: 102405 vertices, 102646 faces slice 180: 108295 vertices, 108556 faces slice 190: 113140 vertices, 113331 faces slice 200: 114894 vertices, 114928 faces slice 210: 114894 vertices, 114928 faces slice 220: 114894 vertices, 114928 faces slice 230: 114894 vertices, 114928 faces slice 240: 114894 vertices, 114928 faces slice 250: 114894 vertices, 114928 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2023:02:18:13:56:14 mri_tessellate N 3 e 0.84 S 0.02 U 1.06 P 129% M 35940 F 0 R 7962 W 0 c 26 w 4 I 0 O 5392 L 1.11 1.11 1.09 @#@FSLOADPOST 2023:02:18:13:56:15 mri_tessellate N 3 1.11 1.11 1.09 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 114894 voxel in cpt #1: X=-34 [v=114894,e=344784,f=229856] located at (27.924017, -6.556826, 37.739925) For the whole surface: X=-34 [v=114894,e=344784,f=229856] One single component has been found nothing to do done @#@FSTIME 2023:02:18:13:56:15 mris_extract_main_component N 2 e 0.53 S 0.16 U 0.53 P 130% M 229256 F 0 R 60644 W 0 c 30 w 10 I 0 O 8088 L 1.11 1.11 1.09 @#@FSLOADPOST 2023:02:18:13:56:15 mris_extract_main_component N 2 1.11 1.11 1.09 #-------------------------------------------- #@# Smooth1 lh Sat Feb 18 13:56:15 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Feb 18 13:56:15 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 4162 of (4162 4165) to complete... Waiting for PID 4165 of (4162 4165) to complete... 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... 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... PIDs (4162 4165) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Feb 18 13:56:18 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Feb 18 13:56:18 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 4210 of (4210 4213) to complete... Waiting for PID 4213 of (4210 4213) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 43.3 mm, total surface area = 61220 mm^2 step 000: RMS=0.149 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.067 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.036 (target=0.015) step 060: RMS=0.035 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 31.145847 mris_inflate stimesec 4.064225 mris_inflate ru_maxrss 183176 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 485691 mris_inflate ru_majflt 16 mris_inflate ru_nswap 0 mris_inflate ru_inblock 2176 mris_inflate ru_oublock 8064 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2688 mris_inflate ru_nivcsw 1165 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 42.8 mm, total surface area = 61612 mm^2 step 000: RMS=0.149 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.038 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.036 (target=0.015) step 060: RMS=0.036 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 31.618373 mris_inflate stimesec 3.908562 mris_inflate ru_maxrss 183824 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 480287 mris_inflate ru_majflt 11 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1560 mris_inflate ru_oublock 8088 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2925 mris_inflate ru_nivcsw 1122 PIDs (4210 4213) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Feb 18 13:56:38 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Feb 18 13:56:38 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 4258 of (4258 4261) to complete... Waiting for PID 4261 of (4258 4261) to complete... mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 scaling brain by 0.350... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.57 (0.00-->7.47) (max @ vno 38356 --> 38357) face area 0.03 +- 0.04 (-0.34-->0.83) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.221, avgs=0 005/300: dt: 0.9000, rms radial error=175.963, avgs=0 010/300: dt: 0.9000, rms radial error=175.407, avgs=0 015/300: dt: 0.9000, rms radial error=174.677, avgs=0 020/300: dt: 0.9000, rms radial error=173.844, avgs=0 025/300: dt: 0.9000, rms radial error=172.953, avgs=0 030/300: dt: 0.9000, rms radial error=172.030, avgs=0 035/300: dt: 0.9000, rms radial error=171.089, avgs=0 040/300: dt: 0.9000, rms radial error=170.141, avgs=0 045/300: dt: 0.9000, rms radial error=169.190, avgs=0 050/300: dt: 0.9000, rms radial error=168.239, avgs=0 055/300: dt: 0.9000, rms radial error=167.294, avgs=0 060/300: dt: 0.9000, rms radial error=166.355, avgs=0 065/300: dt: 0.9000, rms radial error=165.419, avgs=0 070/300: dt: 0.9000, rms radial error=164.488, avgs=0 075/300: dt: 0.9000, rms radial error=163.562, avgs=0 080/300: dt: 0.9000, rms radial error=162.641, avgs=0 085/300: dt: 0.9000, rms radial error=161.725, avgs=0 090/300: dt: 0.9000, rms radial error=160.813, avgs=0 095/300: dt: 0.9000, rms radial error=159.907, avgs=0 100/300: dt: 0.9000, rms radial error=159.005, avgs=0 105/300: dt: 0.9000, rms radial error=158.109, avgs=0 110/300: dt: 0.9000, rms radial error=157.217, avgs=0 115/300: dt: 0.9000, rms radial error=156.330, avgs=0 120/300: dt: 0.9000, rms radial error=155.447, avgs=0 125/300: dt: 0.9000, rms radial error=154.570, avgs=0 130/300: dt: 0.9000, rms radial error=153.697, avgs=0 135/300: dt: 0.9000, rms radial error=152.830, avgs=0 140/300: dt: 0.9000, rms radial error=151.967, avgs=0 145/300: dt: 0.9000, rms radial error=151.108, avgs=0 150/300: dt: 0.9000, rms radial error=150.255, avgs=0 155/300: dt: 0.9000, rms radial error=149.406, avgs=0 160/300: dt: 0.9000, rms radial error=148.562, avgs=0 165/300: dt: 0.9000, rms radial error=147.723, avgs=0 170/300: dt: 0.9000, rms radial error=146.888, avgs=0 175/300: dt: 0.9000, rms radial error=146.058, avgs=0 180/300: dt: 0.9000, rms radial error=145.232, avgs=0 185/300: dt: 0.9000, rms radial error=144.411, avgs=0 190/300: dt: 0.9000, rms radial error=143.595, avgs=0 195/300: dt: 0.9000, rms radial error=142.783, avgs=0 200/300: dt: 0.9000, rms radial error=141.976, avgs=0 205/300: dt: 0.9000, rms radial error=141.173, avgs=0 210/300: dt: 0.9000, rms radial error=140.375, avgs=0 215/300: dt: 0.9000, rms radial error=139.581, avgs=0 220/300: dt: 0.9000, rms radial error=138.792, avgs=0 225/300: dt: 0.9000, rms radial error=138.007, avgs=0 230/300: dt: 0.9000, rms radial error=137.226, avgs=0 235/300: dt: 0.9000, rms radial error=136.450, avgs=0 240/300: dt: 0.9000, rms radial error=135.678, avgs=0 245/300: dt: 0.9000, rms radial error=134.911, avgs=0 250/300: dt: 0.9000, rms radial error=134.148, avgs=0 255/300: dt: 0.9000, rms radial error=133.389, avgs=0 260/300: dt: 0.9000, rms radial error=132.635, avgs=0 265/300: dt: 0.9000, rms radial error=131.884, avgs=0 270/300: dt: 0.9000, rms radial error=131.138, avgs=0 275/300: dt: 0.9000, rms radial error=130.397, avgs=0 280/300: dt: 0.9000, rms radial error=129.659, avgs=0 285/300: dt: 0.9000, rms radial error=128.926, avgs=0 290/300: dt: 0.9000, rms radial error=128.196, avgs=0 295/300: dt: 0.9000, rms radial error=127.471, avgs=0 300/300: dt: 0.9000, rms radial error=126.750, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12745.66 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00048 epoch 2 (K=40.0), pass 1, starting sse = 1828.35 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00028 epoch 3 (K=160.0), pass 1, starting sse = 132.56 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/18 = 0.00585 epoch 4 (K=640.0), pass 1, starting sse = 7.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/21 = 0.00630 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0472 hours FSRUNTIME@ mris_sphere 0.0472 hours 4 threads #VMPC# mris_sphere VmPeak 674712 mris_sphere done mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 scaling brain by 0.350... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.57 (0.00-->8.09) (max @ vno 44180 --> 44207) face area 0.03 +- 0.04 (-0.24-->0.80) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.197, avgs=0 005/300: dt: 0.9000, rms radial error=175.938, avgs=0 010/300: dt: 0.9000, rms radial error=175.383, avgs=0 015/300: dt: 0.9000, rms radial error=174.654, avgs=0 020/300: dt: 0.9000, rms radial error=173.825, avgs=0 025/300: dt: 0.9000, rms radial error=172.940, avgs=0 030/300: dt: 0.9000, rms radial error=172.023, avgs=0 035/300: dt: 0.9000, rms radial error=171.088, avgs=0 040/300: dt: 0.9000, rms radial error=170.146, avgs=0 045/300: dt: 0.9000, rms radial error=169.201, avgs=0 050/300: dt: 0.9000, rms radial error=168.256, avgs=0 055/300: dt: 0.9000, rms radial error=167.315, avgs=0 060/300: dt: 0.9000, rms radial error=166.377, avgs=0 065/300: dt: 0.9000, rms radial error=165.443, avgs=0 070/300: dt: 0.9000, rms radial error=164.513, avgs=0 075/300: dt: 0.9000, rms radial error=163.589, avgs=0 080/300: dt: 0.9000, rms radial error=162.669, avgs=0 085/300: dt: 0.9000, rms radial error=161.754, avgs=0 090/300: dt: 0.9000, rms radial error=160.844, avgs=0 095/300: dt: 0.9000, rms radial error=159.939, avgs=0 100/300: dt: 0.9000, rms radial error=159.039, avgs=0 105/300: dt: 0.9000, rms radial error=158.144, avgs=0 110/300: dt: 0.9000, rms radial error=157.253, avgs=0 115/300: dt: 0.9000, rms radial error=156.368, avgs=0 120/300: dt: 0.9000, rms radial error=155.487, avgs=0 125/300: dt: 0.9000, rms radial error=154.612, avgs=0 130/300: dt: 0.9000, rms radial error=153.742, avgs=0 135/300: dt: 0.9000, rms radial error=152.877, avgs=0 140/300: dt: 0.9000, rms radial error=152.016, avgs=0 145/300: dt: 0.9000, rms radial error=151.160, avgs=0 150/300: dt: 0.9000, rms radial error=150.309, avgs=0 155/300: dt: 0.9000, rms radial error=149.462, avgs=0 160/300: dt: 0.9000, rms radial error=148.620, avgs=0 165/300: dt: 0.9000, rms radial error=147.783, avgs=0 170/300: dt: 0.9000, rms radial error=146.951, avgs=0 175/300: dt: 0.9000, rms radial error=146.123, avgs=0 180/300: dt: 0.9000, rms radial error=145.300, avgs=0 185/300: dt: 0.9000, rms radial error=144.481, avgs=0 190/300: dt: 0.9000, rms radial error=143.667, avgs=0 195/300: dt: 0.9000, rms radial error=142.857, avgs=0 200/300: dt: 0.9000, rms radial error=142.052, avgs=0 205/300: dt: 0.9000, rms radial error=141.251, avgs=0 210/300: dt: 0.9000, rms radial error=140.454, avgs=0 215/300: dt: 0.9000, rms radial error=139.662, avgs=0 220/300: dt: 0.9000, rms radial error=138.875, avgs=0 225/300: dt: 0.9000, rms radial error=138.092, avgs=0 230/300: dt: 0.9000, rms radial error=137.313, avgs=0 235/300: dt: 0.9000, rms radial error=136.538, avgs=0 240/300: dt: 0.9000, rms radial error=135.768, avgs=0 245/300: dt: 0.9000, rms radial error=135.003, avgs=0 250/300: dt: 0.9000, rms radial error=134.241, avgs=0 255/300: dt: 0.9000, rms radial error=133.484, avgs=0 260/300: dt: 0.9000, rms radial error=132.731, avgs=0 265/300: dt: 0.9000, rms radial error=131.982, avgs=0 270/300: dt: 0.9000, rms radial error=131.238, avgs=0 275/300: dt: 0.9000, rms radial error=130.497, avgs=0 280/300: dt: 0.9000, rms radial error=129.761, avgs=0 285/300: dt: 0.9000, rms radial error=129.029, avgs=0 290/300: dt: 0.9000, rms radial error=128.301, avgs=0 295/300: dt: 0.9000, rms radial error=127.577, avgs=0 300/300: dt: 0.9000, rms radial error=126.857, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12779.98 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00045 epoch 2 (K=40.0), pass 1, starting sse = 1836.58 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00034 epoch 3 (K=160.0), pass 1, starting sse = 135.67 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/18 = 0.00555 epoch 4 (K=640.0), pass 1, starting sse = 8.38 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/24 = 0.00579 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0480 hours FSRUNTIME@ mris_sphere 0.0480 hours 4 threads #VMPC# mris_sphere VmPeak 675192 mris_sphere done PIDs (4258 4261) completed and logs appended. #@# Fix Topology lh Sat Feb 18 13:59:30 EST 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Sub-139 lh #@# Fix Topology rh Sat Feb 18 13:59:30 EST 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Sub-139 rh Waiting for PID 4301 of (4301 4304) to complete... Waiting for PID 4304 of (4301 4304) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Sub-139 lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.2.0 7.2.0 before topology correction, eno=-24 (nv=114542, nf=229132, ne=343698, g=13) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 3467 ambiguous faces found in tessellation segmenting defects... 11 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 1 -merging segment 10 into 6 9 defects to be corrected 0 vertices coincident reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.3266 (-4.6633) -vertex loglikelihood: -6.1037 (-3.0519) -normal dot loglikelihood: -3.6161 (-3.6161) -quad curv loglikelihood: -6.1414 (-3.0707) Total Loglikelihood : -25.1879 CORRECTING DEFECT 0 (vertices=32, convex hull=39, v0=17977) After retessellation of defect 0 (v0=17977), euler #=-8 (112548,337103,224547) : difference with theory (-6) = 2 CORRECTING DEFECT 1 (vertices=178, convex hull=168, v0=38419) After retessellation of defect 1 (v0=38419), euler #=-6 (112614,337381,224761) : difference with theory (-5) = 1 CORRECTING DEFECT 2 (vertices=64, convex hull=117, v0=43827) After retessellation of defect 2 (v0=43827), euler #=-5 (112636,337497,224856) : difference with theory (-4) = 1 CORRECTING DEFECT 3 (vertices=167, convex hull=61, v0=67298) After retessellation of defect 3 (v0=67298), euler #=-4 (112665,337609,224940) : difference with theory (-3) = 1 CORRECTING DEFECT 4 (vertices=19, convex hull=24, v0=70492) After retessellation of defect 4 (v0=70492), euler #=-3 (112668,337626,224955) : difference with theory (-2) = 1 CORRECTING DEFECT 5 (vertices=1478, convex hull=559, v0=78252) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 5 (v0=78252), euler #=-1 (113056,339124,226067) : difference with theory (-1) = 0 CORRECTING DEFECT 6 (vertices=13, convex hull=24, v0=78394) After retessellation of defect 6 (v0=78394), euler #=0 (113059,339141,226082) : difference with theory (0) = 0 CORRECTING DEFECT 7 (vertices=22, convex hull=54, v0=79104) After retessellation of defect 7 (v0=79104), euler #=1 (113072,339199,226128) : difference with theory (1) = 0 CORRECTING DEFECT 8 (vertices=26, convex hull=34, v0=80039) After retessellation of defect 8 (v0=80039), euler #=2 (113080,339234,226156) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.06-->7.56) (max @ vno 41596 --> 42700) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.06-->7.56) (max @ vno 41596 --> 42700) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 25 mutations (30.1%), 58 crossovers (69.9%), 27 vertices were eliminated building final representation... 1462 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113080, nf=226156, ne=339234, g=0) writing corrected surface to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 170 intersecting 001: 10 intersecting 002: 9 intersecting 003: 2 intersecting terminating search with 0 intersecting topology fixing took 2.1 minutes FSRUNTIME@ mris_fix_topology lh 0.0352 hours 4 threads #VMPC# mris_fix_topology VmPeak 976684 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 Sub-139 rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.2.0 7.2.0 before topology correction, eno=-34 (nv=114894, nf=229856, ne=344784, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 4326 ambiguous faces found in tessellation segmenting defects... 13 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 1 12 defects to be corrected 0 vertices coincident reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.2829 (-4.6414) -vertex loglikelihood: -6.0968 (-3.0484) -normal dot loglikelihood: -3.6256 (-3.6256) -quad curv loglikelihood: -6.2717 (-3.1359) Total Loglikelihood : -25.2770 CORRECTING DEFECT 0 (vertices=29, convex hull=58, v0=35646) After retessellation of defect 0 (v0=35646), euler #=-8 (112361,336309,223940) : difference with theory (-9) = -1 CORRECTING DEFECT 1 (vertices=390, convex hull=303, v0=36588) normal vector of length zero at vertex 112521 with 3 faces After retessellation of defect 1 (v0=36588), euler #=-6 (112493,336853,224354) : difference with theory (-8) = -2 CORRECTING DEFECT 2 (vertices=23, convex hull=66, v0=47705) After retessellation of defect 2 (v0=47705), euler #=-5 (112502,336906,224399) : difference with theory (-7) = -2 CORRECTING DEFECT 3 (vertices=367, convex hull=266, v0=61071) After retessellation of defect 3 (v0=61071), euler #=-4 (112609,337358,224745) : difference with theory (-6) = -2 CORRECTING DEFECT 4 (vertices=137, convex hull=89, v0=62053) After retessellation of defect 4 (v0=62053), euler #=-4 (112625,337448,224819) : difference with theory (-5) = -1 CORRECTING DEFECT 5 (vertices=28, convex hull=69, v0=67094) After retessellation of defect 5 (v0=67094), euler #=-3 (112642,337521,224876) : difference with theory (-4) = -1 CORRECTING DEFECT 6 (vertices=21, convex hull=46, v0=70552) After retessellation of defect 6 (v0=70552), euler #=-2 (112653,337571,224916) : difference with theory (-3) = -1 CORRECTING DEFECT 7 (vertices=44, convex hull=79, v0=76346) After retessellation of defect 7 (v0=76346), euler #=-1 (112671,337658,224986) : difference with theory (-2) = -1 CORRECTING DEFECT 8 (vertices=358, convex hull=55, v0=77120) After retessellation of defect 8 (v0=77120), euler #=0 (112682,337710,225028) : difference with theory (-1) = -1 CORRECTING DEFECT 9 (vertices=1112, convex hull=526, v0=77146) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 9 (v0=77146), euler #=0 (113110,339315,226205) : difference with theory (0) = 0 CORRECTING DEFECT 10 (vertices=9, convex hull=18, v0=77228) After retessellation of defect 10 (v0=77228), euler #=1 (113112,339325,226214) : difference with theory (1) = 0 CORRECTING DEFECT 11 (vertices=26, convex hull=24, v0=78483) After retessellation of defect 11 (v0=78483), euler #=2 (113114,339336,226224) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.07-->12.23) (max @ vno 37463 --> 38378) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.07-->12.23) (max @ vno 37463 --> 38378) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 49 mutations (31.2%), 108 crossovers (68.8%), 91 vertices were eliminated building final representation... 1780 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113114, nf=226224, ne=339336, g=0) writing corrected surface to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 300 intersecting 001: 15 intersecting 002: 3 intersecting terminating search with 0 intersecting topology fixing took 2.5 minutes FSRUNTIME@ mris_fix_topology rh 0.0412 hours 4 threads #VMPC# mris_fix_topology VmPeak 977188 PIDs (4301 4304) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 113080 - 339234 + 226156 = 2 --> 0 holes F =2V-4: 226156 = 226160-4 (0) 2E=3F: 678468 = 678468 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 113114 - 339336 + 226224 = 2 --> 0 holes F =2V-4: 226224 = 226228-4 (0) 2E=3F: 678672 = 678672 (0) total defect index = 0 Sat Feb 18 14:01:59 EST 2023 setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii cd /home/developer/Desktop/1st_scan_nii/Sub-139/scripts /usr/local/freesurfer/7.2.0/bin/defect2seg --s Sub-139 freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b defect2seg 7.2.0 Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux pid 4357 mri_label2vol --defects /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.orig.nofix /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.defect_labels /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz 1000 0 /home/developer/Desktop/1st_scan_nii/Sub-139/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/mri/surface.defects.mgz mris_defects_pointset -s /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.orig.nofix -d /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.defect_labels -o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.defects.pointset Reading in surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.orig.nofix Reading in defect segmentation /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.defect_labels #VMPC# mris_defects_pointset 548800 mris_defects_pointset done mri_label2vol --defects /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.orig.nofix /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.defect_labels /home/developer/Desktop/1st_scan_nii/Sub-139/mri/surface.defects.mgz 2000 1 /home/developer/Desktop/1st_scan_nii/Sub-139/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 MRIcopyHeader(): source has ctab Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/mri/surface.defects.mgz mris_defects_pointset -s /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.orig.nofix -d /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.defect_labels -o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.defects.pointset Reading in surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.orig.nofix Reading in defect segmentation /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.defect_labels #VMPC# mris_defects_pointset 549052 mris_defects_pointset done Started at Sat Feb 18 14:01:59 EST 2023 Ended at Sat Feb 18 14:02:03 EST 2023 Defect2seg-Run-Time-Sec 4 Defect2seg-Run-Time-Min 0.08 Defect2seg-Run-Time-Hours 0.00 tkmeditfv Sub-139 brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2023:02:18:14:01:59 defect2seg N 2 e 4.04 S 0.67 U 4.72 P 133% M 220192 F 41 R 196291 W 0 c 96 w 320 I 19208 O 368 L 4.35 3.41 2.11 @#@FSLOADPOST 2023:02:18:14:02:03 defect2seg N 2 4.09 3.37 2.10 mris_remesh --remesh --iters 3 --input /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.orig.premesh --output /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708793 remeshing to edge length 0.708793 with 3 iterations avg qual before : 0.892114 after: 0.971188 Removing intersections Remeshed surface quality stats nv0 = 113080 nv = 118080 1.04422 Area 236156 0.30119 0.03357 0.070601 0.5067 Corner 708468 60.00000 8.80516 16.577929 145.8816 Edge 354234 0.84195 0.08216 0.445314 1.2495 Hinge 354234 9.64278 9.78279 0.000000 147.5551 mris_remesh done @#@FSTIME 2023:02:18:14:02:03 mris_remesh N 7 e 31.88 S 0.27 U 33.15 P 104% M 650016 F 14 R 257800 W 0 c 175 w 77 I 3584 O 8304 L 4.09 3.37 2.10 @#@FSLOADPOST 2023:02:18:14:02:35 mris_remesh N 7 2.87 3.14 2.07 mris_remesh --remesh --iters 3 --input /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.orig.premesh --output /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.710763 remeshing to edge length 0.710763 with 3 iterations avg qual before : 0.891925 after: 0.971367 Removing intersections Remeshed surface quality stats nv0 = 113114 nv = 118087 1.04396 Area 236170 0.30273 0.03369 0.051834 0.4859 Corner 708510 60.00000 8.77399 17.217918 140.0020 Edge 354255 0.84404 0.08214 0.280648 1.2641 Hinge 354255 9.70812 9.99260 0.000022 172.4636 mris_remesh done @#@FSTIME 2023:02:18:14:02:35 mris_remesh N 7 e 30.95 S 0.28 U 32.16 P 104% M 651792 F 0 R 243868 W 0 c 152 w 57 I 0 O 8312 L 2.87 3.14 2.07 @#@FSLOADPOST 2023:02:18:14:03:06 mris_remesh N 7 2.13 2.93 2.03 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2023:02:18:14:03:06 mris_remove_intersection N 2 e 2.45 S 0.10 U 2.58 P 109% M 294580 F 15 R 78037 W 0 c 17 w 35 I 3312 O 8312 L 2.13 2.93 2.03 @#@FSLOADPOST 2023:02:18:14:03:09 mris_remove_intersection N 2 2.04 2.90 2.03 rm -f ../surf/lh.inflated /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2023:02:18:14:03:09 mris_remove_intersection N 2 e 2.47 S 0.11 U 2.61 P 110% M 293100 F 0 R 77530 W 0 c 22 w 16 I 0 O 8312 L 2.04 2.90 2.03 @#@FSLOADPOST 2023:02:18:14:03:11 mris_remove_intersection N 2 2.04 2.90 2.03 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Sat Feb 18 14:03:11 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 215245 voxels (1.28%) border gray 234848 voxels (1.40%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 99.7 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 10.3 [30.0 --> 110.0] white_mean = 99.7227 +/- 7.46852, gray_mean = 75.9404 +/- 10.2923 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=177 nbins=178 intensity peaks found at WM=103+-4.3, GM=71+-9.6 white_mode = 103, gray_mode = 71 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.5 (was 105.000000) setting MIN_BORDER_WHITE to 71.0 (was 85.000000) setting MAX_CSF to 50.4 (was 40.000000) setting MAX_GRAY to 95.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 60.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 40.1 (was 40.000000) When placing the white surface white_border_hi = 110.469; white_border_low = 71; white_outside_low = 60.7077; white_inside_hi = 120; white_outside_hi = 110.469; When placing the pial surface pial_border_hi = 60.7077; pial_border_low = 40.1232; pial_outside_low = 10; pial_inside_hi = 95.5315; pial_outside_hi = 55.5616; #VMPC# mris_autodet_gwstats VmPeak 584060 mris_autodet_gwstats done @#@FSTIME 2023:02:18:14:03:11 mris_autodet_gwstats N 8 e 6.69 S 0.15 U 7.40 P 112% M 211012 F 15 R 60020 W 0 c 62 w 44 I 3824 O 8 L 2.04 2.90 2.03 @#@FSLOADPOST 2023:02:18:14:03:18 mris_autodet_gwstats N 8 1.88 2.84 2.01 #-------------------------------------------- #@# AutoDetGWStats rh Sat Feb 18 14:03:18 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 215245 voxels (1.28%) border gray 234848 voxels (1.40%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 99.7 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 10.3 [30.0 --> 110.0] white_mean = 99.7227 +/- 7.46852, gray_mean = 75.9404 +/- 10.2923 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=177 nbins=178 intensity peaks found at WM=103+-4.3, GM=72+-8.7 white_mode = 103, gray_mode = 72 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 61.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.5 (was 105.000000) setting MIN_BORDER_WHITE to 72.0 (was 85.000000) setting MAX_CSF to 51.4 (was 40.000000) setting MAX_GRAY to 95.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 61.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 41.1 (was 40.000000) When placing the white surface white_border_hi = 110.469; white_border_low = 72; white_outside_low = 61.7077; white_inside_hi = 120; white_outside_hi = 110.469; When placing the pial surface pial_border_hi = 61.7077; pial_border_low = 41.1232; pial_outside_low = 10; pial_inside_hi = 95.5315; pial_outside_hi = 56.5616; #VMPC# mris_autodet_gwstats VmPeak 451908 mris_autodet_gwstats done @#@FSTIME 2023:02:18:14:03:18 mris_autodet_gwstats N 8 e 6.75 S 0.10 U 7.55 P 113% M 211052 F 0 R 59920 W 0 c 70 w 36 I 0 O 8 L 1.88 2.84 2.01 @#@FSLOADPOST 2023:02:18:14:03:25 mris_autodet_gwstats N 8 1.81 2.81 2.01 #-------------------------------------------- #@# WhitePreAparc lh Sat Feb 18 14:03:25 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.2.0 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 236156 0.26604 0.06128 0.002648 0.5887 Corner 708468 60.00000 9.34619 8.820903 139.5181 Edge 354234 0.78775 0.11154 0.058587 1.3097 Hinge 354234 6.44585 6.21915 0.000028 142.5388 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 MRIfindBrightNonWM(): 2309 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 MRIcopyHeader(): source has ctab removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5721, nmarked2=6, nripped=5721 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59040: xyz = (-5.84962,-0.141641,81.191) oxyz = (-5.84962,-0.141641,81.191) wxzy = (-5.84962,-0.141641,81.191) pxyz = (0,0,0) CBVO Creating mask 118080 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5721 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5721, nmarked2=6, nripped=5721 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=2 had to be increased for 76 vertices, nripped=5721 mean border=83.2, 12 (12) missing vertices, mean dist 0.3 [0.8 (%38.5)->0.9 (%61.5))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0848 min Finding expansion regions mean absolute distance = 0.86 +- 1.08 3339 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=devel, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=2418256.0, rms=10.096 001: dt: 0.5000, sse=1348715.8, rms=7.379 (26.913%) 002: dt: 0.5000, sse=822129.9, rms=5.572 (24.489%) 003: dt: 0.5000, sse=551505.4, rms=4.356 (21.815%) 004: dt: 0.5000, sse=407402.9, rms=3.540 (18.730%) 005: dt: 0.5000, sse=335238.3, rms=3.046 (13.967%) 006: dt: 0.5000, sse=299962.5, rms=2.770 (9.075%) 007: dt: 0.5000, sse=286108.5, rms=2.648 (4.373%) 008: dt: 0.5000, sse=277846.8, rms=2.573 (2.865%) rms = 2.5439/2.5725, sse=275202.6/277846.8, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=275202.6, rms=2.544 (1.114%) 010: dt: 0.2500, sse=177087.5, rms=1.414 (44.420%) 011: dt: 0.2500, sse=165246.5, rms=1.210 (14.412%) 012: dt: 0.2500, sse=162303.9, rms=1.152 (4.797%) rms = 1.1163/1.1521, sse=160543.1/162303.9, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=160543.1, rms=1.116 (3.103%) rms = 1.0889/1.1163, sse=159258.0/160543.1, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=159258.0, rms=1.089 (2.460%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5721 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5955, nmarked2=59, nripped=5955 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=1 had to be increased for 26 vertices, nripped=5955 mean border=85.4, 16 (1) missing vertices, mean dist -0.2 [0.5 (%66.5)->0.3 (%33.5))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0562 min Finding expansion regions mean absolute distance = 0.40 +- 0.77 2491 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=devel, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=560765.9, rms=4.137 015: dt: 0.5000, sse=329449.7, rms=2.616 (36.755%) 016: dt: 0.5000, sse=283079.4, rms=2.193 (16.172%) 017: dt: 0.5000, sse=266770.5, rms=2.022 (7.780%) rms = 2.1228/2.0225, sse=276339.4/266770.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=220012.2, rms=1.400 (30.788%) 019: dt: 0.2500, sse=201757.4, rms=1.052 (24.869%) 020: dt: 0.2500, sse=197108.8, rms=0.947 (9.998%) rms = 0.9179/0.9465, sse=195536.1/197108.8, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=195536.1, rms=0.918 (3.023%) rms = 0.8922/0.9179, sse=194541.8/195536.1, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=194541.8, rms=0.892 (2.806%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5955 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6078, nmarked2=60, nripped=6078 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 34 vertices, nripped=6078 mean border=87.9, 21 (1) missing vertices, mean dist -0.2 [0.3 (%73.8)->0.2 (%26.2))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0289 min Finding expansion regions mean absolute distance = 0.30 +- 0.45 2725 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=devel, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=445833.2, rms=3.495 023: dt: 0.5000, sse=269181.2, rms=2.074 (40.643%) 024: dt: 0.5000, sse=255776.0, rms=1.934 (6.777%) rms = 1.9414/1.9339, sse=256086.5/255776.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=210402.5, rms=1.301 (32.733%) 026: dt: 0.2500, sse=191720.0, rms=0.925 (28.887%) 027: dt: 0.2500, sse=188916.6, rms=0.855 (7.535%) rms = 0.8420/0.8554, sse=188476.8/188916.6, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=188476.8, rms=0.842 (1.568%) rms = 0.8204/0.8420, sse=187631.4/188476.8, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=187631.4, rms=0.820 (2.562%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6078 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6104, nmarked2=60, nripped=6104 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 24 vertices, nripped=6104 mean border=88.9, 26 (1) missing vertices, mean dist -0.1 [0.2 (%60.4)->0.2 (%39.6))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0172 min Finding expansion regions mean absolute distance = 0.23 +- 0.33 2727 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=devel, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=221690.5, rms=1.549 030: dt: 0.5000, sse=202492.2, rms=1.220 (21.266%) rms = 1.4454/1.2196, sse=214322.1/202492.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=184481.3, rms=0.834 (31.656%) 032: dt: 0.2500, sse=179081.8, rms=0.694 (16.764%) rms = 0.6567/0.6938, sse=177639.3/179081.8, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=177639.3, rms=0.657 (5.353%) rms = 0.6426/0.6567, sse=177001.9/177639.3, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=177001.9, rms=0.643 (2.143%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.49 minutes #VMPC# mris_place_surfaces VmPeak 2134120 mris_place_surface done @#@FSTIME 2023:02:18:14:03:25 mris_place_surface N 18 e 156.70 S 2.97 U 284.50 P 183% M 1680984 F 24 R 471237 W 0 c 2617 w 1316 I 5008 O 8312 L 1.81 2.81 2.01 @#@FSLOADPOST 2023:02:18:14:06:01 mris_place_surface N 18 1.56 2.29 1.93 #-------------------------------------------- #@# WhitePreAparc rh Sat Feb 18 14:06:01 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.2.0 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface with 5 iterations removing intersecting faces 000: 2 intersecting step 1 with no progress (num=4, old_num=2) 001: 4 intersecting 002: 2 intersecting step 1 with no progress (num=7, old_num=2) 003: 7 intersecting terminating search with 0 intersecting Area 236170 0.26699 0.06201 0.000000 0.5770 Corner 708510 60.00000 9.42146 0.014606 179.9384 Edge 354255 0.78906 0.11263 0.000282 1.3624 Hinge 354255 6.48193 6.33375 0.000007 176.5961 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 MRIfindBrightNonWM(): 2309 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 MRIcopyHeader(): source has ctab removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5651, nmarked2=4, nripped=5651 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59044: xyz = (3.12339,3.02827,54.845) oxyz = (3.12339,3.02827,54.845) wxzy = (3.12339,3.02827,54.845) pxyz = (0,0,0) CBVO Creating mask 118087 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5651 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5651, nmarked2=4, nripped=5651 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=2 had to be increased for 68 vertices, nripped=5651 mean border=83.6, 32 (32) missing vertices, mean dist 0.2 [0.7 (%40.0)->0.9 (%60.0))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0844 min Finding expansion regions mean absolute distance = 0.82 +- 1.07 3038 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=devel, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=2514344.5, rms=10.033 001: dt: 0.5000, sse=1404571.5, rms=7.324 (26.997%) 002: dt: 0.5000, sse=899529.2, rms=5.582 (23.792%) 003: dt: 0.5000, sse=614777.8, rms=4.437 (20.499%) 004: dt: 0.5000, sse=475873.9, rms=3.654 (17.653%) 005: dt: 0.5000, sse=392974.7, rms=3.165 (13.381%) 006: dt: 0.5000, sse=353428.4, rms=2.880 (9.001%) 007: dt: 0.5000, sse=347847.9, rms=2.736 (5.007%) 008: dt: 0.5000, sse=334662.4, rms=2.664 (2.638%) rms = 2.6407/2.6638, sse=338121.0/334662.4, time step reduction 1 of 3 to 0.250 0 1 1 009: dt: 0.5000, sse=338121.0, rms=2.641 (0.868%) 010: dt: 0.2500, sse=227895.8, rms=1.471 (44.310%) 011: dt: 0.2500, sse=213736.5, rms=1.269 (13.737%) rms = 1.2230/1.2686, sse=211293.7/213736.5, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=211293.7, rms=1.223 (3.592%) rms = 1.1793/1.2230, sse=208677.5/211293.7, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=208677.5, rms=1.179 (3.578%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5651 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5814, nmarked2=9, nripped=5814 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=1 had to be increased for 78 vertices, nripped=5814 mean border=85.7, 57 (16) missing vertices, mean dist -0.2 [0.4 (%66.4)->0.2 (%33.6))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0532 min Finding expansion regions mean absolute distance = 0.36 +- 0.70 2164 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=devel, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=555440.9, rms=3.863 014: dt: 0.5000, sse=362131.7, rms=2.495 (35.404%) 015: dt: 0.5000, sse=333459.8, rms=2.217 (11.152%) 016: dt: 0.5000, sse=313860.0, rms=2.109 (4.873%) rms = 2.2303/2.1088, sse=325383.6/313860.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=263435.1, rms=1.486 (29.556%) 018: dt: 0.2500, sse=245583.9, rms=1.170 (21.224%) 019: dt: 0.2500, sse=240458.4, rms=1.069 (8.618%) rms = 1.0465/1.0694, sse=240159.5/240458.4, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=240159.5, rms=1.046 (2.145%) rms = 1.0097/1.0465, sse=236536.3/240159.5, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=236536.3, rms=1.010 (3.515%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5814 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5842, nmarked2=9, nripped=5842 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 73 vertices, nripped=5842 mean border=88.0, 62 (15) missing vertices, mean dist -0.2 [0.3 (%73.2)->0.2 (%26.8))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0291 min Finding expansion regions mean absolute distance = 0.28 +- 0.42 3016 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=devel, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=455137.0, rms=3.303 022: dt: 0.5000, sse=313930.1, rms=2.128 (35.565%) rms = 2.0275/2.1283, sse=318560.7/313930.1, time step reduction 1 of 3 to 0.250 0 1 0 023: dt: 0.5000, sse=318560.7, rms=2.028 (4.735%) 024: dt: 0.2500, sse=256372.4, rms=1.154 (43.066%) 025: dt: 0.2500, sse=250808.3, rms=1.015 (12.055%) rms = 0.9945/1.0152, sse=249129.7/250808.3, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=249129.7, rms=0.994 (2.038%) rms = 0.9390/0.9945, sse=249886.3/249129.7, time step reduction 3 of 3 to 0.062 0 1 0 027: dt: 0.1250, sse=249886.3, rms=0.939 (5.575%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5842 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5905, nmarked2=9, nripped=5905 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 64 vertices, nripped=5905 mean border=88.9, 72 (15) missing vertices, mean dist -0.1 [0.2 (%59.4)->0.2 (%40.6))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0173 min Finding expansion regions mean absolute distance = 0.22 +- 0.31 3081 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=devel, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=279254.8, rms=1.544 028: dt: 0.5000, sse=268341.9, rms=1.333 (13.663%) rms = 1.5387/1.3332, sse=268599.7/268341.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=237750.0, rms=0.964 (27.697%) 030: dt: 0.2500, sse=230411.7, rms=0.862 (10.529%) rms = 0.8186/0.8625, sse=234402.8/230411.7, time step reduction 2 of 3 to 0.125 0 1 1 031: dt: 0.2500, sse=234402.8, rms=0.819 (5.079%) rms = 0.7764/0.8186, sse=231078.8/234402.8, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=231078.8, rms=0.776 (5.164%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes removing intersecting faces 000: 1 intersecting step 1 with no progress (num=7, old_num=1) 001: 7 intersecting 002: 3 intersecting step 1 with no progress (num=4, old_num=3) 003: 4 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.41 minutes #VMPC# mris_place_surfaces VmPeak 2109288 mris_place_surface done @#@FSTIME 2023:02:18:14:06:01 mris_place_surface N 18 e 160.12 S 3.42 U 278.89 P 176% M 1656244 F 0 R 435577 W 0 c 2399 w 1156 I 0 O 8312 L 1.56 2.29 1.93 @#@FSLOADPOST 2023:02:18:14:08:42 mris_place_surface N 18 1.42 1.96 1.86 #-------------------------------------------- #@# CortexLabel lh Sat Feb 18 14:08:42 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 7 non-cortical segments detected only using segment with 7682 vertices erasing segment 0 (vno[0] = 20818) erasing segment 2 (vno[0] = 34967) erasing segment 3 (vno[0] = 69614) erasing segment 4 (vno[0] = 71301) erasing segment 5 (vno[0] = 87087) erasing segment 6 (vno[0] = 113525) @#@FSTIME 2023:02:18:14:08:42 mri_label2label N 5 e 13.99 S 0.09 U 14.48 P 104% M 303988 F 17 R 89556 W 0 c 83 w 41 I 4008 O 9512 L 1.42 1.96 1.86 @#@FSLOADPOST 2023:02:18:14:08:56 mri_label2label N 5 1.33 1.92 1.85 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Sat Feb 18 14:08:56 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 10 non-cortical segments detected only using segment with 5202 vertices erasing segment 0 (vno[0] = 20818) erasing segment 2 (vno[0] = 35806) erasing segment 3 (vno[0] = 35866) erasing segment 4 (vno[0] = 60688) erasing segment 5 (vno[0] = 67246) erasing segment 6 (vno[0] = 69614) erasing segment 7 (vno[0] = 71301) erasing segment 8 (vno[0] = 87087) erasing segment 9 (vno[0] = 113525) @#@FSTIME 2023:02:18:14:08:56 mri_label2label N 5 e 13.78 S 0.31 U 14.06 P 104% M 316664 F 0 R 92833 W 0 c 53 w 27 I 0 O 9720 L 1.33 1.92 1.85 @#@FSLOADPOST 2023:02:18:14:09:09 mri_label2label N 5 1.25 1.87 1.84 #-------------------------------------------- #@# CortexLabel rh Sat Feb 18 14:09:09 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 7 non-cortical segments detected only using segment with 7844 vertices erasing segment 1 (vno[0] = 31375) erasing segment 2 (vno[0] = 36429) erasing segment 3 (vno[0] = 54630) erasing segment 4 (vno[0] = 57377) erasing segment 5 (vno[0] = 66521) erasing segment 6 (vno[0] = 97325) @#@FSTIME 2023:02:18:14:09:09 mri_label2label N 5 e 14.09 S 0.13 U 14.53 P 104% M 304324 F 0 R 89599 W 0 c 52 w 24 I 0 O 9296 L 1.25 1.87 1.84 @#@FSLOADPOST 2023:02:18:14:09:23 mri_label2label N 5 1.28 1.84 1.83 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Sat Feb 18 14:09:23 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 MRIcopyHeader(): source has ctab 8 non-cortical segments detected only using segment with 5363 vertices erasing segment 1 (vno[0] = 33814) erasing segment 2 (vno[0] = 36429) erasing segment 3 (vno[0] = 37645) erasing segment 4 (vno[0] = 42572) erasing segment 5 (vno[0] = 54630) erasing segment 6 (vno[0] = 57377) erasing segment 7 (vno[0] = 66521) @#@FSTIME 2023:02:18:14:09:24 mri_label2label N 5 e 14.26 S 0.16 U 14.77 P 104% M 308636 F 0 R 90679 W 0 c 80 w 22 I 0 O 9496 L 1.28 1.84 1.83 @#@FSLOADPOST 2023:02:18:14:09:38 mri_label2label N 5 1.23 1.81 1.82 #-------------------------------------------- #@# Smooth2 lh Sat Feb 18 14:09:38 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Feb 18 14:09:38 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 4946 of (4946 4949) to complete... Waiting for PID 4949 of (4946 4949) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (4946 4949) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Feb 18 14:09:41 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Feb 18 14:09:41 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 4994 of (4994 4997) to complete... Waiting for PID 4997 of (4994 4997) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.3 mm, total surface area = 72020 mm^2 step 000: RMS=0.169 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 36.470353 mris_inflate stimesec 2.806982 mris_inflate ru_maxrss 183540 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49049 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3449 mris_inflate ru_nivcsw 1388 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 42.8 mm, total surface area = 72037 mm^2 step 000: RMS=0.169 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 35.206135 mris_inflate stimesec 3.684942 mris_inflate ru_maxrss 183012 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 457579 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3007 mris_inflate ru_nivcsw 1252 PIDs (4994 4997) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Feb 18 14:10:03 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sat Feb 18 14:10:03 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /home/developer/Desktop/1st_scan_nii/Sub-139/surf reconbatchjobs /home/developer/Desktop/1st_scan_nii/Sub-139/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 5073 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5076 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5079 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5082 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5085 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5088 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5091 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5094 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5097 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5100 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5103 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... Waiting for PID 5106 of (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 15.938*4pi (200.277) --> -15 handles ICI = 120.1, FI = 1228.5, variation=19191.948 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 158 vertices thresholded to be in k1 ~ [-0.19 0.57], k2 ~ [-0.11 0.06] total integrated curvature = 0.691*4pi (8.678) --> 0 handles ICI = 1.5, FI = 7.8, variation=141.176 96 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 130 vertices thresholded to be in [-0.13 0.27] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.024 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 15.526*4pi (195.101) --> -15 handles ICI = 121.0, FI = 1236.6, variation=19339.829 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 127 vertices thresholded to be in k1 ~ [-0.22 3.47], k2 ~ [-0.16 0.09] total integrated curvature = 0.655*4pi (8.233) --> 0 handles ICI = 1.5, FI = 7.8, variation=141.446 112 vertices thresholded to be in [-0.06 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 85 vertices thresholded to be in [-0.14 0.76] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.024 done. PIDs (5073 5076 5079 5082 5085 5088 5091 5094 5097 5100 5103 5106) completed and logs appended. #-------------------------------------------- #@# Sphere lh Sat Feb 18 14:10:44 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Feb 18 14:10:44 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 5177 of (5177 5180) to complete... Waiting for PID 5180 of (5177 5180) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.322... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=devel, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.78 pass 1: epoch 2 of 3 starting distance error %19.77 unfolding complete - removing small folds... starting distance error %19.73 removing remaining folds... final distance error %19.73 MRISunfold() return, current seed 1234 -01: dt=0.0000, 57 negative triangles VmPeak 718408 093: dt=0.9900, 57 negative triangles 094: dt=0.9900, 36 negative triangles 095: dt=0.9900, 36 negative triangles 096: dt=0.9900, 36 negative triangles 097: dt=0.9900, 27 negative triangles 098: dt=0.9900, 29 negative triangles 099: dt=0.9900, 27 negative triangles 100: dt=0.9900, 29 negative triangles 101: dt=0.9900, 28 negative triangles 102: dt=0.9900, 29 negative triangles 103: dt=0.9900, 25 negative triangles 104: dt=0.9900, 27 negative triangles 105: dt=0.9900, 25 negative triangles 106: dt=0.9900, 26 negative triangles 107: dt=0.9900, 28 negative triangles 108: dt=0.9900, 25 negative triangles 109: dt=0.9900, 25 negative triangles 110: dt=0.9900, 22 negative triangles 111: dt=0.9900, 26 negative triangles 112: dt=0.9900, 23 negative triangles 113: dt=0.9900, 23 negative triangles 114: dt=0.9900, 22 negative triangles 115: dt=0.9900, 27 negative triangles 116: dt=0.9900, 22 negative triangles 117: dt=0.9900, 24 negative triangles 118: dt=0.9900, 24 negative triangles 119: dt=0.9900, 23 negative triangles 120: dt=0.9405, 25 negative triangles 121: dt=0.9405, 22 negative triangles 122: dt=0.9405, 24 negative triangles 123: dt=0.9405, 23 negative triangles 124: dt=0.9405, 24 negative triangles 125: dt=0.9405, 22 negative triangles 126: dt=0.9405, 25 negative triangles 127: dt=0.9405, 25 negative triangles 128: dt=0.9405, 23 negative triangles 129: dt=0.9405, 23 negative triangles 130: dt=0.8935, 22 negative triangles 131: dt=0.8935, 21 negative triangles 132: dt=0.8935, 22 negative triangles 133: dt=0.8935, 24 negative triangles 134: dt=0.8935, 20 negative triangles 135: dt=0.8935, 21 negative triangles 136: dt=0.8935, 20 negative triangles 137: dt=0.8935, 21 negative triangles 138: dt=0.8935, 20 negative triangles 139: dt=0.8935, 21 negative triangles 140: dt=0.8935, 18 negative triangles 141: dt=0.8935, 21 negative triangles 142: dt=0.8935, 16 negative triangles 143: dt=0.8935, 15 negative triangles 144: dt=0.8935, 17 negative triangles 145: dt=0.8935, 16 negative triangles 146: dt=0.8935, 17 negative triangles 147: dt=0.8935, 16 negative triangles 148: dt=0.8935, 17 negative triangles 149: dt=0.8935, 16 negative triangles 150: dt=0.8935, 18 negative triangles 151: dt=0.8935, 16 negative triangles 152: dt=0.8935, 17 negative triangles 153: dt=0.8488, 15 negative triangles 154: dt=0.8488, 13 negative triangles 155: dt=0.8488, 12 negative triangles 156: dt=0.8488, 12 negative triangles 157: dt=0.8488, 12 negative triangles 158: dt=0.8488, 10 negative triangles 159: dt=0.8488, 10 negative triangles 160: dt=0.8488, 11 negative triangles 161: dt=0.8488, 9 negative triangles 162: dt=0.8488, 7 negative triangles 163: dt=0.8488, 6 negative triangles 164: dt=0.8488, 9 negative triangles 165: dt=0.8488, 5 negative triangles 166: dt=0.8488, 3 negative triangles 167: dt=0.8488, 3 negative triangles 168: dt=0.8488, 6 negative triangles 169: dt=0.8488, 3 negative triangles 170: dt=0.8488, 3 negative triangles 171: dt=0.8488, 3 negative triangles 172: dt=0.8488, 3 negative triangles 173: dt=0.8488, 5 negative triangles 174: dt=0.8488, 3 negative triangles 175: dt=0.8488, 2 negative triangles 176: dt=0.8488, 2 negative triangles 177: dt=0.8488, 1 negative triangles 178: dt=0.8488, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1120 hours FSRUNTIME@ mris_sphere 0.1120 hours 4 threads #VMPC# mris_sphere VmPeak 718408 mris_sphere done mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.2.0 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.321... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=devel, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.46 pass 1: epoch 2 of 3 starting distance error %19.44 unfolding complete - removing small folds... starting distance error %19.38 removing remaining folds... final distance error %19.41 MRISunfold() return, current seed 1234 -01: dt=0.0000, 29 negative triangles VmPeak 718384 174: dt=0.9900, 29 negative triangles 175: dt=0.9900, 25 negative triangles 176: dt=0.9900, 25 negative triangles 177: dt=0.9900, 26 negative triangles 178: dt=0.9900, 25 negative triangles 179: dt=0.9900, 25 negative triangles 180: dt=0.9900, 24 negative triangles 181: dt=0.9900, 24 negative triangles 182: dt=0.9900, 25 negative triangles 183: dt=0.9900, 24 negative triangles 184: dt=0.9900, 25 negative triangles 185: dt=0.9900, 24 negative triangles 186: dt=0.9900, 24 negative triangles 187: dt=0.9900, 25 negative triangles 188: dt=0.9900, 24 negative triangles 189: dt=0.9900, 26 negative triangles 190: dt=0.9405, 24 negative triangles 191: dt=0.9405, 24 negative triangles 192: dt=0.9405, 25 negative triangles 193: dt=0.9405, 23 negative triangles 194: dt=0.9405, 23 negative triangles 195: dt=0.9405, 25 negative triangles 196: dt=0.9405, 22 negative triangles 197: dt=0.9405, 25 negative triangles 198: dt=0.9405, 24 negative triangles 199: dt=0.9405, 24 negative triangles 200: dt=0.9405, 26 negative triangles 201: dt=0.9405, 24 negative triangles 202: dt=0.9405, 22 negative triangles 203: dt=0.9405, 23 negative triangles 204: dt=0.9405, 24 negative triangles 205: dt=0.9405, 23 negative triangles 206: dt=0.8935, 22 negative triangles 207: dt=0.8935, 24 negative triangles 208: dt=0.8935, 24 negative triangles 209: dt=0.8935, 23 negative triangles 210: dt=0.8935, 22 negative triangles 211: dt=0.8935, 25 negative triangles 212: dt=0.8935, 23 negative triangles 213: dt=0.8935, 25 negative triangles 214: dt=0.8935, 28 negative triangles 215: dt=0.8935, 26 negative triangles 216: dt=0.8488, 26 negative triangles 217: dt=0.8488, 24 negative triangles 218: dt=0.8488, 25 negative triangles 219: dt=0.8488, 25 negative triangles 220: dt=0.8488, 24 negative triangles 221: dt=0.8488, 26 negative triangles 222: dt=0.8488, 24 negative triangles 223: dt=0.8488, 23 negative triangles 224: dt=0.8488, 27 negative triangles 225: dt=0.8488, 24 negative triangles 226: dt=0.8064, 24 negative triangles 227: dt=0.8064, 26 negative triangles 228: dt=0.8064, 26 negative triangles 229: dt=0.8064, 27 negative triangles 230: dt=0.8064, 24 negative triangles 231: dt=0.8064, 24 negative triangles 232: dt=0.8064, 24 negative triangles 233: dt=0.8064, 25 negative triangles 234: dt=0.8064, 25 negative triangles 235: dt=0.8064, 25 negative triangles 236: dt=0.7660, 25 negative triangles 237: dt=0.7660, 24 negative triangles 238: dt=0.7660, 25 negative triangles 239: dt=0.7660, 24 negative triangles 240: dt=0.7660, 27 negative triangles 241: dt=0.7660, 26 negative triangles 242: dt=0.7660, 28 negative triangles 243: dt=0.7660, 29 negative triangles 244: dt=0.7660, 27 negative triangles 245: dt=0.7660, 27 negative triangles 246: dt=0.7277, 25 negative triangles expanding nbhd size to 1 247: dt=0.9900, 27 negative triangles 248: dt=0.9900, 27 negative triangles 249: dt=0.9900, 23 negative triangles 250: dt=0.9900, 26 negative triangles 251: dt=0.9900, 22 negative triangles 252: dt=0.9900, 19 negative triangles 253: dt=0.9900, 22 negative triangles 254: dt=0.9900, 22 negative triangles 255: dt=0.9900, 21 negative triangles 256: dt=0.9900, 21 negative triangles 257: dt=0.9900, 22 negative triangles 258: dt=0.9900, 22 negative triangles 259: dt=0.9900, 22 negative triangles 260: dt=0.9900, 23 negative triangles 261: dt=0.9900, 24 negative triangles 262: dt=0.9405, 24 negative triangles 263: dt=0.9405, 24 negative triangles 264: dt=0.9405, 24 negative triangles 265: dt=0.9405, 24 negative triangles 266: dt=0.9405, 24 negative triangles 267: dt=0.9405, 24 negative triangles 268: dt=0.9405, 24 negative triangles 269: dt=0.9405, 23 negative triangles 270: dt=0.9405, 23 negative triangles 271: dt=0.9405, 23 negative triangles 272: dt=0.8935, 22 negative triangles 273: dt=0.8935, 23 negative triangles 274: dt=0.8935, 23 negative triangles 275: dt=0.8935, 23 negative triangles 276: dt=0.8935, 23 negative triangles 277: dt=0.8935, 23 negative triangles 278: dt=0.8935, 23 negative triangles 279: dt=0.8935, 23 negative triangles 280: dt=0.8935, 22 negative triangles 281: dt=0.8935, 21 negative triangles 282: dt=0.8488, 22 negative triangles 283: dt=0.8488, 22 negative triangles 284: dt=0.8488, 22 negative triangles 285: dt=0.8488, 22 negative triangles 286: dt=0.8488, 22 negative triangles 287: dt=0.8488, 22 negative triangles 288: dt=0.8488, 22 negative triangles 289: dt=0.8488, 22 negative triangles 290: dt=0.8488, 21 negative triangles 291: dt=0.8488, 22 negative triangles 292: dt=0.8064, 22 negative triangles 293: dt=0.8064, 21 negative triangles 294: dt=0.8064, 21 negative triangles 295: dt=0.8064, 20 negative triangles 296: dt=0.8064, 20 negative triangles 297: dt=0.8064, 20 negative triangles 298: dt=0.8064, 20 negative triangles 299: dt=0.8064, 20 negative triangles 300: dt=0.8064, 19 negative triangles 301: dt=0.8064, 18 negative triangles 302: dt=0.8064, 19 negative triangles 303: dt=0.8064, 18 negative triangles 304: dt=0.8064, 19 negative triangles 305: dt=0.8064, 18 negative triangles 306: dt=0.8064, 18 negative triangles 307: dt=0.8064, 18 negative triangles 308: dt=0.8064, 18 negative triangles 309: dt=0.8064, 18 negative triangles 310: dt=0.8064, 17 negative triangles 311: dt=0.8064, 19 negative triangles 312: dt=0.8064, 18 negative triangles 313: dt=0.8064, 19 negative triangles 314: dt=0.8064, 19 negative triangles 315: dt=0.8064, 18 negative triangles 316: dt=0.8064, 18 negative triangles 317: dt=0.8064, 17 negative triangles 318: dt=0.8064, 19 negative triangles 319: dt=0.8064, 18 negative triangles 320: dt=0.7660, 19 negative triangles 321: dt=0.7660, 17 negative triangles 322: dt=0.7660, 18 negative triangles 323: dt=0.7660, 17 negative triangles 324: dt=0.7660, 16 negative triangles 325: dt=0.7660, 17 negative triangles 326: dt=0.7660, 18 negative triangles 327: dt=0.7660, 17 negative triangles 328: dt=0.7660, 19 negative triangles 329: dt=0.7660, 18 negative triangles 330: dt=0.7660, 19 negative triangles 331: dt=0.7660, 19 negative triangles 332: dt=0.7660, 18 negative triangles 333: dt=0.7660, 18 negative triangles 334: dt=0.7277, 16 negative triangles 335: dt=0.7277, 17 negative triangles 336: dt=0.7277, 18 negative triangles 337: dt=0.7277, 16 negative triangles 338: dt=0.7277, 17 negative triangles 339: dt=0.7277, 19 negative triangles 340: dt=0.7277, 19 negative triangles 341: dt=0.7277, 17 negative triangles 342: dt=0.7277, 17 negative triangles 343: dt=0.7277, 19 negative triangles 344: dt=0.6914, 18 negative triangles 345: dt=0.6914, 19 negative triangles 346: dt=0.6914, 17 negative triangles 347: dt=0.6914, 18 negative triangles 348: dt=0.6914, 19 negative triangles 349: dt=0.6914, 19 negative triangles 350: dt=0.6914, 19 negative triangles 351: dt=0.6914, 18 negative triangles 352: dt=0.6914, 17 negative triangles 353: dt=0.6914, 19 negative triangles 354: dt=0.6568, 18 negative triangles 355: dt=0.6568, 17 negative triangles 356: dt=0.6568, 18 negative triangles 357: dt=0.6568, 18 negative triangles 358: dt=0.6568, 19 negative triangles 359: dt=0.6568, 19 negative triangles 360: dt=0.6568, 17 negative triangles 361: dt=0.6568, 18 negative triangles 362: dt=0.6568, 18 negative triangles 363: dt=0.6568, 19 negative triangles 364: dt=0.6239, 19 negative triangles 365: dt=0.6239, 19 negative triangles 366: dt=0.6239, 18 negative triangles 367: dt=0.6239, 19 negative triangles 368: dt=0.6239, 19 negative triangles 369: dt=0.6239, 17 negative triangles 370: dt=0.6239, 19 negative triangles 371: dt=0.6239, 16 negative triangles 372: dt=0.6239, 17 negative triangles 373: dt=0.6239, 17 negative triangles 374: dt=0.5927, 18 negative triangles 375: dt=0.5927, 17 negative triangles 376: dt=0.5927, 17 negative triangles 377: dt=0.5927, 18 negative triangles 378: dt=0.5927, 17 negative triangles 379: dt=0.5927, 17 negative triangles 380: dt=0.5927, 18 negative triangles 381: dt=0.5927, 18 negative triangles 382: dt=0.5927, 19 negative triangles 383: dt=0.5927, 18 negative triangles 384: dt=0.5631, 19 negative triangles 385: dt=0.5631, 19 negative triangles 386: dt=0.5631, 17 negative triangles 387: dt=0.5631, 18 negative triangles 388: dt=0.5631, 18 negative triangles 389: dt=0.5631, 19 negative triangles 390: dt=0.5631, 17 negative triangles 391: dt=0.5631, 18 negative triangles 392: dt=0.5631, 19 negative triangles 393: dt=0.5631, 17 negative triangles 394: dt=0.5350, 19 negative triangles 395: dt=0.5350, 18 negative triangles 396: dt=0.5350, 19 negative triangles 397: dt=0.5350, 19 negative triangles 398: dt=0.5350, 19 negative triangles 399: dt=0.5350, 19 negative triangles 400: dt=0.5350, 19 negative triangles 401: dt=0.5350, 17 negative triangles 402: dt=0.5350, 19 negative triangles 403: dt=0.5350, 19 negative triangles 404: dt=0.5082, 18 negative triangles 405: dt=0.5082, 19 negative triangles 406: dt=0.5082, 19 negative triangles 407: dt=0.5082, 17 negative triangles 408: dt=0.5082, 19 negative triangles 409: dt=0.5082, 19 negative triangles 410: dt=0.5082, 17 negative triangles 411: dt=0.5082, 18 negative triangles 412: dt=0.5082, 17 negative triangles 413: dt=0.5082, 18 negative triangles 414: dt=0.4828, 18 negative triangles 415: dt=0.4828, 19 negative triangles 416: dt=0.4828, 19 negative triangles 417: dt=0.4828, 19 negative triangles 418: dt=0.4828, 18 negative triangles 419: dt=0.4828, 17 negative triangles 420: dt=0.4828, 19 negative triangles 421: dt=0.4828, 19 negative triangles 422: dt=0.4828, 18 negative triangles 423: dt=0.4828, 17 negative triangles 424: dt=0.4587, 17 negative triangles 425: dt=0.4587, 19 negative triangles 426: dt=0.4587, 19 negative triangles 427: dt=0.4587, 19 negative triangles 428: dt=0.4587, 19 negative triangles 429: dt=0.4587, 17 negative triangles 430: dt=0.4587, 18 negative triangles 431: dt=0.4587, 19 negative triangles 432: dt=0.4587, 19 negative triangles 433: dt=0.4587, 19 negative triangles 434: dt=0.4357, 18 negative triangles 435: dt=0.4357, 18 negative triangles 436: dt=0.4357, 19 negative triangles 437: dt=0.4357, 18 negative triangles 438: dt=0.4357, 18 negative triangles 439: dt=0.4357, 18 negative triangles 440: dt=0.4357, 17 negative triangles 441: dt=0.4357, 17 negative triangles 442: dt=0.4357, 17 negative triangles 443: dt=0.4357, 17 negative triangles 444: dt=0.4139, 19 negative triangles 445: dt=0.4139, 19 negative triangles 446: dt=0.4139, 18 negative triangles 447: dt=0.4139, 18 negative triangles 448: dt=0.4139, 17 negative triangles 449: dt=0.4139, 17 negative triangles 450: dt=0.4139, 17 negative triangles 451: dt=0.4139, 17 negative triangles 452: dt=0.4139, 17 negative triangles 453: dt=0.4139, 17 negative triangles 454: dt=0.3932, 18 negative triangles 455: dt=0.3932, 16 negative triangles 456: dt=0.3932, 17 negative triangles 457: dt=0.3932, 18 negative triangles 458: dt=0.3932, 18 negative triangles 459: dt=0.3932, 17 negative triangles 460: dt=0.3932, 16 negative triangles 461: dt=0.3932, 18 negative triangles 462: dt=0.3932, 16 negative triangles 463: dt=0.3932, 18 negative triangles 464: dt=0.3736, 17 negative triangles 465: dt=0.3736, 16 negative triangles 466: dt=0.3736, 16 negative triangles 467: dt=0.3736, 16 negative triangles 468: dt=0.3736, 16 negative triangles 469: dt=0.3736, 17 negative triangles 470: dt=0.3736, 17 negative triangles 471: dt=0.3736, 17 negative triangles 472: dt=0.3736, 17 negative triangles 473: dt=0.3736, 16 negative triangles 474: dt=0.3549, 17 negative triangles 475: dt=0.3549, 16 negative triangles 476: dt=0.3549, 16 negative triangles 477: dt=0.3549, 17 negative triangles 478: dt=0.3549, 17 negative triangles 479: dt=0.3549, 19 negative triangles 480: dt=0.3549, 19 negative triangles 481: dt=0.3549, 17 negative triangles 482: dt=0.3549, 17 negative triangles 483: dt=0.3549, 17 negative triangles 484: dt=0.3372, 17 negative triangles 485: dt=0.3372, 17 negative triangles 486: dt=0.3372, 17 negative triangles 487: dt=0.3372, 17 negative triangles 488: dt=0.3372, 17 negative triangles 489: dt=0.3372, 16 negative triangles 490: dt=0.3372, 15 negative triangles 491: dt=0.3372, 15 negative triangles 492: dt=0.3372, 15 negative triangles 493: dt=0.3372, 15 negative triangles 494: dt=0.3372, 15 negative triangles 495: dt=0.3372, 16 negative triangles 496: dt=0.3372, 15 negative triangles 497: dt=0.3372, 15 negative triangles 498: dt=0.3372, 15 negative triangles 499: dt=0.3372, 15 negative triangles 500: dt=0.3203, 15 negative triangles 501: dt=0.3203, 16 negative triangles 502: dt=0.3203, 17 negative triangles 503: dt=0.3203, 17 negative triangles 504: dt=0.3203, 15 negative triangles 505: dt=0.3203, 15 negative triangles 506: dt=0.3203, 16 negative triangles 507: dt=0.3203, 17 negative triangles 508: dt=0.3203, 16 negative triangles 509: dt=0.3203, 16 negative triangles 510: dt=0.3043, 15 negative triangles 511: dt=0.3043, 17 negative triangles 512: dt=0.3043, 16 negative triangles 513: dt=0.3043, 17 negative triangles 514: dt=0.3043, 17 negative triangles 515: dt=0.3043, 17 negative triangles 516: dt=0.3043, 15 negative triangles 517: dt=0.3043, 17 negative triangles 518: dt=0.3043, 15 negative triangles 519: dt=0.3043, 17 negative triangles 520: dt=0.2891, 17 negative triangles 521: dt=0.2891, 16 negative triangles 522: dt=0.2891, 16 negative triangles 523: dt=0.2891, 15 negative triangles 524: dt=0.2891, 17 negative triangles 525: dt=0.2891, 17 negative triangles 526: dt=0.2891, 17 negative triangles 527: dt=0.2891, 17 negative triangles 528: dt=0.2891, 17 negative triangles 529: dt=0.2891, 16 negative triangles 530: dt=0.2746, 17 negative triangles 531: dt=0.2746, 17 negative triangles 532: dt=0.2746, 17 negative triangles 533: dt=0.2746, 17 negative triangles 534: dt=0.2746, 17 negative triangles 535: dt=0.2746, 17 negative triangles 536: dt=0.2746, 17 negative triangles 537: dt=0.2746, 18 negative triangles 538: dt=0.2746, 18 negative triangles 539: dt=0.2746, 15 negative triangles 540: dt=0.2609, 15 negative triangles 541: dt=0.2609, 15 negative triangles 542: dt=0.2609, 15 negative triangles 543: dt=0.2609, 15 negative triangles 544: dt=0.2609, 15 negative triangles 545: dt=0.2609, 15 negative triangles 546: dt=0.2609, 15 negative triangles 547: dt=0.2609, 17 negative triangles 548: dt=0.2609, 17 negative triangles 549: dt=0.2609, 17 negative triangles 550: dt=0.2478, 17 negative triangles 551: dt=0.2478, 16 negative triangles 552: dt=0.2478, 16 negative triangles 553: dt=0.2478, 15 negative triangles 554: dt=0.2478, 17 negative triangles 555: dt=0.2478, 17 negative triangles 556: dt=0.2478, 18 negative triangles 557: dt=0.2478, 17 negative triangles 558: dt=0.2478, 18 negative triangles 559: dt=0.2478, 16 negative triangles 560: dt=0.2354, 18 negative triangles 561: dt=0.2354, 18 negative triangles 562: dt=0.2354, 18 negative triangles 563: dt=0.2354, 18 negative triangles 564: dt=0.2354, 18 negative triangles 565: dt=0.2354, 18 negative triangles 566: dt=0.2354, 18 negative triangles 567: dt=0.2354, 17 negative triangles 568: dt=0.2354, 16 negative triangles 569: dt=0.2354, 17 negative triangles 570: dt=0.2237, 17 negative triangles 571: dt=0.2237, 18 negative triangles 572: dt=0.2237, 17 negative triangles 573: dt=0.2237, 17 negative triangles 574: dt=0.2237, 17 negative triangles 575: dt=0.2237, 17 negative triangles 576: dt=0.2237, 17 negative triangles 577: dt=0.2237, 17 negative triangles 578: dt=0.2237, 17 negative triangles 579: dt=0.2237, 17 negative triangles 580: dt=0.2125, 17 negative triangles 581: dt=0.2125, 17 negative triangles 582: dt=0.2125, 17 negative triangles 583: dt=0.2125, 16 negative triangles 584: dt=0.2125, 16 negative triangles 585: dt=0.2125, 16 negative triangles 586: dt=0.2125, 17 negative triangles 587: dt=0.2125, 17 negative triangles 588: dt=0.2125, 17 negative triangles 589: dt=0.2125, 17 negative triangles 590: dt=0.2019, 17 negative triangles 591: dt=0.2019, 17 negative triangles 592: dt=0.2019, 17 negative triangles 593: dt=0.2019, 16 negative triangles 594: dt=0.2019, 16 negative triangles 595: dt=0.2019, 16 negative triangles 596: dt=0.2019, 16 negative 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10 negative triangles 1120: dt=0.0155, 10 negative triangles 1121: dt=0.0155, 10 negative triangles 1122: dt=0.0155, 10 negative triangles 1123: dt=0.0155, 11 negative triangles 1124: dt=0.0155, 9 negative triangles 1125: dt=0.0155, 9 negative triangles 1126: dt=0.0155, 9 negative triangles 1127: dt=0.0155, 10 negative triangles 1128: dt=0.0155, 10 negative triangles 1129: dt=0.0148, 10 negative triangles 1130: dt=0.0148, 10 negative triangles 1131: dt=0.0148, 11 negative triangles 1132: dt=0.0148, 11 negative triangles 1133: dt=0.0148, 9 negative triangles 1134: dt=0.0148, 9 negative triangles 1135: dt=0.0148, 10 negative triangles 1136: dt=0.0148, 10 negative triangles 1137: dt=0.0148, 10 negative triangles 1138: dt=0.0148, 10 negative triangles 1139: dt=0.0140, 10 negative triangles 1140: dt=0.0140, 11 negative triangles 1141: dt=0.0140, 9 negative triangles 1142: dt=0.0140, 9 negative triangles 1143: dt=0.0140, 9 negative triangles 1144: dt=0.0140, 10 negative triangles 1145: dt=0.0140, 10 negative triangles 1146: dt=0.0140, 10 negative triangles 1147: dt=0.0140, 10 negative triangles 1148: dt=0.0140, 10 negative triangles 1149: dt=0.0133, 11 negative triangles 1150: dt=0.0133, 9 negative triangles 1151: dt=0.0133, 9 negative triangles 1152: dt=0.0133, 9 negative triangles 1153: dt=0.0133, 9 negative triangles 1154: dt=0.0133, 9 negative triangles 1155: dt=0.0133, 9 negative triangles 1156: dt=0.0133, 9 negative triangles 1157: dt=0.0133, 9 negative triangles 1158: dt=0.0133, 9 negative triangles 1159: dt=0.0127, 9 negative triangles 1160: dt=0.0127, 9 negative triangles 1161: dt=0.0127, 9 negative triangles 1162: dt=0.0127, 9 negative triangles 1163: dt=0.0127, 9 negative triangles 1164: dt=0.0127, 9 negative triangles 1165: dt=0.0127, 9 negative triangles 1166: dt=0.0127, 9 negative triangles 1167: dt=0.0127, 9 negative triangles 1168: dt=0.0127, 9 negative triangles 1169: dt=0.0120, 9 negative triangles 1170: dt=0.0120, 9 negative triangles 1171: dt=0.0120, 9 negative triangles 1172: dt=0.0120, 9 negative triangles 1173: dt=0.0120, 9 negative triangles 1174: dt=0.0120, 9 negative triangles 1175: 11 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1823 hours FSRUNTIME@ mris_sphere 0.1823 hours 4 threads #VMPC# mris_sphere VmPeak 718384 mris_sphere done PIDs (5177 5180) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Feb 18 14:21:40 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sat Feb 18 14:21:40 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 5235 of (5235 5238) to complete... Waiting for PID 5238 of (5235 5238) to complete... mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/developer/Desktop/1st_scan_nii/Sub-139/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.2.0 7.2.0 reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=devel, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=devel, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=devel, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.430 curvature mean = 0.039, std = 0.818 curvature mean = 0.013, std = 0.875 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (6.00, -8.50, 11.50) sse = 190645.4, elapsed since starting=0.3087 min MRISrigidBodyAlignGlobal() done 0.31 min curvature mean = 0.019, std = 0.847 curvature mean = 0.005, std = 0.953 curvature mean = 0.018, std = 0.859 curvature mean = 0.002, std = 0.982 curvature mean = 0.017, std = 0.862 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.019, std = 0.253 curvature mean = 0.044, std = 0.251 curvature mean = 0.054, std = 0.409 curvature mean = 0.040, std = 0.309 curvature mean = 0.025, std = 0.629 curvature mean = 0.040, std = 0.337 curvature mean = 0.011, std = 0.773 curvature mean = 0.039, std = 0.349 curvature mean = 0.003, std = 0.868 MRISregister() return, current seed 0 -01: dt=0.0000, 2 negative triangles VmPeak 758184 106: dt=0.9900, 2 negative triangles expanding nbhd size to 1 107: dt=0.9900, 2 negative triangles 108: dt=0.9900, 1 negative triangles 109: dt=0.9900, 2 negative triangles 110: dt=0.9900, 1 negative triangles 111: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.14 hours #VMPC# mris_register VmPeak 758184 FSRUNTIME@ mris_register 0.1431 hours 4 threads mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/developer/Desktop/1st_scan_nii/Sub-139/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.2.0 7.2.0 reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=devel, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=devel, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=devel, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.442 curvature mean = 0.043, std = 0.809 curvature mean = 0.010, std = 0.876 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (15.50, -5.00, 15.50) sse = 203704.5, elapsed since starting=0.3142 min MRISrigidBodyAlignGlobal() done 0.32 min curvature mean = 0.018, std = 0.834 curvature mean = 0.003, std = 0.955 curvature mean = 0.016, std = 0.846 curvature mean = 0.001, std = 0.982 curvature mean = 0.015, std = 0.849 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.034, std = 4.254 curvature mean = 0.039, std = 0.244 curvature mean = 0.006, std = 0.028 curvature mean = 0.035, std = 0.302 curvature mean = 0.004, std = 0.047 curvature mean = 0.035, std = 0.328 curvature mean = 0.000, std = 0.248 curvature mean = 0.034, std = 0.340 curvature mean = 0.000, std = 0.233 MRISregister() return, current seed 0 -01: dt=0.0000, 32 negative triangles VmPeak 722828 107: dt=0.9900, 32 negative triangles expanding nbhd size to 1 108: dt=0.9900, 35 negative triangles 109: dt=0.9900, 31 negative triangles 110: dt=0.9900, 33 negative triangles 111: dt=0.9900, 35 negative triangles 112: dt=0.9900, 35 negative triangles 113: dt=0.9900, 31 negative triangles 114: dt=0.9900, 30 negative triangles 115: dt=0.9900, 31 negative triangles 116: dt=0.9900, 30 negative triangles 117: dt=0.9900, 30 negative triangles 118: dt=0.9900, 29 negative triangles 119: dt=0.9900, 28 negative triangles 120: dt=0.9900, 27 negative triangles 121: dt=0.9900, 27 negative triangles 122: dt=0.9900, 27 negative triangles 123: dt=0.9900, 26 negative triangles 124: dt=0.9900, 27 negative triangles 125: dt=0.9900, 27 negative triangles 126: dt=0.9900, 28 negative triangles 127: dt=0.9900, 29 negative triangles 128: dt=0.9900, 30 negative triangles 129: dt=0.9900, 29 negative triangles 130: dt=0.9900, 29 negative triangles 131: dt=0.9900, 30 negative triangles 132: dt=0.9900, 30 negative triangles 133: dt=0.9405, 30 negative triangles 134: dt=0.9405, 31 negative triangles 135: dt=0.9405, 31 negative triangles 136: dt=0.9405, 30 negative triangles 137: dt=0.9405, 31 negative triangles 138: dt=0.9405, 30 negative triangles 139: dt=0.9405, 29 negative triangles 140: dt=0.9405, 31 negative triangles 141: dt=0.9405, 31 negative triangles 142: dt=0.9405, 28 negative triangles 143: dt=0.8935, 30 negative triangles 144: dt=0.8935, 30 negative triangles 145: dt=0.8935, 27 negative triangles 146: dt=0.8935, 31 negative triangles 147: dt=0.8935, 31 negative triangles 148: dt=0.8935, 31 negative triangles 149: dt=0.8935, 30 negative triangles 150: dt=0.8935, 29 negative triangles 151: dt=0.8935, 31 negative triangles 152: dt=0.8935, 31 negative triangles 153: dt=0.8488, 28 negative triangles 154: dt=0.8488, 30 negative triangles 155: dt=0.8488, 29 negative triangles 156: dt=0.8488, 29 negative triangles 157: dt=0.8488, 30 negative triangles 158: dt=0.8488, 31 negative triangles 159: dt=0.8488, 30 negative triangles 160: dt=0.8488, 28 negative triangles 161: dt=0.8488, 27 negative triangles 162: dt=0.8488, 31 negative triangles 163: dt=0.8064, 29 negative triangles 164: dt=0.8064, 29 negative triangles 165: dt=0.8064, 28 negative triangles 166: dt=0.8064, 29 negative triangles 167: dt=0.8064, 27 negative triangles 168: dt=0.8064, 31 negative triangles 169: dt=0.8064, 29 negative triangles 170: dt=0.8064, 27 negative triangles 171: dt=0.8064, 29 negative triangles 172: dt=0.8064, 29 negative triangles 173: dt=0.7660, 29 negative triangles 174: dt=0.7660, 30 negative triangles 175: dt=0.7660, 30 negative triangles 176: dt=0.7660, 29 negative triangles 177: dt=0.7660, 28 negative triangles 178: dt=0.7660, 29 negative triangles 179: dt=0.7660, 31 negative triangles 180: dt=0.7660, 30 negative triangles 181: dt=0.7660, 31 negative triangles 182: dt=0.7660, 27 negative triangles 183: dt=0.7277, 30 negative triangles 184: dt=0.7277, 29 negative triangles 185: dt=0.7277, 28 negative triangles 186: dt=0.7277, 30 negative triangles 187: dt=0.7277, 29 negative triangles 188: dt=0.7277, 30 negative triangles 189: dt=0.7277, 29 negative triangles 190: dt=0.7277, 27 negative triangles 191: dt=0.7277, 29 negative triangles 192: dt=0.7277, 29 negative triangles 193: dt=0.6914, 29 negative triangles 194: dt=0.6914, 27 negative triangles 195: dt=0.6914, 29 negative triangles 196: dt=0.6914, 30 negative triangles 197: dt=0.6914, 28 negative triangles 198: dt=0.6914, 30 negative triangles 199: dt=0.6914, 29 negative triangles 200: dt=0.6914, 31 negative triangles 201: dt=0.6914, 29 negative triangles 202: dt=0.6914, 30 negative triangles 203: dt=0.6568, 31 negative triangles 204: dt=0.6568, 29 negative triangles 205: dt=0.6568, 29 negative triangles 206: dt=0.6568, 29 negative triangles 207: dt=0.6568, 28 negative triangles 208: dt=0.6568, 28 negative triangles 209: dt=0.6568, 28 negative triangles 210: dt=0.6568, 27 negative triangles 211: dt=0.6568, 30 negative triangles 212: dt=0.6568, 28 negative triangles 213: dt=0.6239, 31 negative triangles 214: dt=0.6239, 31 negative triangles 215: dt=0.6239, 31 negative triangles 216: dt=0.6239, 29 negative triangles 217: dt=0.6239, 29 negative triangles 218: dt=0.6239, 29 negative triangles 219: dt=0.6239, 31 negative triangles 220: dt=0.6239, 29 negative triangles 221: dt=0.6239, 28 negative triangles 222: dt=0.6239, 28 negative triangles 223: dt=0.5927, 29 negative triangles 224: dt=0.5927, 29 negative triangles 225: dt=0.5927, 29 negative triangles 226: dt=0.5927, 29 negative triangles 227: dt=0.5927, 29 negative triangles 228: dt=0.5927, 29 negative triangles 229: dt=0.5927, 31 negative triangles 230: dt=0.5927, 29 negative triangles 231: dt=0.5927, 30 negative triangles 232: dt=0.5927, 28 negative triangles 233: dt=0.5631, 30 negative triangles 234: dt=0.5631, 29 negative triangles 235: dt=0.5631, 28 negative triangles 236: dt=0.5631, 28 negative triangles 237: dt=0.5631, 27 negative triangles 238: dt=0.5631, 30 negative triangles 239: dt=0.5631, 29 negative triangles 240: dt=0.5631, 28 negative triangles 241: dt=0.5631, 28 negative triangles 242: dt=0.5631, 30 negative triangles 243: dt=0.5350, 30 negative triangles 244: dt=0.5350, 29 negative triangles 245: dt=0.5350, 26 negative triangles 246: dt=0.5350, 26 negative triangles 247: dt=0.5350, 28 negative triangles 248: dt=0.5350, 27 negative triangles 249: dt=0.5350, 29 negative triangles 250: dt=0.5350, 28 negative triangles 251: dt=0.5350, 28 negative triangles 252: dt=0.5350, 28 negative triangles 253: dt=0.5082, 28 negative triangles 254: dt=0.5082, 27 negative triangles 255: dt=0.5082, 29 negative triangles 256: dt=0.5082, 29 negative triangles 257: dt=0.5082, 27 negative triangles 258: dt=0.5082, 28 negative triangles 259: dt=0.5082, 27 negative triangles 260: dt=0.5082, 28 negative triangles 261: dt=0.5082, 26 negative triangles 262: dt=0.5082, 27 negative triangles 263: dt=0.4828, 29 negative triangles 264: dt=0.4828, 26 negative triangles 265: dt=0.4828, 27 negative triangles 266: dt=0.4828, 28 negative triangles 267: dt=0.4828, 28 negative triangles 268: dt=0.4828, 27 negative triangles 269: dt=0.4828, 29 negative triangles 270: dt=0.4828, 27 negative triangles 271: dt=0.4828, 29 negative triangles 272: dt=0.4828, 29 negative triangles 273: dt=0.4587, 27 negative triangles 274: dt=0.4587, 28 negative triangles 275: dt=0.4587, 27 negative triangles 276: dt=0.4587, 28 negative triangles 277: dt=0.4587, 27 negative triangles 278: dt=0.4587, 29 negative triangles 279: dt=0.4587, 28 negative triangles 280: dt=0.4587, 29 negative triangles 281: dt=0.4587, 29 negative triangles 282: dt=0.4587, 27 negative triangles 283: dt=0.4587, 25 negative triangles 284: dt=0.4587, 27 negative triangles 285: dt=0.4587, 28 negative triangles 286: dt=0.4587, 29 negative triangles 287: dt=0.4587, 28 negative triangles 288: dt=0.4587, 27 negative triangles 289: dt=0.4587, 27 negative triangles 290: dt=0.4587, 29 negative triangles 291: dt=0.4587, 29 negative triangles 292: dt=0.4587, 27 negative triangles 293: dt=0.4357, 27 negative triangles 294: dt=0.4357, 26 negative triangles 295: dt=0.4357, 25 negative triangles 296: dt=0.4357, 26 negative triangles 297: dt=0.4357, 27 negative triangles 298: dt=0.4357, 27 negative triangles 299: dt=0.4357, 28 negative triangles 300: dt=0.4357, 27 negative triangles 301: dt=0.4357, 27 negative triangles 302: dt=0.4357, 25 negative triangles 303: dt=0.4139, 26 negative triangles 304: dt=0.4139, 27 negative triangles 305: dt=0.4139, 26 negative triangles 306: dt=0.4139, 29 negative triangles 307: dt=0.4139, 26 negative triangles 308: dt=0.4139, 28 negative triangles 309: dt=0.4139, 26 negative triangles 310: dt=0.4139, 28 negative triangles 311: dt=0.4139, 27 negative triangles 312: dt=0.4139, 29 negative triangles 313: dt=0.3932, 28 negative triangles 314: dt=0.3932, 29 negative triangles 315: dt=0.3932, 26 negative triangles 316: dt=0.3932, 28 negative triangles 317: dt=0.3932, 25 negative triangles 318: dt=0.3932, 27 negative triangles 319: dt=0.3932, 27 negative triangles 320: dt=0.3932, 29 negative triangles 321: dt=0.3932, 29 negative triangles 322: dt=0.3932, 29 negative triangles 323: dt=0.3736, 27 negative triangles 324: dt=0.3736, 26 negative triangles 325: dt=0.3736, 27 negative triangles 326: dt=0.3736, 27 negative triangles 327: dt=0.3736, 28 negative triangles 328: dt=0.3736, 27 negative triangles 329: dt=0.3736, 27 negative triangles 330: dt=0.3736, 29 negative triangles 331: dt=0.3736, 27 negative triangles 332: dt=0.3736, 29 negative triangles 333: dt=0.3549, 27 negative triangles 334: dt=0.3549, 25 negative triangles 335: dt=0.3549, 27 negative triangles 336: dt=0.3549, 28 negative triangles 337: dt=0.3549, 29 negative triangles 338: dt=0.3549, 28 negative triangles 339: dt=0.3549, 28 negative triangles 340: dt=0.3549, 29 negative triangles 341: dt=0.3549, 25 negative triangles 342: dt=0.3549, 27 negative triangles 343: dt=0.3372, 27 negative triangles 344: dt=0.3372, 25 negative triangles 345: dt=0.3372, 25 negative triangles 346: dt=0.3372, 25 negative triangles 347: dt=0.3372, 25 negative triangles 348: dt=0.3372, 29 negative triangles 349: dt=0.3372, 27 negative triangles 350: dt=0.3372, 27 negative triangles 351: dt=0.3372, 27 negative triangles 352: dt=0.3372, 28 negative triangles 353: dt=0.3203, 27 negative triangles 354: dt=0.3203, 27 negative triangles 355: dt=0.3203, 26 negative triangles 356: dt=0.3203, 25 negative triangles 357: dt=0.3203, 28 negative triangles 358: dt=0.3203, 28 negative triangles 359: dt=0.3203, 27 negative triangles 360: dt=0.3203, 29 negative triangles 361: dt=0.3203, 29 negative triangles 362: dt=0.3203, 29 negative triangles 363: dt=0.3043, 29 negative triangles 364: dt=0.3043, 29 negative triangles 365: dt=0.3043, 28 negative triangles 366: dt=0.3043, 27 negative triangles 367: dt=0.3043, 27 negative triangles 368: dt=0.3043, 28 negative triangles 369: dt=0.3043, 27 negative triangles 370: dt=0.3043, 28 negative triangles 371: dt=0.3043, 28 negative triangles 372: dt=0.3043, 29 negative triangles 373: dt=0.2891, 28 negative triangles 374: dt=0.2891, 27 negative triangles 375: dt=0.2891, 27 negative triangles 376: dt=0.2891, 28 negative triangles 377: dt=0.2891, 27 negative triangles 378: dt=0.2891, 28 negative triangles 379: dt=0.2891, 27 negative triangles 380: dt=0.2891, 27 negative triangles 381: dt=0.2891, 27 negative triangles 382: dt=0.2891, 28 negative triangles 383: dt=0.2746, 27 negative triangles 384: dt=0.2746, 29 negative triangles 385: dt=0.2746, 28 negative triangles 386: dt=0.2746, 27 negative triangles 387: dt=0.2746, 29 negative triangles 388: dt=0.2746, 29 negative triangles 389: dt=0.2746, 29 negative triangles 390: dt=0.2746, 28 negative triangles 391: dt=0.2746, 26 negative triangles 392: dt=0.2746, 27 negative triangles 393: dt=0.2609, 28 negative triangles 394: dt=0.2609, 28 negative triangles 395: dt=0.2609, 26 negative triangles 396: dt=0.2609, 29 negative triangles 397: dt=0.2609, 28 negative triangles 398: dt=0.2609, 29 negative triangles 399: dt=0.2609, 28 negative triangles 400: dt=0.2609, 28 negative triangles 401: dt=0.2609, 27 negative triangles 402: dt=0.2609, 28 negative triangles 403: dt=0.2478, 28 negative triangles 404: dt=0.2478, 29 negative triangles 405: dt=0.2478, 27 negative triangles 406: dt=0.2478, 29 negative triangles 407: dt=0.2478, 26 negative triangles 408: dt=0.2478, 25 negative triangles 409: dt=0.2478, 25 negative triangles 410: dt=0.2478, 25 negative triangles 411: dt=0.2478, 27 negative triangles 412: dt=0.2478, 27 negative triangles 413: dt=0.2354, 27 negative triangles 414: dt=0.2354, 29 negative triangles 415: dt=0.2354, 29 negative triangles 416: dt=0.2354, 29 negative triangles 417: dt=0.2354, 29 negative triangles 418: dt=0.2354, 29 negative triangles 419: dt=0.2354, 29 negative triangles 420: dt=0.2354, 27 negative triangles 421: dt=0.2354, 26 negative triangles 422: dt=0.2354, 26 negative triangles 423: dt=0.2237, 26 negative triangles 424: dt=0.2237, 24 negative triangles 425: dt=0.2237, 28 negative triangles 426: dt=0.2237, 28 negative triangles 427: dt=0.2237, 26 negative triangles 428: dt=0.2237, 27 negative triangles 429: dt=0.2237, 26 negative triangles 430: dt=0.2237, 26 negative triangles 431: dt=0.2237, 26 negative triangles 432: dt=0.2237, 26 negative triangles 433: dt=0.2237, 25 negative triangles 434: dt=0.2125, 26 negative triangles 435: dt=0.2125, 25 negative triangles 436: dt=0.2125, 26 negative triangles 437: dt=0.2125, 26 negative triangles 438: dt=0.2125, 25 negative triangles 439: dt=0.2125, 24 negative triangles 440: dt=0.2125, 25 negative triangles 441: dt=0.2125, 24 negative triangles 442: dt=0.2125, 24 negative triangles 443: dt=0.2125, 25 negative triangles 444: dt=0.2019, 28 negative triangles 445: dt=0.2019, 24 negative triangles 446: dt=0.2019, 26 negative triangles 447: dt=0.2019, 27 negative triangles 448: dt=0.2019, 27 negative triangles 449: dt=0.2019, 26 negative triangles 450: dt=0.2019, 27 negative triangles 451: dt=0.2019, 25 negative triangles 452: dt=0.2019, 23 negative triangles 453: dt=0.2019, 23 negative triangles 454: dt=0.2019, 24 negative triangles 455: dt=0.2019, 25 negative triangles 456: dt=0.2019, 24 negative triangles 457: dt=0.2019, 24 negative triangles 458: dt=0.2019, 23 negative triangles 459: dt=0.2019, 24 negative triangles 460: dt=0.2019, 26 negative triangles 461: dt=0.2019, 25 negative triangles 462: dt=0.1918, 25 negative triangles 463: dt=0.1918, 25 negative triangles 464: dt=0.1918, 25 negative triangles 465: dt=0.1918, 23 negative triangles 466: dt=0.1918, 23 negative triangles 467: dt=0.1918, 25 negative triangles 468: dt=0.1918, 23 negative triangles 469: dt=0.1918, 23 negative triangles 470: dt=0.1918, 27 negative triangles 471: dt=0.1918, 23 negative triangles 472: dt=0.1822, 25 negative triangles 473: dt=0.1822, 27 negative triangles 474: dt=0.1822, 25 negative triangles 475: dt=0.1822, 26 negative triangles 476: dt=0.1822, 25 negative triangles 477: dt=0.1822, 25 negative triangles 478: dt=0.1822, 25 negative triangles 479: dt=0.1822, 25 negative triangles 480: dt=0.1822, 25 negative triangles 481: dt=0.1822, 25 negative triangles 482: dt=0.1731, 25 negative triangles 483: dt=0.1731, 25 negative triangles 484: dt=0.1731, 25 negative triangles 485: dt=0.1731, 25 negative triangles 486: dt=0.1731, 25 negative triangles 487: dt=0.1731, 25 negative triangles 488: dt=0.1731, 25 negative triangles 489: dt=0.1731, 23 negative triangles 490: dt=0.1731, 25 negative triangles 491: dt=0.1731, 25 negative triangles 492: dt=0.1644, 24 negative triangles 493: dt=0.1644, 23 negative triangles 494: dt=0.1644, 23 negative triangles 495: dt=0.1644, 24 negative triangles 496: dt=0.1644, 24 negative triangles 497: dt=0.1644, 26 negative triangles 498: dt=0.1644, 27 negative triangles 499: dt=0.1644, 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triangles 1024: dt=0.0108, 25 negative triangles 1025: dt=0.0108, 25 negative triangles 1026: dt=0.0108, 25 negative triangles 1027: dt=0.0108, 25 negative triangles 1028: dt=0.0108, 25 negative triangles 1029: dt=0.0108, 24 negative triangles 1030: dt=0.0108, 23 negative triangles 1031: dt=0.0108, 23 negative triangles 1032: dt=0.0108, 23 negative triangles 1033: dt=0.0108, 23 negative triangles 1034: dt=0.0103, 23 negative triangles 1035: dt=0.0103, 23 negative triangles 1036: dt=0.0103, 24 negative triangles 1037: dt=0.0103, 22 negative triangles 1038: dt=0.0103, 22 negative triangles 1039: dt=0.0103, 24 negative triangles 1040: dt=0.0103, 24 negative triangles 1041: dt=0.0103, 23 negative triangles 1042: dt=0.0103, 23 negative triangles 1043: dt=0.0103, 24 negative triangles 1044: dt=0.0098, 24 negative triangles 1045: dt=0.0098, 25 negative triangles 1046: dt=0.0098, 25 negative triangles 1047: dt=0.0098, 24 negative triangles 1048: dt=0.0098, 25 negative triangles 1049: dt=0.0098, 25 negative triangles 1050: dt=0.0098, 25 negative triangles 1051: dt=0.0098, 25 negative triangles 1052: dt=0.0098, 25 negative triangles 1053: dt=0.0098, 25 negative triangles 1054: dt=0.0098, 25 negative triangles 1055: dt=0.0098, 25 negative triangles 1056: dt=0.0098, 25 negative triangles 1057: dt=0.0098, 25 negative triangles 1058: dt=0.0098, 25 negative triangles 1059: dt=0.0098, 25 negative triangles 1060: dt=0.0098, 25 negative triangles 1061: dt=0.0098, 25 negative triangles 1062: dt=0.0098, 25 negative triangles 1063: dt=0.0098, 25 negative triangles 1064: dt=0.0098, 24 negative triangles 1065: dt=0.0098, 24 negative triangles 1066: dt=0.0098, 25 negative triangles 1067: dt=0.0098, 23 negative triangles 1068: dt=0.0098, 23 negative triangles 1069: dt=0.0098, 24 negative triangles 1070: dt=0.0098, 24 negative triangles 1071: dt=0.0098, 24 negative triangles 1072: dt=0.0098, 24 negative triangles 1073: dt=0.0098, 24 negative triangles 1074: dt=0.0098, 24 negative triangles 1075: dt=0.0098, 25 negative triangles 1076: dt=0.0098, 25 negative triangles 1077: dt=0.0098, 24 negative triangles 1078: dt=0.0098, 25 negative triangles 1079: dt=0.0098, 25 negative triangles 1080: dt=0.0098, 23 negative triangles 1081: dt=0.0098, 23 negative triangles 1082: dt=0.0098, 23 negative triangles 1083: dt=0.0098, 23 negative triangles 1084: dt=0.0098, 23 negative triangles 1085: dt=0.0098, 25 negative triangles 1086: dt=0.0098, 25 negative triangles 1087: dt=0.0098, 25 negative triangles 1088: dt=0.0098, 25 negative triangles 1089: dt=0.0098, 25 negative triangles 1090: dt=0.0098, 25 negative triangles 1091: dt=0.0098, 25 negative triangles 1092: dt=0.0098, 24 negative triangles 1093: dt=0.0098, 25 negative triangles 1094: dt=0.0098, 25 negative triangles 1095: dt=0.0098, 25 negative triangles 1096: dt=0.0098, 23 negative triangles 1097: dt=0.0098, 23 negative triangles 1098: dt=0.0098, 25 negative triangles 1099: dt=0.0098, 25 negative triangles 1100: dt=0.0098, 25 negative triangles 1101: dt=0.0098, 25 negative triangles 1102: dt=0.0098, 25 negative triangles 1103: dt=0.0098, 25 negative triangles 1104: dt=0.0098, 25 negative triangles 1105: dt=0.0098, 25 negative triangles 1106: dt=0.0098, 25 negative triangles writing registered surface to ../surf/rh.sphere.reg... 1107: dt=0.0098, 25 negative triangles 1108: 25 negative triangles registration took 0.19 hours #VMPC# mris_register VmPeak 722828 FSRUNTIME@ mris_register 0.1892 hours 4 threads PIDs (5235 5238) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sat Feb 18 14:33:01 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sat Feb 18 14:33:01 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 5286 of (5286 5289) to complete... Waiting for PID 5289 of (5286 5289) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (5286 5289) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sat Feb 18 14:33:03 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mrisp_paint -a 5 /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Sat Feb 18 14:33:03 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mrisp_paint -a 5 /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 5334 of (5334 5337) to complete... Waiting for PID 5337 of (5334 5337) to complete... mrisp_paint -a 5 /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/7.2.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/7.2.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (5334 5337) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sat Feb 18 14:33:03 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.2.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Sat Feb 18 14:33:03 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.2.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 5382 of (5382 5385) to complete... Waiting for PID 5385 of (5382 5385) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.2.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /usr/local/freesurfer/7.2.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 1108 labels changed using aseg relabeling using gibbs priors... 000: 2767 changed, 118080 examined... 001: 631 changed, 11841 examined... 002: 149 changed, 3634 examined... 003: 55 changed, 942 examined... 004: 17 changed, 324 examined... 005: 8 changed, 110 examined... 006: 1 changed, 47 examined... 007: 0 changed, 6 examined... 237 labels changed using aseg 000: 97 total segments, 39 labels (108 vertices) changed 001: 59 total segments, 1 labels (1 vertices) changed 002: 58 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1789 vertices marked for relabeling... 1789 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.2.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /usr/local/freesurfer/7.2.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 968 labels changed using aseg relabeling using gibbs priors... 000: 2525 changed, 118087 examined... 001: 538 changed, 11086 examined... 002: 113 changed, 3158 examined... 003: 33 changed, 715 examined... 004: 13 changed, 204 examined... 005: 1 changed, 77 examined... 006: 0 changed, 7 examined... 166 labels changed using aseg 000: 75 total segments, 37 labels (148 vertices) changed 001: 40 total segments, 3 labels (14 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1742 vertices marked for relabeling... 1742 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 12 seconds. PIDs (5382 5385) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Sat Feb 18 14:33:16 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.2.0 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 236156 0.33402 0.11315 0.001474 2.0651 Corner 708468 60.00000 12.96878 1.093052 176.5162 Edge 354234 0.88718 0.18703 0.038435 3.2301 Hinge 354234 9.53038 9.73766 0.000027 179.7843 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 MRIfindBrightNonWM(): 2309 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRIcopyHeader(): source has ctab MRISripBasalGanglia(): -2 2 0.5 ripped 364 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59040: xyz = (-5.16139,-0.127429,81.4839) oxyz = (-5.16139,-0.127429,81.4839) wxzy = (-5.16139,-0.127429,81.4839) pxyz = (0,0,0) CBVO Creating mask 118080 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=2 had to be increased for 60 vertices, nripped=8284 mean border=83.1, 44 (44) missing vertices, mean dist 0.3 [1.2 (%16.0)->0.6 (%84.0))] %59 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0781 min Finding expansion regions mean absolute distance = 0.72 +- 1.04 2484 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=devel, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1414886.5, rms=7.553 001: dt: 0.5000, sse=616717.4, rms=4.557 (39.663%) 002: dt: 0.5000, sse=355014.9, rms=2.975 (34.718%) 003: dt: 0.5000, sse=285179.5, rms=2.377 (20.108%) 004: dt: 0.5000, sse=260721.4, rms=2.127 (10.510%) rms = 2.1519/2.1271, sse=263691.9/260721.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=213354.6, rms=1.519 (28.585%) 006: dt: 0.2500, sse=194344.9, rms=1.186 (21.952%) 007: dt: 0.2500, sse=189667.0, rms=1.089 (8.108%) rms = 1.0568/1.0895, sse=188370.4/189667.0, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=188370.4, rms=1.057 (3.003%) rms = 1.0323/1.0568, sse=187346.9/188370.4, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=187346.9, rms=1.032 (2.316%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=1 had to be increased for 37 vertices, nripped=8284 mean border=85.2, 46 (23) missing vertices, mean dist -0.2 [0.5 (%63.8)->0.2 (%36.2))] %68 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0562 min Finding expansion regions mean absolute distance = 0.40 +- 0.78 2096 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=devel, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=492688.5, rms=3.793 010: dt: 0.5000, sse=299493.4, rms=2.363 (37.689%) 011: dt: 0.5000, sse=262278.8, rms=1.975 (16.417%) 012: dt: 0.5000, sse=251551.0, rms=1.859 (5.890%) rms = 1.9892/1.8590, sse=262416.3/251551.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=212686.7, rms=1.271 (31.630%) 014: dt: 0.2500, sse=198721.1, rms=0.972 (23.517%) 015: dt: 0.2500, sse=195301.5, rms=0.907 (6.745%) rms = 0.8961/0.9065, sse=194769.9/195301.6, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=194769.9, rms=0.896 (1.149%) rms = 0.8848/0.8961, sse=194252.7/194769.9, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=194252.7, rms=0.885 (1.262%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 33 vertices, nripped=8284 mean border=87.9, 49 (17) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0293 min Finding expansion regions mean absolute distance = 0.31 +- 0.47 2450 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=devel, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=453284.0, rms=3.581 018: dt: 0.5000, sse=273513.1, rms=2.134 (40.414%) 019: dt: 0.5000, sse=255873.5, rms=1.938 (9.161%) rms = 1.9213/1.9381, sse=253668.1/255873.5, time step reduction 1 of 3 to 0.250 0 0 1 020: dt: 0.5000, sse=253668.1, rms=1.921 (0.868%) 021: dt: 0.2500, sse=196538.6, rms=1.026 (46.618%) 022: dt: 0.2500, sse=192826.7, rms=0.881 (14.126%) rms = 0.8673/0.8807, sse=189314.6/192826.7, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=189314.6, rms=0.867 (1.526%) rms = 0.8395/0.8673, sse=188321.9/189314.6, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=188321.9, rms=0.839 (3.207%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 71.0000000; outside_low = 60.7077410; outside_hi = 110.4685130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 28 vertices, nripped=8284 mean border=88.8, 42 (17) missing vertices, mean dist -0.1 [0.2 (%60.6)->0.2 (%39.4))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0181 min Finding expansion regions mean absolute distance = 0.23 +- 0.33 2632 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=devel, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=222401.8, rms=1.572 025: dt: 0.5000, sse=205673.5, rms=1.236 (21.358%) rms = 1.4480/1.2359, sse=215301.2/205673.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=187150.7, rms=0.859 (30.473%) 027: dt: 0.2500, sse=181380.2, rms=0.715 (16.786%) rms = 0.6803/0.7150, sse=179275.4/181380.2, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=179275.4, rms=0.680 (4.866%) rms = 0.6692/0.6803, sse=178916.4/179275.4, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=178916.4, rms=0.669 (1.623%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 2.14 minutes #VMPC# mris_place_surfaces VmPeak 2040832 mris_place_surface done @#@FSTIME 2023:02:18:14:33:16 mris_place_surface N 25 e 135.63 S 2.47 U 251.59 P 187% M 1600556 F 3 R 421855 W 0 c 2224 w 1140 I 664 O 8312 L 2.45 3.21 3.27 @#@FSLOADPOST 2023:02:18:14:35:31 mris_place_surface N 25 1.80 2.67 3.06 #-------------------------------------------- #@# WhiteSurfs rh Sat Feb 18 14:35:31 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.2.0 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 236170 0.33428 0.11231 0.000000 2.4824 Corner 708510 60.00000 12.97942 0.587870 178.4046 Edge 354255 0.88749 0.18573 0.000325 3.4122 Hinge 354255 9.56892 10.01472 0.000025 179.9165 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 MRIfindBrightNonWM(): 2309 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRIcopyHeader(): source has ctab MRISripBasalGanglia(): -2 2 0.5 ripped 222 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59044: xyz = (3.13423,3.16779,54.7142) oxyz = (3.13423,3.16779,54.7142) wxzy = (3.13423,3.16779,54.7142) pxyz = (0,0,0) CBVO Creating mask 118087 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=2 had to be increased for 97 vertices, nripped=8262 mean border=83.5, 62 (62) missing vertices, mean dist 0.3 [1.1 (%16.9)->0.6 (%83.1))] %59 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0774 min Finding expansion regions mean absolute distance = 0.68 +- 1.03 2387 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=devel, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1484318.8, rms=7.155 001: dt: 0.5000, sse=609404.0, rms=4.308 (39.790%) 002: dt: 0.5000, sse=383571.3, rms=2.904 (32.597%) 003: dt: 0.5000, sse=320834.7, rms=2.468 (14.992%) 004: dt: 0.5000, sse=275147.1, rms=2.252 (8.759%) rms = 2.2986/2.2521, sse=279485.3/275147.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=222621.0, rms=1.633 (27.497%) 006: dt: 0.2500, sse=202179.0, rms=1.308 (19.923%) 007: dt: 0.2500, sse=197070.7, rms=1.217 (6.923%) rms = 1.1705/1.2170, sse=197236.9/197070.7, time step reduction 2 of 3 to 0.125 0 1 1 008: dt: 0.2500, sse=197236.9, rms=1.171 (3.817%) rms = 1.1349/1.1705, sse=196111.2/197236.9, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=196111.2, rms=1.135 (3.039%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=1 had to be increased for 72 vertices, nripped=8262 mean border=85.4, 80 (21) missing vertices, mean dist -0.2 [0.4 (%64.1)->0.2 (%35.9))] %68 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0535 min Finding expansion regions mean absolute distance = 0.36 +- 0.73 2010 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=devel, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=462060.9, rms=3.582 010: dt: 0.5000, sse=297188.3, rms=2.313 (35.436%) 011: dt: 0.5000, sse=269098.9, rms=2.027 (12.376%) 012: dt: 0.5000, sse=268291.5, rms=1.968 (2.886%) rms = 2.0758/1.9681, sse=270710.1/268291.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=220570.8, rms=1.366 (30.577%) 014: dt: 0.2500, sse=201952.6, rms=1.050 (23.158%) 015: dt: 0.2500, sse=198957.8, rms=0.988 (5.859%) rms = 0.9787/0.9884, sse=198180.7/198957.8, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=198180.7, rms=0.979 (0.978%) rms = 0.9471/0.9787, sse=197029.5/198180.7, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=197029.5, rms=0.947 (3.235%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 59 vertices, nripped=8262 mean border=87.9, 73 (7) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.2 (%26.5))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0292 min Finding expansion regions mean absolute distance = 0.29 +- 0.44 2606 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=devel, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=419444.3, rms=3.353 018: dt: 0.5000, sse=275551.1, rms=2.133 (36.399%) 019: dt: 0.5000, sse=261154.6, rms=1.985 (6.930%) rms = 1.9980/1.9848, sse=262361.5/261154.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=215544.2, rms=1.369 (31.040%) 021: dt: 0.2500, sse=197336.1, rms=1.006 (26.470%) 022: dt: 0.2500, sse=195331.7, rms=0.943 (6.335%) rms = 0.9241/0.9427, sse=193782.0/195331.7, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=193782.0, rms=0.924 (1.969%) rms = 0.8899/0.9241, sse=192704.4/193782.0, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=192704.4, rms=0.890 (3.699%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4685130; border_low = 72.0000000; outside_low = 61.7077410; outside_hi = 110.4685130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 51 vertices, nripped=8262 mean border=88.8, 75 (6) missing vertices, mean dist -0.1 [0.2 (%59.5)->0.2 (%40.5))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0171 min Finding expansion regions mean absolute distance = 0.22 +- 0.32 2352 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=devel, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=223219.0, rms=1.545 025: dt: 0.5000, sse=214626.9, rms=1.324 (14.316%) rms = 1.4867/1.3237, sse=229167.8/214626.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=192638.8, rms=0.932 (29.591%) 027: dt: 0.2500, sse=190264.2, rms=0.805 (13.625%) rms = 0.7654/0.8050, sse=185057.7/190264.2, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=185057.8, rms=0.765 (4.927%) rms = 0.7173/0.7654, sse=183729.3/185057.7, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=183729.3, rms=0.717 (6.283%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.16 minutes #VMPC# mris_place_surfaces VmPeak 2115932 mris_place_surface done @#@FSTIME 2023:02:18:14:35:31 mris_place_surface N 25 e 137.35 S 2.34 U 255.07 P 187% M 1675864 F 0 R 476942 W 0 c 2789 w 1158 I 0 O 8312 L 1.80 2.67 3.06 @#@FSLOADPOST 2023:02:18:14:37:49 mris_place_surface N 25 1.72 2.33 2.87 #-------------------------------------------- #@# T1PialSurf lh Sat Feb 18 14:37:49 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.2.0 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 236156 0.33550 0.12482 0.001263 2.5967 Corner 708468 60.00000 14.14979 0.452339 178.7391 Edge 354234 0.89025 0.20307 0.020280 3.6859 Hinge 354234 9.57016 9.92666 0.000005 179.7843 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 MRIfindBrightNonWM(): 2309 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 67.8274 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 vertex 59040: xyz = (-5.05008,-0.10048,81.4492) oxyz = (-5.05008,-0.10048,81.4492) wxzy = (-5.05008,-0.10048,81.4492) pxyz = (-5.05008,-0.10048,81.4492) CBVO Creating mask 118080 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 60.7077410; border_low = 40.1232190; outside_low = 10.0000000; outside_hi = 55.5616110; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=2 had to be increased for 69 vertices, nripped=5513 mean border=59.4, 61 (61) missing vertices, mean dist 1.6 [1.0 (%0.0)->2.7 (%100.0))] %18 local maxima, %39 large gradients and %38 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0561 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=devel, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=20610594.0, rms=30.142 001: dt: 0.5000, sse=15081824.0, rms=25.746 (14.586%) 002: dt: 0.5000, sse=10926932.0, rms=21.867 (15.067%) 003: dt: 0.5000, sse=7998625.0, rms=18.653 (14.696%) 004: dt: 0.5000, sse=5997831.5, rms=16.091 (13.735%) 005: dt: 0.5000, sse=4538420.0, rms=13.927 (13.451%) 006: dt: 0.5000, sse=3363231.5, rms=11.900 (14.553%) 007: dt: 0.5000, sse=2392305.2, rms=9.917 (16.664%) 008: dt: 0.5000, sse=1630361.9, rms=8.023 (19.092%) 009: dt: 0.5000, sse=1106648.2, rms=6.404 (20.182%) 010: dt: 0.5000, sse=803873.4, rms=5.243 (18.137%) 011: dt: 0.5000, sse=668405.2, rms=4.628 (11.726%) 012: dt: 0.5000, sse=602247.2, rms=4.293 (7.236%) 013: dt: 0.5000, sse=572111.1, rms=4.129 (3.813%) 014: dt: 0.5000, sse=553898.1, rms=4.025 (2.523%) rms = 3.9753/4.0251, sse=545650.2/553898.1, time step reduction 1 of 3 to 0.250 0 0 1 015: dt: 0.5000, sse=545650.2, rms=3.975 (1.236%) 016: dt: 0.2500, sse=411784.6, rms=3.112 (21.707%) 017: dt: 0.2500, sse=384940.7, rms=2.910 (6.510%) 018: dt: 0.2500, sse=378759.4, rms=2.859 (1.729%) rms = 2.8317/2.8595, sse=375471.0/378759.4, time step reduction 2 of 3 to 0.125 0 0 1 019: dt: 0.2500, sse=375471.0, rms=2.832 (0.971%) 020: dt: 0.1250, sse=366904.5, rms=2.760 (2.537%) rms = 2.7487/2.7599, sse=365692.2/366904.5, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=365692.2, rms=2.749 (0.406%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 60.7077410; border_low = 40.1232190; outside_low = 10.0000000; outside_hi = 55.5616110; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=1 had to be increased for 9060 vertices, nripped=5513 mean border=57.8, 1344 (11) missing vertices, mean dist 0.1 [0.1 (%39.7)->0.4 (%60.3))] %31 local maxima, %30 large gradients and %34 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0161 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=devel, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=541179.2, rms=3.739 022: dt: 0.5000, sse=507271.8, rms=3.524 (5.738%) rms = 3.6003/3.5241, sse=516842.6/507271.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=425708.4, rms=2.963 (15.915%) 024: dt: 0.2500, sse=396297.2, rms=2.735 (7.693%) 025: dt: 0.2500, sse=388428.0, rms=2.669 (2.429%) rms = 2.6550/2.6688, sse=386858.3/388428.0, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=386858.2, rms=2.655 (0.520%) 027: dt: 0.1250, sse=379984.5, rms=2.593 (2.319%) rms = 2.5860/2.5934, sse=379224.2/379984.5, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=379224.2, rms=2.586 (0.284%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 60.7077410; border_low = 40.1232190; outside_low = 10.0000000; outside_hi = 55.5616110; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 10225 vertices, nripped=5513 mean border=56.9, 1557 (5) missing vertices, mean dist 0.1 [0.1 (%41.4)->0.3 (%58.6))] %41 local maxima, %20 large gradients and %34 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0092 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=devel, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=437427.4, rms=3.024 rms = 3.3920/3.0240, sse=490814.2/437427.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=398508.6, rms=2.720 (10.054%) 030: dt: 0.2500, sse=388590.5, rms=2.637 (3.068%) rms = 2.6289/2.6365, sse=387543.5/388590.5, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=387543.4, rms=2.629 (0.289%) rms = 2.5877/2.6289, sse=382968.2/387543.5, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=382968.2, rms=2.588 (1.568%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 60.7077410; border_low = 40.1232190; outside_low = 10.0000000; outside_hi = 55.5616110; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118080 Gdiag_no=-1 vno start=0, stop=118080 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8798 vertices, nripped=5513 mean border=56.3, 3604 (4) missing vertices, mean dist 0.1 [0.1 (%45.0)->0.3 (%55.0))] %45 local maxima, %15 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0063 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=devel, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=404077.0, rms=2.762 rms = 3.0648/2.7618, sse=442932.0/404077.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=390063.8, rms=2.645 (4.218%) rms = 2.6044/2.6453, sse=384803.0/390063.8, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=384803.0, rms=2.604 (1.548%) rms = 2.5566/2.6044, sse=379369.0/384803.0, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=379369.0, rms=2.557 (1.834%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 7 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 1.92 minutes #VMPC# mris_place_surfaces VmPeak 1427712 mris_place_surface done @#@FSTIME 2023:02:18:14:37:49 mris_place_surface N 28 e 122.63 S 2.28 U 237.81 P 195% M 975348 F 0 R 270539 W 0 c 2396 w 1124 I 0 O 8312 L 1.72 2.33 2.87 @#@FSLOADPOST 2023:02:18:14:39:51 mris_place_surface N 28 1.56 2.05 2.70 #-------------------------------------------- #@# T1PialSurf rh Sat Feb 18 14:39:51 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.2.0 7.2.0 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 236170 0.33597 0.12464 0.000859 2.4824 Corner 708510 60.00000 14.17898 0.381982 178.4046 Edge 354255 0.89083 0.20303 0.021779 3.9362 Hinge 354255 9.60562 10.12346 0.000022 179.7648 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=17420, wmmin=5, clip=110 MRIfindBrightNonWM(): 2309 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 68.3274 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 vertex 59044: xyz = (3.12922,3.18932,54.7329) oxyz = (3.12922,3.18932,54.7329) wxzy = (3.12922,3.18932,54.7329) pxyz = (3.12922,3.18932,54.7329) CBVO Creating mask 118087 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 61.7077410; border_low = 41.1232190; outside_low = 10.0000000; outside_hi = 56.5616110; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=2 had to be increased for 135 vertices, nripped=5643 mean border=60.2, 81 (81) missing vertices, mean dist 1.6 [0.7 (%0.0)->2.6 (%100.0))] %18 local maxima, %39 large gradients and %38 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0559 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=devel, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=19496624.0, rms=29.328 001: dt: 0.5000, sse=14052911.0, rms=24.858 (15.243%) 002: dt: 0.5000, sse=10014779.0, rms=20.932 (15.791%) 003: dt: 0.5000, sse=7234599.5, rms=17.731 (15.296%) 004: dt: 0.5000, sse=5383534.5, rms=15.229 (14.112%) 005: dt: 0.5000, sse=4072070.5, rms=13.169 (13.521%) 006: dt: 0.5000, sse=3028061.8, rms=11.263 (14.475%) 007: dt: 0.5000, sse=2172584.5, rms=9.417 (16.394%) 008: dt: 0.5000, sse=1500631.2, rms=7.659 (18.662%) 009: dt: 0.5000, sse=1040728.8, rms=6.173 (19.400%) 010: dt: 0.5000, sse=760291.1, rms=5.056 (18.101%) 011: dt: 0.5000, sse=626669.1, rms=4.423 (12.522%) 012: dt: 0.5000, sse=561054.7, rms=4.074 (7.883%) 013: dt: 0.5000, sse=540224.4, rms=3.954 (2.952%) 014: dt: 0.5000, sse=521485.9, rms=3.843 (2.819%) rms = 3.8141/3.8425, sse=517457.9/521485.9, time step reduction 1 of 3 to 0.250 0 0 1 015: dt: 0.5000, sse=517457.9, rms=3.814 (0.739%) 016: dt: 0.2500, sse=398106.3, rms=3.013 (21.017%) 017: dt: 0.2500, sse=373494.2, rms=2.820 (6.384%) rms = 2.7724/2.8202, sse=367852.9/373494.2, time step reduction 2 of 3 to 0.125 0 0 1 018: dt: 0.2500, sse=367852.8, rms=2.772 (1.695%) 019: dt: 0.1250, sse=359158.1, rms=2.698 (2.700%) rms = 2.6844/2.6976, sse=357705.3/359158.0, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=357705.2, rms=2.684 (0.490%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 61.7077410; border_low = 41.1232190; outside_low = 10.0000000; outside_hi = 56.5616110; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8894 vertices, nripped=5643 mean border=58.6, 1395 (10) missing vertices, mean dist 0.1 [0.1 (%42.5)->0.5 (%57.5))] %29 local maxima, %32 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0167 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=devel, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=548881.6, rms=3.778 021: dt: 0.5000, sse=499107.3, rms=3.466 (8.270%) rms = 3.5298/3.4659, sse=506685.3/499107.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=428419.4, rms=2.976 (14.148%) 023: dt: 0.2500, sse=402984.0, rms=2.780 (6.575%) 024: dt: 0.2500, sse=396575.1, rms=2.727 (1.915%) rms = 2.7177/2.7266, sse=395622.5/396575.1, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=395622.5, rms=2.718 (0.329%) rms = 2.6761/2.7177, sse=390933.9/395622.5, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=390933.8, rms=2.676 (1.529%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 61.7077410; border_low = 41.1232190; outside_low = 10.0000000; outside_hi = 56.5616110; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9955 vertices, nripped=5643 mean border=57.7, 1684 (9) missing vertices, mean dist 0.1 [0.1 (%41.8)->0.3 (%58.2))] %40 local maxima, %21 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0092 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=devel, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=457789.2, rms=3.162 rms = 3.4937/3.1625, sse=507640.5/457789.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=420167.8, rms=2.883 (8.849%) 028: dt: 0.2500, sse=410368.8, rms=2.805 (2.697%) rms = 2.8109/2.8049, sse=411018.5/410368.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 2.7897/2.8049, sse=408540.1/410368.8, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=408540.1, rms=2.790 (0.540%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5314870; border_hi = 61.7077410; border_low = 41.1232190; outside_low = 10.0000000; outside_hi = 56.5616110; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118087 Gdiag_no=-1 vno start=0, stop=118087 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8659 vertices, nripped=5643 mean border=57.1, 3542 (8) missing vertices, mean dist 0.1 [0.1 (%45.5)->0.3 (%54.5))] %45 local maxima, %15 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0057 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=devel, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=426180.9, rms=2.925 rms = 3.1048/2.9251, sse=449469.5/426180.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=408803.1, rms=2.788 (4.681%) 031: dt: 0.2500, sse=397152.8, rms=2.697 (3.273%) 032: dt: 0.2500, sse=390191.9, rms=2.642 (2.052%) rms = 2.5941/2.6416, sse=384264.8/390191.9, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=384264.8, rms=2.594 (1.797%) 034: dt: 0.1250, sse=377816.8, rms=2.536 (2.233%) rms = 2.5123/2.5362, sse=375031.2/377816.7, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=375031.2, rms=2.512 (0.940%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 10 intersecting step 1 with no progress (num=14, old_num=10) 001: 14 intersecting 002: 8 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 1.99 minutes #VMPC# mris_place_surfaces VmPeak 1426024 mris_place_surface done @#@FSTIME 2023:02:18:14:39:51 mris_place_surface N 28 e 126.97 S 2.38 U 243.18 P 193% M 973932 F 0 R 270258 W 0 c 2360 w 1214 I 0 O 8312 L 1.56 2.05 2.70 @#@FSLOADPOST 2023:02:18:14:41:58 mris_place_surface N 28 1.60 1.95 2.58 #@# white curv lh Sat Feb 18 14:41:58 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2023:02:18:14:41:58 mris_place_surface N 5 e 1.40 S 0.11 U 1.63 P 124% M 162848 F 0 R 44053 W 0 c 8 w 20 I 0 O 928 L 1.60 1.95 2.58 @#@FSLOADPOST 2023:02:18:14:42:00 mris_place_surface N 5 1.55 1.93 2.57 #@# white area lh Sat Feb 18 14:42:00 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2023:02:18:14:42:00 mris_place_surface N 3 e 0.48 S 0.09 U 0.70 P 165% M 162676 F 0 R 44028 W 0 c 19 w 15 I 0 O 928 L 1.55 1.93 2.57 @#@FSLOADPOST 2023:02:18:14:42:00 mris_place_surface N 3 1.55 1.93 2.57 #@# pial curv lh Sat Feb 18 14:42:00 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2023:02:18:14:42:00 mris_place_surface N 5 e 1.40 S 0.08 U 1.67 P 124% M 163128 F 0 R 43905 W 0 c 9 w 15 I 0 O 928 L 1.55 1.93 2.57 @#@FSLOADPOST 2023:02:18:14:42:02 mris_place_surface N 5 1.55 1.93 2.57 #@# pial area lh Sat Feb 18 14:42:02 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2023:02:18:14:42:02 mris_place_surface N 3 e 0.49 S 0.13 U 0.71 P 170% M 162868 F 0 R 43864 W 0 c 10 w 14 I 0 O 928 L 1.55 1.93 2.57 @#@FSLOADPOST 2023:02:18:14:42:02 mris_place_surface N 3 1.55 1.93 2.57 #@# thickness lh Sat Feb 18 14:42:02 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 118080 vertices processed 25000 of 118080 vertices processed 50000 of 118080 vertices processed 75000 of 118080 vertices processed 100000 of 118080 vertices processed 0 of 118080 vertices processed 25000 of 118080 vertices processed 50000 of 118080 vertices processed 75000 of 118080 vertices processed 100000 of 118080 vertices processed thickness calculation complete, 25:228 truncations. 57842 vertices at 0 distance 106926 vertices at 1 distance 48757 vertices at 2 distance 15135 vertices at 3 distance 4905 vertices at 4 distance 1685 vertices at 5 distance 540 vertices at 6 distance 188 vertices at 7 distance 71 vertices at 8 distance 26 vertices at 9 distance 16 vertices at 10 distance 7 vertices at 11 distance 9 vertices at 12 distance 7 vertices at 13 distance 7 vertices at 14 distance 13 vertices at 15 distance 10 vertices at 16 distance 2 vertices at 17 distance 4 vertices at 18 distance 6 vertices at 19 distance 4 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2023:02:18:14:42:02 mris_place_surface N 6 e 22.37 S 0.07 U 22.73 P 101% M 162884 F 0 R 50192 W 0 c 70 w 16 I 0 O 928 L 1.55 1.93 2.57 @#@FSLOADPOST 2023:02:18:14:42:25 mris_place_surface N 6 1.36 1.86 2.53 #@# area and vertex vol lh Sat Feb 18 14:42:25 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /home/developer/Desktop/1st_scan_nii/Sub-139/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume Sub-139 lh /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.volume masking with /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Total face volume 192984 Total vertex volume 192773 (mask=0) #@# Sub-139 lh 192773 vertexvol Done @#@FSTIME 2023:02:18:14:42:25 vertexvol N 4 e 1.15 S 0.16 U 1.44 P 139% M 271104 F 31 R 79978 W 0 c 19 w 85 I 6696 O 2784 L 1.36 1.86 2.53 @#@FSLOADPOST 2023:02:18:14:42:26 vertexvol N 4 1.36 1.86 2.53 #@# white curv rh Sat Feb 18 14:42:26 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2023:02:18:14:42:26 mris_place_surface N 5 e 1.34 S 0.10 U 1.55 P 123% M 162688 F 0 R 44125 W 0 c 14 w 13 I 0 O 928 L 1.36 1.86 2.53 @#@FSLOADPOST 2023:02:18:14:42:27 mris_place_surface N 5 1.36 1.86 2.53 #@# white area rh Sat Feb 18 14:42:27 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2023:02:18:14:42:27 mris_place_surface N 3 e 0.54 S 0.13 U 0.82 P 176% M 163100 F 0 R 43902 W 0 c 7 w 22 I 0 O 928 L 1.36 1.86 2.53 @#@FSLOADPOST 2023:02:18:14:42:28 mris_place_surface N 3 1.36 1.86 2.53 #@# pial curv rh Sat Feb 18 14:42:28 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2023:02:18:14:42:28 mris_place_surface N 5 e 1.36 S 0.15 U 1.54 P 124% M 163116 F 0 R 43978 W 0 c 15 w 15 I 0 O 928 L 1.36 1.86 2.53 @#@FSLOADPOST 2023:02:18:14:42:29 mris_place_surface N 5 1.36 1.86 2.53 #@# pial area rh Sat Feb 18 14:42:29 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2023:02:18:14:42:29 mris_place_surface N 3 e 0.55 S 0.09 U 0.87 P 176% M 163160 F 0 R 43905 W 0 c 14 w 22 I 0 O 928 L 1.36 1.86 2.53 @#@FSLOADPOST 2023:02:18:14:42:30 mris_place_surface N 3 1.33 1.84 2.52 #@# thickness rh Sat Feb 18 14:42:30 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 118087 vertices processed 25000 of 118087 vertices processed 50000 of 118087 vertices processed 75000 of 118087 vertices processed 100000 of 118087 vertices processed 0 of 118087 vertices processed 25000 of 118087 vertices processed 50000 of 118087 vertices processed 75000 of 118087 vertices processed 100000 of 118087 vertices processed thickness calculation complete, 79:312 truncations. 59048 vertices at 0 distance 106698 vertices at 1 distance 48931 vertices at 2 distance 14600 vertices at 3 distance 4528 vertices at 4 distance 1485 vertices at 5 distance 486 vertices at 6 distance 153 vertices at 7 distance 52 vertices at 8 distance 38 vertices at 9 distance 35 vertices at 10 distance 21 vertices at 11 distance 19 vertices at 12 distance 20 vertices at 13 distance 21 vertices at 14 distance 14 vertices at 15 distance 6 vertices at 16 distance 1 vertices at 17 distance 6 vertices at 18 distance 4 vertices at 19 distance 8 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2023:02:18:14:42:30 mris_place_surface N 6 e 22.74 S 0.13 U 23.06 P 102% M 163092 F 0 R 50162 W 0 c 92 w 23 I 0 O 928 L 1.33 1.84 2.52 @#@FSLOADPOST 2023:02:18:14:42:53 mris_place_surface N 6 1.31 1.80 2.49 #@# area and vertex vol rh Sat Feb 18 14:42:53 EST 2023 cd /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /home/developer/Desktop/1st_scan_nii/Sub-139/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume Sub-139 rh /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.volume masking with /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Total face volume 191975 Total vertex volume 191785 (mask=0) #@# Sub-139 rh 191785 vertexvol Done @#@FSTIME 2023:02:18:14:42:53 vertexvol N 4 e 1.12 S 0.22 U 1.39 P 143% M 271284 F 0 R 76861 W 0 c 32 w 46 I 0 O 2784 L 1.31 1.80 2.49 @#@FSLOADPOST 2023:02:18:14:42:54 vertexvol N 4 1.31 1.80 2.49 #----------------------------------------- #@# Curvature Stats lh Sat Feb 18 14:42:54 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Sub-139 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Sub-139/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 216 ] Gb_filter = 0 WARN: S lookup min: -0.011201 WARN: S explicit min: 0.000000 vertex = 642 @#@FSTIME 2023:02:18:14:42:54 mris_curvature_stats N 11 e 2.10 S 0.08 U 2.46 P 121% M 162796 F 17 R 44166 W 0 c 132 w 40 I 3528 O 7464 L 1.31 1.80 2.49 @#@FSLOADPOST 2023:02:18:14:42:56 mris_curvature_stats N 11 1.29 1.79 2.49 #----------------------------------------- #@# Curvature Stats rh Sat Feb 18 14:42:56 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Sub-139 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Sub-139/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 207 ] Gb_filter = 0 WARN: S lookup min: -0.282177 WARN: S explicit min: 0.000000 vertex = 667 @#@FSTIME 2023:02:18:14:42:56 mris_curvature_stats N 11 e 1.93 S 0.13 U 2.25 P 123% M 163132 F 0 R 44111 W 0 c 78 w 24 I 0 O 7464 L 1.29 1.79 2.49 @#@FSLOADPOST 2023:02:18:14:42:58 mris_curvature_stats N 11 1.29 1.79 2.49 #-------------------------------------------- #@# Cortical ribbon mask Sat Feb 18 14:42:58 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon Sub-139 SUBJECTS_DIR is /home/developer/Desktop/1st_scan_nii loading input data... Running hemis serially Processing left hemi MRIcopyHeader(): source has ctab computing distance to left white surface MRIcopyHeader(): source has ctab computing distance to left pial surface Processing right hemi MRIcopyHeader(): source has ctab computing distance to right white surface MRIcopyHeader(): source has ctab computing distance to right pial surface hemi masks overlap voxels = 138 MRIcopyHeader(): source has ctab writing volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/ribbon.mgz mris_volmask took 2.85 minutes writing ribbon files MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab @#@FSTIME 2023:02:18:14:42:58 mris_volmask N 12 e 170.87 S 0.50 U 171.77 P 100% M 916792 F 16 R 500982 W 0 c 728 w 74 I 4064 O 736 L 1.29 1.79 2.49 @#@FSLOADPOST 2023:02:18:14:45:49 mris_volmask N 12 1.09 1.47 2.24 #----------------------------------------- #@# Cortical Parc 2 lh Sat Feb 18 14:45:49 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.2.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Sat Feb 18 14:45:49 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.2.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 6193 of (6193 6196) to complete... Waiting for PID 6196 of (6193 6196) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.2.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /usr/local/freesurfer/7.2.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 99 labels changed using aseg relabeling using gibbs priors... 000: 7999 changed, 118080 examined... 001: 1759 changed, 30934 examined... 002: 531 changed, 9360 examined... 003: 219 changed, 2987 examined... 004: 108 changed, 1268 examined... 005: 50 changed, 608 examined... 006: 25 changed, 284 examined... 007: 13 changed, 153 examined... 008: 7 changed, 80 examined... 009: 6 changed, 42 examined... 010: 2 changed, 33 examined... 011: 1 changed, 10 examined... 012: 0 changed, 6 examined... 44 labels changed using aseg 000: 208 total segments, 120 labels (1412 vertices) changed 001: 93 total segments, 5 labels (18 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 21 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1229 vertices marked for relabeling... 1229 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.2.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /usr/local/freesurfer/7.2.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 4 labels changed using aseg relabeling using gibbs priors... 000: 7915 changed, 118087 examined... 001: 1825 changed, 31267 examined... 002: 525 changed, 9924 examined... 003: 216 changed, 3112 examined... 004: 107 changed, 1250 examined... 005: 51 changed, 608 examined... 006: 27 changed, 316 examined... 007: 16 changed, 161 examined... 008: 16 changed, 102 examined... 009: 8 changed, 87 examined... 010: 4 changed, 47 examined... 011: 2 changed, 24 examined... 012: 0 changed, 16 examined... 5 labels changed using aseg 000: 206 total segments, 119 labels (1491 vertices) changed 001: 92 total segments, 5 labels (26 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 30 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1309 vertices marked for relabeling... 1309 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. PIDs (6193 6196) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sat Feb 18 14:46:06 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.2.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Sat Feb 18 14:46:06 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.2.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 6241 of (6241 6244) to complete... Waiting for PID 6244 of (6241 6244) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 lh ../surf/lh.sphere.reg /usr/local/freesurfer/7.2.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /usr/local/freesurfer/7.2.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 1545 labels changed using aseg relabeling using gibbs priors... 000: 1760 changed, 118080 examined... 001: 401 changed, 8376 examined... 002: 120 changed, 2308 examined... 003: 54 changed, 724 examined... 004: 29 changed, 321 examined... 005: 15 changed, 159 examined... 006: 9 changed, 77 examined... 007: 9 changed, 52 examined... 008: 2 changed, 44 examined... 009: 0 changed, 14 examined... 241 labels changed using aseg 000: 49 total segments, 16 labels (99 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 807 vertices marked for relabeling... 807 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub-139 rh ../surf/rh.sphere.reg /usr/local/freesurfer/7.2.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.2.0 7.2.0 reading atlas from /usr/local/freesurfer/7.2.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... MRIcopyHeader(): source has ctab 1512 labels changed using aseg relabeling using gibbs priors... 000: 1706 changed, 118087 examined... 001: 377 changed, 8118 examined... 002: 101 changed, 2136 examined... 003: 46 changed, 598 examined... 004: 21 changed, 275 examined... 005: 17 changed, 104 examined... 006: 13 changed, 80 examined... 007: 9 changed, 76 examined... 008: 6 changed, 49 examined... 009: 7 changed, 33 examined... 010: 5 changed, 33 examined... 011: 4 changed, 17 examined... 012: 1 changed, 18 examined... 013: 1 changed, 7 examined... 014: 0 changed, 7 examined... 251 labels changed using aseg 000: 46 total segments, 13 labels (86 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 845 vertices marked for relabeling... 845 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. PIDs (6241 6244) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sat Feb 18 14:46:19 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts pctsurfcon --s Sub-139 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sat Feb 18 14:46:19 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts pctsurfcon --s Sub-139 --rh-only Waiting for PID 6289 of (6289 6292) to complete... Waiting for PID 6292 of (6289 6292) to complete... pctsurfcon --s Sub-139 --lh-only Log file is /home/developer/Desktop/1st_scan_nii/Sub-139/scripts/pctsurfcon.log Sat Feb 18 14:46:19 EST 2023 setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii cd /home/developer/Desktop/1st_scan_nii/Sub-139/scripts /usr/local/freesurfer/7.2.0/bin/pctsurfcon pctsurfcon 7.2.0 Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/7.2.0 mri_vol2surf --mov /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6289/lh.wm.mgh --regheader Sub-139 --cortex srcvol = /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99948 -0.02990 0.01209 -0.00002; 0.00846 0.11869 0.99290 -0.00002; 0.03112 -0.99248 0.11838 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Reading surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 63088 Masking with /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6289/lh.wm.mgh Dim: 118080 1 1 mri_vol2surf --mov /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6289/lh.gm.mgh --projfrac 0.3 --regheader Sub-139 --cortex srcvol = /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99948 -0.02990 0.01209 -0.00002; 0.00846 0.11869 0.99290 -0.00002; 0.03112 -0.99248 0.11838 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Reading surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Done reading source surface Reading thickness /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 74051 Masking with /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6289/lh.gm.mgh Dim: 118080 1 1 mri_concat /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6289/lh.wm.mgh /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6289/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.w-g.pct.mgh mri_segstats --in /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.w-g.pct.mgh --annot Sub-139 lh aparc --sum /home/developer/Desktop/1st_scan_nii/Sub-139/stats/lh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.w-g.pct.mgh --annot Sub-139 lh aparc --sum /home/developer/Desktop/1st_scan_nii/Sub-139/stats/lh.w-g.pct.stats --snr sysname Linux hostname developer-VirtualBox machine x86_64 user developer whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.annot Seg base 1000 Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.w-g.pct.mgh Vertex Area is 0.670989 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s Sub-139 --rh-only Log file is /home/developer/Desktop/1st_scan_nii/Sub-139/scripts/pctsurfcon.log Sat Feb 18 14:46:19 EST 2023 setenv SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii cd /home/developer/Desktop/1st_scan_nii/Sub-139/scripts /usr/local/freesurfer/7.2.0/bin/pctsurfcon pctsurfcon 7.2.0 Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/7.2.0 mri_vol2surf --mov /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6292/rh.wm.mgh --regheader Sub-139 --cortex srcvol = /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99948 -0.02990 0.01209 -0.00002; 0.00846 0.11869 0.99290 -0.00002; 0.03112 -0.99248 0.11838 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Reading surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 63481 Masking with /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6292/rh.wm.mgh Dim: 118087 1 1 mri_vol2surf --mov /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6292/rh.gm.mgh --projfrac 0.3 --regheader Sub-139 --cortex srcvol = /home/developer/Desktop/1st_scan_nii/Sub-139/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/developer/Desktop/1st_scan_nii/Sub-139/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99948 -0.02990 0.01209 -0.00002; 0.00846 0.11869 0.99290 -0.00002; 0.03112 -0.99248 0.11838 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Reading surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Done reading source surface Reading thickness /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 73787 Masking with /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6292/rh.gm.mgh Dim: 118087 1 1 mri_concat /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6292/rh.wm.mgh /home/developer/Desktop/1st_scan_nii/Sub-139/surf/tmp.pctsurfcon.6292/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.w-g.pct.mgh mri_segstats --in /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.w-g.pct.mgh --annot Sub-139 rh aparc --sum /home/developer/Desktop/1st_scan_nii/Sub-139/stats/rh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.w-g.pct.mgh --annot Sub-139 rh aparc --sum /home/developer/Desktop/1st_scan_nii/Sub-139/stats/rh.w-g.pct.stats --snr sysname Linux hostname developer-VirtualBox machine x86_64 user developer whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.annot Seg base 2000 Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.w-g.pct.mgh Vertex Area is 0.671928 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (6289 6292) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sat Feb 18 14:46:22 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... MRIcopyHeader(): source has ctab 2140 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... MRIcopyHeader(): source has ctab 1660 voxels changed to hypointensity... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 3791 hypointense voxels neighboring cortex changed @#@FSTIME 2023:02:18:14:46:22 mri_relabel_hypointensities N 3 e 21.70 S 0.35 U 22.59 P 105% M 447744 F 17 R 321015 W 0 c 91 w 64 I 4232 O 568 L 1.84 1.63 2.27 @#@FSLOADPOST 2023:02:18:14:46:44 mri_relabel_hypointensities N 3 1.68 1.61 2.25 #----------------------------------------- #@# APas-to-ASeg Sat Feb 18 14:46:44 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /home/developer/Desktop/1st_scan_nii/Sub-139/mri/ribbon.mgz --threads 4 --lh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label --lh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white --lh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial --rh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label --rh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white --rh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii outvol aseg.mgz 4 avail.processors, using 4 Loading aseg.presurf.hypos.mgz MRIcopyHeader(): source has ctab Loading /home/developer/Desktop/1st_scan_nii/Sub-139/mri/ribbon.mgz Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Done loading 0 64 128 192 1 2 193 3 4 194 5 6 195 7 196 8 9 197 10 198 11 12 65 199 13 200 201 14 15 16 66 202 203 67 204 129 205 206 207 17 208 18 209 210 19 211 20 68 212 21 22 213 23 214 24 215 25 216 26 27 217 28 218 29 219 30 220 31 221 69 32 222 33 34 223 35 224 36 225 37 226 38 227 39 228 70 40 229 230 41 231 42 232 43 233 44 234 235 45 46 236 71 47 237 48 238 49 239 50 240 51 241 52 242 72 53 243 54 55 244 245 56 57 246 247 58 59 248 60 249 61 250 62 251 252 130 253 254 255 73 63 74 75 131 76 77 78 132 79 80 81 82 83 84 133 85 86 87 134 88 89 135 90 136 91 137 92 93 94 138 139 95 96 97 140 98 141 99 142 100 101 143 102 103 144 104 105 106 145 107 146 108 147 109 148 110 149 111 150 112 151 113 152 153 114 154 155 115 156 157 116 158 159 117 160 118 161 119 162 163 120 164 121 165 166 122 167 123 168 169 124 170 125 171 172 126 173 174 175 127 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 96652 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1028132 mri_surf2volseg done @#@FSTIME 2023:02:18:14:46:44 mri_surf2volseg N 20 e 8.28 S 0.83 U 13.88 P 177% M 821088 F 19 R 235060 W 0 c 693 w 101 I 21168 O 608 L 1.68 1.61 2.25 @#@FSLOADPOST 2023:02:18:14:46:52 mri_surf2volseg N 20 1.73 1.62 2.24 mri_brainvol_stats Sub-139 ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1409721.0 #CBVS2 BrainSegVol 985155.0 #CBVS2 BrainSegVolNotVent 970918.0 #CBVS2 SupraTentVol 873492.0 #CBVS2 SupraTentVolNotVent 859255.0 #CBVS2 lhCtxGM 193015.6 #CBVS2 rhCtxGM 192073.4 #CBVS2 lhCerebralWM 214504.5 #CBVS2 rhCerebralWM 212221.5 #CBVS2 SubCortGMVol 48552.0 #CBVS2 CerebellumVol 111663.0 #CBVS2 CerebellumGMVol 87662.0 #CBVS2 VentChorVol 11357.0 #CBVS2 3rd4th5thCSF 2880.0 #CBVS2 AllCSF 14237.0 #CBVS2 CCVol 3633.0 @#@FSTIME 2023:02:18:14:46:52 mri_brainvol_stats N 1 e 2.48 S 0.24 U 4.38 P 186% M 212136 F 17 R 103888 W 0 c 64 w 79 I 6136 O 8 L 1.73 1.62 2.24 @#@FSLOADPOST 2023:02:18:14:46:55 mri_brainvol_stats N 1 1.83 1.65 2.25 #----------------------------------------- #@# AParc-to-ASeg aparc Sat Feb 18 14:46:55 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.annot 1000 --lh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label --lh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white --lh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial --rh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.annot 2000 --rh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label --rh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white --rh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii outvol aparc+aseg.mgz 4 avail.processors, using 4 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7920 vertices from lh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.annot Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8040 vertices from rh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.annot Done loading 0 64 192 128 1 2 3 4 5 6 7 8 193 9 10 194 11 195 12 196 13 197 14 198 15 199 16 200 17 18 201 19 202 20 203 21 204 22 205 23 206 24 25 26 27 28 29 30 31 32 207 33 208 34 209 35 36 210 37 38 39 211 40 212 41 213 42 43 44 214 45 215 46 216 47 217 48 218 49 50 219 51 220 52 221 53 222 54 223 55 224 56 57 225 58 226 59 227 60 228 61 62 229 230 231 232 233 234 235 236 65 237 238 239 63 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 66 67 68 129 69 70 130 71 72 131 73 132 74 133 75 134 76 135 136 77 137 78 138 79 139 80 140 81 141 82 142 83 143 84 144 145 85 146 86 147 87 148 149 88 150 89 151 90 152 153 91 154 92 155 156 93 157 94 158 159 95 160 96 161 97 162 98 163 99 164 100 101 165 102 166 103 104 167 105 168 106 107 169 108 170 109 171 110 172 111 112 173 113 174 114 175 115 176 116 117 177 118 178 119 179 120 180 121 181 122 182 123 183 184 124 185 186 125 187 188 189 190 126 191 127 nrelabeled = 383972 ndotcheck = 22297 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1012196 mri_surf2volseg done @#@FSTIME 2023:02:18:14:46:55 mri_surf2volseg N 25 e 90.45 S 0.66 U 176.42 P 195% M 805084 F 2 R 228776 W 0 c 972 w 65 I 376 O 696 L 1.83 1.65 2.25 @#@FSLOADPOST 2023:02:18:14:48:25 mri_surf2volseg N 25 1.88 1.72 2.21 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Sat Feb 18 14:48:25 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label --lh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white --lh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial --rh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label --rh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white --rh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii outvol aparc.a2009s+aseg.mgz 4 avail.processors, using 4 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7920 vertices from lh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.a2009s.annot Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8040 vertices from rh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.a2009s.annot Done loading 0 128 64 192 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 193 16 194 17 195 18 196 19 197 20 198 21 199 22 200 23 201 24 202 25 203 26 204 27 205 28 206 29 207 30 31 208 32 33 209 34 35 210 36 211 37 212 38 39 213 40 214 215 41 216 42 217 43 218 219 44 220 45 221 46 222 47 223 48 224 49 225 50 226 51 52 227 53 228 54 65 229 55 230 56 231 57 232 58 233 59 60 234 61 235 62 236 237 238 239 240 241 242 243 244 245 246 63 247 248 249 250 251 252 253 254 255 66 67 68 129 69 70 130 71 72 131 73 132 74 133 75 134 76 135 77 136 78 137 79 138 80 139 81 140 82 141 142 83 143 84 144 85 145 146 86 147 87 148 88 149 89 150 151 90 152 91 153 154 92 155 93 156 157 94 158 95 159 96 160 97 161 98 162 99 163 100 164 101 102 165 103 166 104 105 167 106 168 107 108 169 109 170 110 111 171 112 172 113 173 114 174 115 116 175 117 176 118 177 119 178 120 179 121 180 122 181 123 182 124 183 125 184 126 185 186 127 187 188 189 190 191 nrelabeled = 383972 ndotcheck = 22297 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1012284 mri_surf2volseg done @#@FSTIME 2023:02:18:14:48:25 mri_surf2volseg N 25 e 88.84 S 0.50 U 175.49 P 198% M 805136 F 0 R 222592 W 0 c 771 w 82 I 0 O 752 L 1.88 1.72 2.21 @#@FSLOADPOST 2023:02:18:14:49:54 mri_surf2volseg N 25 2.08 1.84 2.21 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Sat Feb 18 14:49:54 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label --lh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white --lh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial --rh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label --rh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white --rh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii outvol aparc.DKTatlas+aseg.mgz 4 avail.processors, using 4 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7920 vertices from lh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.DKTatlas.annot Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8040 vertices from rh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.DKTatlas.annot Done loading 0 192 128 64 1 2 3 4 5 6 7 8 9 10 193 11 194 12 195 13 196 14 197 15 198 16 199 17 200 18 201 202 19 203 204 20 205 206 21 207 22 208 23 209 24 210 25 211 26 212 27 213 28 214 29 215 30 216 31 217 32 218 33 219 220 34 221 35 222 36 223 37 224 38 225 226 39 227 40 228 41 229 42 230 43 231 232 44 233 45 234 46 235 47 236 48 237 49 238 239 50 240 51 241 52 242 53 243 54 244 55 56 245 246 57 247 58 248 59 249 60 250 61 251 62 252 253 254 255 65 63 66 67 68 129 69 70 130 71 72 131 73 132 74 133 75 134 76 135 77 136 78 137 79 138 80 139 81 140 82 141 83 142 84 143 144 85 145 86 146 87 147 148 88 149 89 150 90 151 152 91 153 92 154 155 93 156 94 157 158 95 159 96 160 97 161 98 162 99 163 100 101 164 102 165 103 104 166 105 167 106 107 168 108 109 169 110 170 111 171 112 172 113 173 114 115 174 116 175 117 176 118 119 177 178 120 121 179 122 180 123 181 124 182 125 183 126 184 185 127 186 187 188 189 190 191 nrelabeled = 383972 ndotcheck = 22297 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1012196 mri_surf2volseg done @#@FSTIME 2023:02:18:14:49:54 mri_surf2volseg N 25 e 90.89 S 2.20 U 177.61 P 197% M 805128 F 0 R 225436 W 0 c 832 w 90 I 0 O 696 L 2.08 1.84 2.21 @#@FSLOADPOST 2023:02:18:14:51:25 mri_surf2volseg N 25 2.10 1.93 2.20 #----------------------------------------- #@# WMParc Sat Feb 18 14:51:25 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 4 --lh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.annot 3000 --lh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label --lh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white --lh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial --rh-annot /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.annot 4000 --rh-cortex-mask /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label --rh-white /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white --rh-pial /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii outvol wmparc.mgz 4 avail.processors, using 4 Loading aparc+aseg.mgz MRIcopyHeader(): source has ctab Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7920 vertices from lh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/lh.aparc.annot Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white Loading /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8040 vertices from rh hemi Loading /home/developer/Desktop/1st_scan_nii/Sub-139/label/rh.aparc.annot Done loading 0 128 64 192 193 65 1 2 194 3 66 195 4 196 5 197 6 198 7 199 8 9 200 10 201 11 202 12 203 67 13 204 14 205 15 206 16 207 17 208 18 209 19 210 20 211 21 212 22 213 68 23 214 24 215 25 216 26 217 27 218 28 219 29 220 30 221 31 222 32 223 33 224 34 225 35 226 36 227 37 228 38 229 69 39 230 40 231 41 232 42 233 43 234 44 235 45 236 46 237 47 238 48 239 49 50 240 51 52 241 242 53 54 243 55 244 56 70 57 245 58 246 59 247 60 248 61 249 62 250 63 251 252 253 254 255 129 71 72 130 73 131 74 132 75 133 76 134 77 135 78 136 79 80 137 81 82 138 83 139 84 85 140 86 141 87 142 88 89 143 90 91 144 92 93 145 94 146 95 96 147 97 148 98 99 149 100 150 101 151 102 152 103 153 104 154 105 155 106 156 107 157 108 158 159 109 160 110 161 162 111 163 164 112 165 113 166 167 114 168 169 115 170 171 116 172 117 173 174 118 175 176 119 177 120 178 179 121 180 122 181 123 182 124 183 184 125 185 186 187 126 188 189 190 191 127 nrelabeled = 423093 ndotcheck = 3336 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1012196 mri_surf2volseg done @#@FSTIME 2023:02:18:14:51:25 mri_surf2volseg N 25 e 37.55 S 0.46 U 72.52 P 194% M 805440 F 0 R 244820 W 0 c 569 w 73 I 0 O 792 L 2.10 1.93 2.20 @#@FSLOADPOST 2023:02:18:14:52:03 mri_surf2volseg N 25 2.06 1.94 2.19 mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Sub-139 --surf-wm-vol --ctab /usr/local/freesurfer/7.2.0/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.2.0 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Sub-139 --surf-wm-vol --ctab /usr/local/freesurfer/7.2.0/WMParcStatsLUT.txt --etiv sysname Linux hostname developer-VirtualBox machine x86_64 user developer whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2023:02:18:14:52:03 mri_segstats N 24 e 329.19 S 0.68 U 678.77 P 206% M 239844 F 1 R 1208041 W 0 c 1638 w 23 I 2928 O 24 L 2.06 1.94 2.19 @#@FSLOADPOST 2023:02:18:14:57:32 mri_segstats N 24 2.12 2.12 2.19 #----------------------------------------- #@# Parcellation Stats lh Sat Feb 18 14:57:32 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 lh pial #----------------------------------------- #@# Parcellation Stats rh Sat Feb 18 14:57:32 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 rh pial Waiting for PID 6726 of (6726 6729 6732 6735) to complete... Waiting for PID 6729 of (6726 6729 6732 6735) to complete... Waiting for PID 6732 of (6726 6729 6732 6735) to complete... Waiting for PID 6735 of (6726 6729 6732 6735) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 192984 Total vertex volume 192773 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 1266 853 1872 2.337 0.377 0.090 0.014 6 0.8 bankssts 645 410 1115 2.571 0.552 0.126 0.015 8 0.4 caudalanteriorcingulate 2696 1821 4897 2.546 0.433 0.123 0.022 27 2.6 caudalmiddlefrontal 1673 1104 2186 1.900 0.477 0.137 0.030 19 2.2 cuneus 491 315 1593 3.455 0.784 0.089 0.029 4 0.5 entorhinal 3709 2527 7516 2.707 0.556 0.127 0.025 44 3.8 fusiform 5494 3763 9999 2.447 0.437 0.124 0.023 58 5.4 inferiorparietal 4166 2898 8722 2.627 0.594 0.126 0.025 49 4.5 inferiortemporal 1532 1026 2393 2.095 0.742 0.122 0.028 20 1.5 isthmuscingulate 6068 4047 9269 2.136 0.512 0.133 0.028 73 6.9 lateraloccipital 3703 2537 6514 2.543 0.590 0.133 0.030 42 4.8 lateralorbitofrontal 3751 2719 5206 1.852 0.536 0.149 0.034 49 5.4 lingual 2348 1651 4273 2.336 0.485 0.129 0.036 34 3.7 medialorbitofrontal 3369 2461 7846 2.669 0.538 0.130 0.024 44 3.3 middletemporal 927 551 1755 2.692 0.672 0.084 0.015 6 0.6 parahippocampal 1973 1200 2973 2.351 0.554 0.088 0.016 10 1.4 paracentral 2235 1505 3925 2.414 0.400 0.109 0.018 21 1.6 parsopercularis 1031 708 2154 2.503 0.640 0.149 0.031 16 1.3 parsorbitalis 1829 1264 3139 2.323 0.467 0.123 0.022 19 1.8 parstriangularis 2070 1400 1752 1.479 0.437 0.141 0.025 28 2.3 pericalcarine 5904 3686 7497 1.884 0.562 0.102 0.016 48 4.2 postcentral 1597 1109 2898 2.399 0.574 0.125 0.024 18 1.6 posteriorcingulate 6918 4196 11470 2.556 0.499 0.098 0.017 47 4.8 precentral 5476 3794 9091 2.295 0.460 0.122 0.023 55 5.7 precuneus 782 526 1441 2.518 0.608 0.144 0.028 13 0.9 rostralanteriorcingulate 6953 4989 12064 2.264 0.419 0.139 0.028 98 8.5 rostralmiddlefrontal 8364 5557 16157 2.655 0.460 0.115 0.022 78 7.6 superiorfrontal 7823 5215 12617 2.188 0.478 0.121 0.022 77 7.5 superiorparietal 4826 3210 9889 2.764 0.566 0.098 0.014 36 3.1 superiortemporal 5659 3973 10678 2.502 0.435 0.133 0.025 66 6.1 supramarginal 310 229 811 2.789 0.450 0.157 0.039 6 0.4 frontalpole 623 442 2194 3.681 0.489 0.131 0.022 7 0.6 temporalpole 595 374 924 2.323 0.503 0.117 0.025 6 0.5 transversetemporal 3354 2300 5946 2.632 0.700 0.124 0.034 36 4.2 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 192984 Total vertex volume 192773 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 1266 762 1872 2.337 0.377 0.116 0.038 26 1.7 bankssts 645 461 1115 2.571 0.552 0.176 0.082 37 1.4 caudalanteriorcingulate 2696 2051 4897 2.546 0.433 0.126 0.026 38 2.9 caudalmiddlefrontal 1673 1322 2186 1.900 0.477 0.128 0.029 18 2.1 cuneus 491 606 1593 3.455 0.784 0.286 0.088 16 2.3 entorhinal 3709 3098 7516 2.707 0.556 0.136 0.036 88 5.0 fusiform 5494 4449 9999 2.447 0.437 0.140 0.044 83 7.1 inferiorparietal 4166 3626 8722 2.627 0.594 0.145 0.063 101 5.7 inferiortemporal 1532 1274 2393 2.095 0.742 0.157 0.047 42 2.8 isthmuscingulate 6068 4746 9269 2.136 0.512 0.135 0.034 163 8.2 lateraloccipital 3703 2747 6514 2.543 0.590 0.134 0.036 145 5.1 lateralorbitofrontal 3751 3223 5206 1.852 0.536 0.152 0.042 95 5.9 lingual 2348 2143 4273 2.336 0.485 0.160 0.039 55 3.9 medialorbitofrontal 3369 3314 7846 2.669 0.538 0.154 0.029 48 4.4 middletemporal 927 804 1755 2.692 0.672 0.173 0.051 17 2.7 parahippocampal 1973 1374 2973 2.351 0.554 0.094 0.018 13 1.5 paracentral 2235 1801 3925 2.414 0.400 0.126 0.026 36 2.3 parsopercularis 1031 977 2154 2.503 0.640 0.160 0.035 18 1.5 parsorbitalis 1829 1456 3139 2.323 0.467 0.135 0.027 26 2.0 parstriangularis 2070 1139 1752 1.479 0.437 0.125 0.036 93 2.8 pericalcarine 5904 4415 7497 1.884 0.562 0.115 0.021 60 5.2 postcentral 1597 1317 2898 2.399 0.574 0.164 0.048 106 2.3 posteriorcingulate 6918 4739 11470 2.556 0.499 0.098 0.019 76 5.4 precentral 5476 4178 9091 2.295 0.460 0.127 0.030 104 7.0 precuneus 782 656 1441 2.518 0.608 0.164 0.047 19 1.3 rostralanteriorcingulate 6953 5730 12064 2.264 0.419 0.150 0.033 137 9.5 rostralmiddlefrontal 8364 6572 16157 2.655 0.460 0.124 0.034 97 8.0 superiorfrontal 7823 6277 12617 2.188 0.478 0.136 0.028 101 9.2 superiorparietal 4826 3842 9889 2.764 0.566 0.120 0.026 63 5.2 superiortemporal 5659 4609 10678 2.502 0.435 0.138 0.033 93 7.5 supramarginal 310 360 811 2.789 0.450 0.180 0.031 3 0.4 frontalpole 623 753 2194 3.681 0.489 0.163 0.028 8 0.7 temporalpole 595 473 924 2.323 0.503 0.129 0.032 6 0.9 transversetemporal 3354 2262 5946 2.632 0.700 0.156 0.053 83 6.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 191975 Total vertex volume 191785 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 1035 684 1620 2.416 0.395 0.098 0.017 6 0.7 bankssts 868 585 1728 2.410 0.744 0.129 0.020 12 0.8 caudalanteriorcingulate 3129 2117 5311 2.400 0.387 0.117 0.023 29 3.0 caudalmiddlefrontal 2233 1491 2892 1.856 0.386 0.132 0.028 26 2.7 cuneus 418 267 1438 3.513 0.628 0.092 0.017 2 0.3 entorhinal 3512 2394 7630 2.749 0.534 0.124 0.024 39 3.5 fusiform 6079 4245 10901 2.386 0.431 0.131 0.026 75 6.3 inferiorparietal 3972 2864 8476 2.623 0.572 0.129 0.027 48 4.3 inferiortemporal 1329 893 1968 1.991 0.721 0.118 0.023 16 1.3 isthmuscingulate 5957 4059 9202 2.091 0.425 0.135 0.026 72 6.7 lateraloccipital 4002 2777 6451 2.308 0.603 0.147 0.044 55 8.4 lateralorbitofrontal 4230 2855 5929 1.974 0.544 0.135 0.030 49 5.4 lingual 2462 1756 4073 2.258 0.533 0.143 0.038 43 4.3 medialorbitofrontal 3989 2840 8584 2.600 0.508 0.123 0.021 48 3.7 middletemporal 856 516 1655 2.681 0.750 0.084 0.017 6 0.5 parahippocampal 2150 1228 3235 2.396 0.520 0.096 0.016 14 1.6 paracentral 1642 1087 2573 2.332 0.382 0.113 0.019 15 1.1 parsopercularis 880 644 1874 2.490 0.428 0.144 0.030 12 1.1 parsorbitalis 1851 1327 3611 2.466 0.473 0.139 0.026 25 2.0 parstriangularis 2187 1447 2033 1.556 0.438 0.120 0.024 21 2.1 pericalcarine 6148 3920 8217 1.908 0.546 0.104 0.019 49 5.0 postcentral 1437 1000 2672 2.491 0.621 0.135 0.026 20 1.6 posteriorcingulate 7568 4793 12771 2.464 0.523 0.102 0.017 56 5.4 precentral 5865 3926 9523 2.262 0.492 0.117 0.022 55 5.2 precuneus 787 550 1645 2.600 0.550 0.133 0.024 12 0.8 rostralanteriorcingulate 6265 4500 10732 2.209 0.448 0.139 0.028 86 7.5 rostralmiddlefrontal 7929 5249 15733 2.714 0.478 0.111 0.021 66 7.1 superiorfrontal 7581 5080 12014 2.132 0.496 0.118 0.021 74 6.6 superiorparietal 4541 3028 9409 2.780 0.500 0.106 0.018 37 3.4 superiortemporal 4693 3184 8387 2.445 0.495 0.122 0.022 51 4.5 supramarginal 360 271 811 2.547 0.418 0.170 0.035 7 0.5 frontalpole 608 457 2381 3.856 0.595 0.144 0.032 7 0.7 temporalpole 505 310 796 2.354 0.555 0.128 0.039 6 0.7 transversetemporal 2979 2016 5508 2.722 0.642 0.121 0.035 38 4.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Sub-139 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 191975 Total vertex volume 191785 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 1035 647 1620 2.416 0.395 0.100 0.027 9 1.1 bankssts 868 797 1728 2.410 0.744 0.194 0.060 79 2.0 caudalanteriorcingulate 3129 2309 5311 2.400 0.387 0.126 0.028 55 3.5 caudalmiddlefrontal 2233 1762 2892 1.856 0.386 0.139 0.038 41 3.4 cuneus 418 541 1438 3.513 0.628 0.276 0.075 15 1.7 entorhinal 3512 3084 7630 2.749 0.534 0.147 0.035 289 5.4 fusiform 6079 4913 10901 2.386 0.431 0.146 0.036 136 9.1 inferiorparietal 3972 3543 8476 2.623 0.572 0.160 0.036 145 6.4 inferiortemporal 1329 1123 1968 1.991 0.721 0.156 0.040 47 2.2 isthmuscingulate 5957 4814 9202 2.091 0.425 0.140 0.032 337 8.1 lateraloccipital 4002 3051 6451 2.308 0.603 0.161 0.049 105 8.0 lateralorbitofrontal 4230 3382 5929 1.974 0.544 0.146 0.038 302 6.5 lingual 2462 2002 4073 2.258 0.533 0.147 0.041 62 3.7 medialorbitofrontal 3989 3699 8584 2.600 0.508 0.149 0.029 56 5.0 middletemporal 856 699 1655 2.681 0.750 0.136 0.034 11 1.4 parahippocampal 2150 1484 3235 2.396 0.520 0.106 0.018 18 1.8 paracentral 1642 1135 2573 2.332 0.382 0.130 0.033 25 2.1 parsopercularis 880 842 1874 2.490 0.428 0.161 0.033 21 1.2 parsorbitalis 1851 1631 3611 2.466 0.473 0.150 0.032 22 2.7 parstriangularis 2187 1329 2033 1.556 0.438 0.111 0.026 33 2.3 pericalcarine 6148 4785 8217 1.908 0.546 0.122 0.024 66 6.2 postcentral 1437 1161 2672 2.491 0.621 0.149 0.037 46 2.3 posteriorcingulate 7568 5480 12771 2.464 0.523 0.109 0.022 164 6.5 precentral 5865 4471 9523 2.262 0.492 0.132 0.030 95 7.3 precuneus 787 756 1645 2.600 0.550 0.189 0.057 48 2.0 rostralanteriorcingulate 6265 5348 10732 2.209 0.448 0.158 0.034 203 8.5 rostralmiddlefrontal 7929 6322 15733 2.714 0.478 0.126 0.026 134 7.8 superiorfrontal 7581 6125 12014 2.132 0.496 0.132 0.026 98 8.2 superiorparietal 4541 3705 9409 2.780 0.500 0.135 0.030 57 5.9 superiortemporal 4693 3711 8387 2.445 0.495 0.137 0.031 71 6.1 supramarginal 360 373 811 2.547 0.418 0.190 0.043 13 0.5 frontalpole 608 781 2381 3.856 0.595 0.183 0.044 6 1.2 temporalpole 505 391 796 2.354 0.555 0.114 0.032 3 0.7 transversetemporal 2979 1975 5508 2.722 0.642 0.168 0.063 140 8.0 insula PIDs (6726 6729 6732 6735) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Feb 18 14:57:44 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Sub-139 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sat Feb 18 14:57:44 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Sub-139 rh white Waiting for PID 6790 of (6790 6793) to complete... Waiting for PID 6793 of (6790 6793) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Sub-139 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 192984 Total vertex volume 192773 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 1193 877 1938 2.193 0.441 0.149 0.029 21 1.6 G_and_S_frontomargin 1162 768 2272 2.489 0.446 0.121 0.023 13 1.1 G_and_S_occipital_inf 1680 963 2427 2.174 0.535 0.095 0.018 11 1.4 G_and_S_paracentral 1444 958 2695 2.468 0.451 0.116 0.019 14 1.0 G_and_S_subcentral 683 492 1444 2.394 0.550 0.156 0.034 13 0.9 G_and_S_transv_frontopol 1878 1287 3452 2.563 0.493 0.129 0.022 23 1.9 G_and_S_cingul-Ant 902 615 1583 2.584 0.352 0.105 0.014 5 0.7 G_and_S_cingul-Mid-Ant 1278 878 2205 2.531 0.433 0.119 0.022 11 1.2 G_and_S_cingul-Mid-Post 593 407 1472 2.804 0.523 0.141 0.036 8 0.7 G_cingul-Post-dorsal 291 189 570 2.417 0.783 0.135 0.039 5 0.5 G_cingul-Post-ventral 1660 1095 2145 1.778 0.526 0.143 0.031 22 2.2 G_cuneus 1356 896 2697 2.573 0.369 0.115 0.020 14 1.0 G_front_inf-Opercular 510 331 1094 2.703 0.492 0.137 0.026 7 0.5 G_front_inf-Orbital 979 697 2111 2.385 0.407 0.147 0.031 16 1.4 G_front_inf-Triangul 3410 2380 7260 2.449 0.426 0.147 0.031 55 4.3 G_front_middle 5549 3598 12195 2.800 0.429 0.119 0.024 60 5.4 G_front_sup 624 417 1189 2.826 0.723 0.131 0.036 8 0.7 G_Ins_lg_and_S_cent_ins 616 433 1806 3.202 0.653 0.136 0.041 9 0.9 G_insular_short 1855 1260 3787 2.386 0.471 0.138 0.026 28 2.1 G_occipital_middle 1061 680 1818 2.279 0.532 0.133 0.026 12 1.1 G_occipital_sup 1746 1146 3865 2.864 0.515 0.134 0.030 26 2.1 G_oc-temp_lat-fusifor 2691 1922 3888 1.816 0.541 0.154 0.035 39 4.2 G_oc-temp_med-Lingual 1101 669 2677 3.017 0.641 0.089 0.023 9 0.9 G_oc-temp_med-Parahip 2358 1655 5300 2.568 0.650 0.143 0.038 39 3.5 G_orbital 2158 1514 5152 2.637 0.479 0.146 0.029 34 2.7 G_pariet_inf-Angular 2863 2059 6429 2.588 0.439 0.145 0.028 42 3.5 G_pariet_inf-Supramar 3010 2035 6175 2.367 0.490 0.142 0.028 44 3.6 G_parietal_sup 2176 1287 3011 1.935 0.548 0.107 0.019 22 1.8 G_postcentral 2590 1414 5152 2.809 0.417 0.090 0.017 18 1.6 G_precentral 2735 1884 5573 2.459 0.442 0.130 0.025 36 2.9 G_precuneus 782 574 1741 2.369 0.520 0.163 0.056 19 2.1 G_rectus 734 481 1107 2.188 0.742 0.136 0.062 12 1.5 G_subcallosal 469 280 855 2.443 0.478 0.108 0.024 4 0.4 G_temp_sup-G_T_transv 1552 1064 4383 2.975 0.546 0.123 0.019 20 1.3 G_temp_sup-Lateral 606 415 1488 3.344 0.586 0.072 0.011 2 0.3 G_temp_sup-Plan_polar 860 558 1496 2.598 0.367 0.089 0.015 4 0.6 G_temp_sup-Plan_tempo 2059 1497 5522 2.819 0.602 0.142 0.030 31 2.7 G_temporal_inf 2041 1519 5555 2.766 0.451 0.144 0.031 36 2.5 G_temporal_middle 188 131 262 2.230 0.479 0.098 0.010 1 0.1 Lat_Fis-ant-Horizont 413 279 542 2.138 0.327 0.080 0.009 1 0.2 Lat_Fis-ant-Vertical 968 649 1236 2.445 0.456 0.125 0.026 8 1.1 Lat_Fis-post 2039 1328 2468 1.711 0.429 0.139 0.030 28 2.6 Pole_occipital 1347 976 4548 3.424 0.663 0.142 0.027 19 1.5 Pole_temporal 2249 1670 2344 1.657 0.499 0.140 0.027 26 2.9 S_calcarine 2918 1928 3117 1.885 0.618 0.099 0.018 16 2.2 S_central 1158 750 1470 2.137 0.362 0.074 0.009 4 0.5 S_cingul-Marginalis 631 430 990 2.745 0.478 0.112 0.021 4 0.7 S_circular_insula_ant 1232 829 1914 2.818 0.675 0.093 0.015 7 0.8 S_circular_insula_inf 1474 972 1903 2.510 0.394 0.098 0.017 7 1.1 S_circular_insula_sup 865 571 1278 2.601 0.419 0.103 0.017 5 0.6 S_collat_transv_ant 438 326 656 2.467 0.498 0.169 0.043 6 0.8 S_collat_transv_post 2166 1524 3074 2.238 0.372 0.125 0.022 19 2.3 S_front_inf 1100 781 1679 2.189 0.387 0.123 0.027 11 1.1 S_front_middle 2440 1666 3442 2.297 0.443 0.104 0.017 15 1.9 S_front_sup 318 228 442 2.244 0.525 0.122 0.018 2 0.3 S_interm_prim-Jensen 3102 2026 3805 2.089 0.376 0.097 0.015 16 2.0 S_intrapariet_and_P_trans 924 625 1072 2.088 0.351 0.129 0.027 8 1.0 S_oc_middle_and_Lunatus 1019 693 1237 2.101 0.331 0.118 0.021 7 0.9 S_oc_sup_and_transversal 578 388 684 2.203 0.385 0.125 0.022 5 0.6 S_occipital_ant 806 554 1139 2.261 0.344 0.104 0.017 5 0.5 S_oc-temp_lat 1527 1024 2053 2.246 0.471 0.107 0.020 11 1.1 S_oc-temp_med_and_Lingual 413 295 483 1.907 0.380 0.136 0.021 4 0.4 S_orbital_lateral 598 422 730 2.226 0.489 0.128 0.018 5 0.5 S_orbital_med-olfact 1284 906 2120 2.514 0.524 0.138 0.029 13 1.6 S_orbital-H_Shaped 1460 993 1801 2.023 0.477 0.114 0.022 11 1.5 S_parieto_occipital 1150 730 1007 1.709 0.565 0.117 0.019 16 0.8 S_pericallosal 3228 2161 4033 2.020 0.420 0.103 0.016 21 2.2 S_postcentral 1282 846 1916 2.425 0.366 0.100 0.013 8 0.8 S_precentral-inf-part 1218 784 1686 2.515 0.409 0.091 0.011 6 0.6 S_precentral-sup-part 566 391 730 2.209 0.372 0.109 0.014 4 0.3 S_suborbital 1397 953 2020 2.237 0.381 0.123 0.022 13 1.4 S_subparietal 1248 856 1610 2.234 0.418 0.119 0.019 10 1.0 S_temporal_inf 4825 3253 7294 2.409 0.378 0.103 0.017 31 3.5 S_temporal_sup 336 230 461 2.556 0.484 0.113 0.013 2 0.3 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Sub-139 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 191975 Total vertex volume 191785 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 787 623 1411 2.145 0.391 0.158 0.031 12 1.2 G_and_S_frontomargin 1053 730 1798 2.174 0.330 0.123 0.021 14 0.9 G_and_S_occipital_inf 1361 760 1952 2.167 0.557 0.103 0.021 11 1.2 G_and_S_paracentral 1379 947 2536 2.374 0.425 0.128 0.022 15 1.2 G_and_S_subcentral 880 654 1862 2.362 0.446 0.152 0.030 15 1.2 G_and_S_transv_frontopol 2250 1593 4200 2.595 0.421 0.112 0.019 19 1.8 G_and_S_cingul-Ant 1030 711 2143 2.830 0.462 0.113 0.022 8 0.9 G_and_S_cingul-Mid-Ant 1189 803 2146 2.619 0.409 0.115 0.025 11 1.1 G_and_S_cingul-Mid-Post 475 305 1164 2.897 0.543 0.148 0.033 7 0.7 G_cingul-Post-dorsal 281 179 536 2.291 0.694 0.137 0.035 4 0.4 G_cingul-Post-ventral 2193 1469 2862 1.789 0.456 0.139 0.031 28 2.9 G_cuneus 949 649 1998 2.438 0.392 0.120 0.022 12 0.9 G_front_inf-Opercular 272 221 745 2.703 0.369 0.161 0.031 4 0.3 G_front_inf-Orbital 814 597 1947 2.668 0.435 0.161 0.034 15 1.1 G_front_inf-Triangul 3157 2262 6739 2.397 0.461 0.144 0.029 50 4.0 G_front_middle 5543 3526 12356 2.838 0.425 0.119 0.023 59 5.4 G_front_sup 555 359 1164 2.911 0.866 0.127 0.063 17 1.4 G_Ins_lg_and_S_cent_ins 546 389 1728 3.105 0.567 0.139 0.034 8 0.7 G_insular_short 1940 1377 4315 2.481 0.454 0.145 0.026 30 2.3 G_occipital_middle 1444 994 2657 2.271 0.564 0.145 0.029 20 1.8 G_occipital_sup 1776 1163 3820 2.724 0.460 0.117 0.022 21 1.7 G_oc-temp_lat-fusifor 2503 1687 3690 1.946 0.570 0.140 0.033 33 3.5 G_oc-temp_med-Lingual 1008 631 2903 3.190 0.740 0.107 0.025 9 0.9 G_oc-temp_med-Parahip 2359 1622 4853 2.373 0.553 0.138 0.036 35 3.3 G_orbital 2268 1638 5193 2.522 0.491 0.147 0.032 39 2.9 G_pariet_inf-Angular 2280 1548 4914 2.572 0.508 0.132 0.024 35 2.3 G_pariet_inf-Supramar 2785 1866 5124 2.251 0.477 0.124 0.022 33 2.6 G_parietal_sup 2235 1376 3469 2.050 0.515 0.112 0.022 23 2.3 G_postcentral 2943 1764 6005 2.677 0.510 0.102 0.018 26 2.2 G_precentral 2848 1897 5417 2.321 0.532 0.126 0.024 34 2.8 G_precuneus 791 609 1585 2.202 0.644 0.200 0.065 25 2.7 G_rectus 496 372 710 2.086 0.662 0.162 0.064 8 1.3 G_subcallosal 362 204 638 2.511 0.429 0.113 0.030 4 0.3 G_temp_sup-G_T_transv 1549 1079 4414 3.062 0.404 0.140 0.028 22 1.8 G_temp_sup-Lateral 868 572 1843 2.975 0.750 0.104 0.026 6 0.7 G_temp_sup-Plan_polar 718 479 1251 2.499 0.445 0.089 0.011 4 0.4 G_temp_sup-Plan_tempo 1974 1458 5269 2.785 0.590 0.143 0.033 33 2.7 G_temporal_inf 2259 1668 5962 2.747 0.494 0.136 0.025 35 2.4 G_temporal_middle 337 232 490 2.313 0.389 0.126 0.019 3 0.3 Lat_Fis-ant-Horizont 287 204 346 1.981 0.423 0.111 0.013 2 0.1 Lat_Fis-ant-Vertical 1300 876 1603 2.294 0.439 0.119 0.026 11 1.4 Lat_Fis-post 2815 1835 3665 1.816 0.484 0.139 0.031 36 3.8 Pole_occipital 1457 1139 4954 3.285 0.710 0.150 0.031 20 1.8 Pole_temporal 2382 1608 2578 1.813 0.482 0.114 0.022 21 2.2 S_calcarine 2922 1913 3051 1.782 0.603 0.093 0.017 15 2.1 S_central 1147 773 1643 2.197 0.471 0.095 0.014 6 0.7 S_cingul-Marginalis 521 352 733 2.651 0.430 0.103 0.022 2 0.5 S_circular_insula_ant 1082 719 1507 2.673 0.523 0.094 0.018 6 0.8 S_circular_insula_inf 1216 808 1664 2.533 0.436 0.106 0.020 6 1.1 S_circular_insula_sup 851 569 1246 2.498 0.384 0.093 0.011 4 0.4 S_collat_transv_ant 347 242 395 2.130 0.277 0.141 0.032 3 0.4 S_collat_transv_post 1839 1242 2505 2.127 0.369 0.115 0.020 16 1.5 S_front_inf 1702 1205 2386 2.169 0.423 0.127 0.026 16 1.9 S_front_middle 1970 1311 2792 2.379 0.419 0.102 0.019 13 1.6 S_front_sup 217 161 378 2.644 0.679 0.127 0.029 1 0.3 S_interm_prim-Jensen 2823 1881 3381 1.993 0.367 0.104 0.016 19 1.9 S_intrapariet_and_P_trans 814 563 968 1.928 0.330 0.130 0.023 9 0.8 S_oc_middle_and_Lunatus 1119 769 1555 2.181 0.369 0.123 0.026 9 1.1 S_oc_sup_and_transversal 529 374 774 2.150 0.444 0.128 0.022 5 0.5 S_occipital_ant 751 540 1485 2.655 0.552 0.125 0.026 6 0.8 S_oc-temp_lat 1691 1117 2538 2.390 0.431 0.104 0.018 12 1.1 S_oc-temp_med_and_Lingual 296 203 349 1.978 0.400 0.120 0.024 3 0.3 S_orbital_lateral 1001 733 1117 1.949 0.567 0.182 0.066 18 3.7 S_orbital_med-olfact 1212 830 1996 2.469 0.487 0.127 0.028 11 1.5 S_orbital-H_Shaped 2133 1414 2813 2.163 0.412 0.112 0.020 15 1.9 S_parieto_occipital 1330 871 1116 1.632 0.513 0.125 0.019 20 1.1 S_pericallosal 2677 1726 3068 2.004 0.473 0.098 0.016 14 1.8 S_postcentral 2039 1319 2683 2.286 0.294 0.099 0.014 13 1.2 S_precentral-inf-part 1430 921 2038 2.438 0.465 0.097 0.013 8 0.9 S_precentral-sup-part 122 91 154 2.078 0.154 0.169 0.021 2 0.2 S_suborbital 1201 812 1620 2.155 0.423 0.106 0.017 8 0.8 S_subparietal 1201 820 1525 2.292 0.403 0.119 0.019 9 1.0 S_temporal_inf 4927 3232 6939 2.340 0.366 0.097 0.016 27 3.3 S_temporal_sup 239 172 412 3.006 0.345 0.134 0.016 2 0.2 S_temporal_transverse PIDs (6790 6793) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sat Feb 18 14:57:52 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Sub-139 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sat Feb 18 14:57:52 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Sub-139 rh white Waiting for PID 6838 of (6838 6841) to complete... Waiting for PID 6841 of (6838 6841) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Sub-139 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 192984 Total vertex volume 192773 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 1312 849 2487 2.671 0.517 0.117 0.017 14 1.0 caudalanteriorcingulate 2918 1969 5198 2.527 0.438 0.124 0.022 29 2.7 caudalmiddlefrontal 2234 1486 2938 1.916 0.480 0.133 0.029 24 2.8 cuneus 458 289 1358 3.288 0.687 0.084 0.028 3 0.4 entorhinal 3419 2299 6523 2.663 0.526 0.126 0.026 40 3.5 fusiform 5597 3832 10314 2.458 0.444 0.124 0.023 58 5.4 inferiorparietal 4139 2931 9474 2.710 0.628 0.126 0.026 49 4.5 inferiortemporal 1499 1006 2369 2.118 0.740 0.121 0.028 19 1.5 isthmuscingulate 6087 4050 9336 2.145 0.510 0.134 0.028 73 7.0 lateraloccipital 4128 2913 7673 2.511 0.628 0.144 0.036 62 6.2 lateralorbitofrontal 3862 2813 5332 1.841 0.534 0.151 0.034 52 5.8 lingual 1988 1406 3523 2.257 0.521 0.140 0.043 34 3.5 medialorbitofrontal 4670 3322 9823 2.596 0.524 0.125 0.022 56 4.3 middletemporal 921 548 1761 2.702 0.637 0.081 0.013 5 0.5 parahippocampal 2238 1359 3459 2.399 0.551 0.087 0.016 11 1.5 paracentral 2132 1431 3673 2.430 0.384 0.108 0.018 20 1.5 parsopercularis 956 642 1909 2.677 0.550 0.119 0.020 9 0.8 parsorbitalis 2192 1516 3554 2.234 0.443 0.125 0.023 24 2.2 parstriangularis 2035 1375 1727 1.483 0.439 0.141 0.025 28 2.3 pericalcarine 6665 4181 8587 1.931 0.568 0.104 0.017 55 4.9 postcentral 1735 1200 3038 2.404 0.584 0.126 0.025 19 1.8 posteriorcingulate 6830 4144 11334 2.558 0.500 0.099 0.017 46 4.9 precentral 5427 3761 9272 2.315 0.458 0.124 0.023 56 5.7 precuneus 1235 834 2164 2.489 0.601 0.130 0.025 17 1.2 rostralanteriorcingulate 5102 3670 9259 2.305 0.420 0.144 0.030 71 6.6 rostralmiddlefrontal 9194 6169 17348 2.557 0.485 0.118 0.023 93 8.6 superiorfrontal 6484 4323 10488 2.185 0.478 0.117 0.021 61 6.0 superiorparietal 6344 4249 13486 2.803 0.646 0.102 0.016 50 4.5 superiortemporal 5219 3670 9580 2.476 0.444 0.135 0.025 61 5.8 supramarginal 602 379 934 2.324 0.504 0.119 0.025 6 0.5 transversetemporal 2538 1745 4854 2.778 0.612 0.114 0.026 22 2.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Sub-139 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/developer/Desktop/1st_scan_nii/Sub-139/mri/wm.mgz... reading input surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... reading input pial surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.pial... reading input white surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 191975 Total vertex volume 191785 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) 952 639 1871 2.425 0.733 0.130 0.020 13 0.9 caudalanteriorcingulate 3269 2204 5573 2.408 0.390 0.118 0.023 31 3.1 caudalmiddlefrontal 2745 1827 3603 1.906 0.408 0.135 0.029 32 3.4 cuneus 384 243 1331 3.500 0.606 0.092 0.015 2 0.3 entorhinal 3203 2149 6464 2.689 0.471 0.120 0.023 35 3.0 fusiform 6083 4257 10952 2.378 0.433 0.131 0.026 75 6.3 inferiorparietal 4251 3077 9568 2.670 0.614 0.129 0.027 52 4.7 inferiortemporal 1335 895 1972 2.000 0.707 0.117 0.023 16 1.3 isthmuscingulate 5949 4063 9126 2.081 0.428 0.135 0.027 72 6.8 lateraloccipital 4210 2942 7000 2.273 0.578 0.148 0.043 60 8.4 lateralorbitofrontal 4153 2804 5788 1.971 0.546 0.135 0.030 48 5.2 lingual 1998 1481 3529 2.213 0.569 0.165 0.049 44 4.7 medialorbitofrontal 4735 3347 9614 2.546 0.512 0.121 0.021 54 4.2 middletemporal 926 564 1787 2.664 0.747 0.085 0.017 6 0.6 parahippocampal 2280 1308 3515 2.408 0.514 0.094 0.016 15 1.6 paracentral 1857 1240 2914 2.295 0.405 0.113 0.019 18 1.3 parsopercularis 766 537 1508 2.510 0.405 0.129 0.027 7 0.9 parsorbitalis 1862 1337 3659 2.483 0.461 0.140 0.027 25 2.1 parstriangularis 2106 1394 1988 1.565 0.445 0.121 0.024 21 2.2 pericalcarine 6739 4298 8858 1.901 0.536 0.103 0.018 52 5.3 postcentral 1493 1042 2732 2.480 0.623 0.134 0.026 20 1.6 posteriorcingulate 7287 4605 12264 2.461 0.527 0.103 0.017 54 5.4 precentral 6046 4050 9970 2.261 0.500 0.117 0.022 58 5.4 precuneus 1058 729 1985 2.491 0.571 0.129 0.025 15 1.0 rostralanteriorcingulate 4505 3218 7670 2.206 0.457 0.139 0.028 62 5.3 rostralmiddlefrontal 9963 6724 19252 2.638 0.487 0.115 0.022 89 9.2 superiorfrontal 6259 4192 10080 2.157 0.497 0.116 0.020 60 5.3 superiorparietal 5926 3993 13128 2.868 0.607 0.110 0.020 50 4.6 superiortemporal 4483 3051 8159 2.462 0.497 0.123 0.022 51 4.5 supramarginal 510 311 814 2.371 0.560 0.126 0.038 6 0.7 transversetemporal 2714 1837 5109 2.784 0.643 0.119 0.034 34 3.7 insula PIDs (6838 6841) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Sat Feb 18 14:57:59 EST 2023 /home/developer/Desktop/1st_scan_nii/Sub-139 mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject Sub-139 setting seed for random number genererator to 1234 7.2.0 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject Sub-139 sysname Linux hostname developer-VirtualBox machine x86_64 user developer whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1054039 mm^3 (det: 1.848229 ) Computing euler number orig.nofix lheno = -24, rheno = -34 orig.nofix lhholes = 13, rhholes = 18 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2023:02:18:14:57:59 mri_segstats N 32 e 98.49 S 1.35 U 370.46 P 377% M 292028 F 0 R 753022 W 0 c 4003 w 42 I 16144 O 24 L 2.09 2.11 2.19 @#@FSLOADPOST 2023:02:18:14:59:38 mri_segstats N 32 3.54 2.64 2.37 /home/developer/Desktop/1st_scan_nii/Sub-139/label #-------------------------------------------- #@# BA_exvivo Labels lh Sat Feb 18 14:59:38 EST 2023 mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA1_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA2_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA3a_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA3b_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA4a_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 6924 of (6924 6927 6930 6933 6936) to complete... Waiting for PID 6927 of (6924 6927 6930 6933 6936) to complete... Waiting for PID 6930 of (6924 6927 6930 6933 6936) to complete... Waiting for PID 6933 of (6924 6927 6930 6933 6936) to complete... Waiting for PID 6936 of (6924 6927 6930 6933 6936) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA1_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4196 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA2_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8147 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA3a_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4107 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA3b_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6065 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA4a_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5887 mri_label2label: Done PIDs (6924 6927 6930 6933 6936) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA4p_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA6_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA44_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA45_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 6978 of (6978 6981 6984 6987) to complete... Waiting for PID 6981 of (6978 6981 6984 6987) to complete... Waiting for PID 6984 of (6978 6981 6984 6987) to complete... Waiting for PID 6987 of (6978 6981 6984 6987) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA4p_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4127 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA6_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13821 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA44_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA45_exvivo.label --trgsubject Sub-139 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 342 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3764 mri_label2label: Done PIDs (6978 6981 6984 6987) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.V1_exvivo.label --trgsubject Sub-139 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.V2_exvivo.label --trgsubject Sub-139 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.MT_exvivo.label --trgsubject Sub-139 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject Sub-139 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject Sub-139 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 7027 of (7027 7030 7033 7036 7039) to complete... Waiting for PID 7030 of (7027 7030 7033 7036 7039) to complete... Waiting for PID 7033 of (7027 7030 7033 7036 7039) to complete... Waiting for PID 7036 of (7027 7030 7033 7036 7039) to complete... Waiting for PID 7039 of (7027 7030 7033 7036 7039) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.V1_exvivo.label --trgsubject Sub-139 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 772 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5413 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.V2_exvivo.label --trgsubject Sub-139 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 1088 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9202 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.MT_exvivo.label --trgsubject Sub-139 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2110 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject Sub-139 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1333 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject Sub-139 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1205 mri_label2label: Done PIDs (7027 7030 7033 7036 7039) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 7093 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... /usr/local/freesurfer/7.2.0/bin/reconbatchjobs: line 77: 7093 Killed exec $JOB >> $LOG 2>&1 /usr/local/freesurfer/7.2.0/bin/reconbatchjobs: line 77: 7111 Killed exec $JOB >> $LOG 2>&1 Waiting for PID 7096 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... /usr/local/freesurfer/7.2.0/bin/reconbatchjobs: line 77: 7102 Killed exec $JOB >> $LOG 2>&1 Waiting for PID 7099 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... Waiting for PID 7102 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... Waiting for PID 7105 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... Waiting for PID 7108 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... Waiting for PID 7111 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... Waiting for PID 7114 of (7093 7096 7099 7102 7105 7108 7111 7114) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 414 points in source label. mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 764 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1915 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 2101 points in source label. mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 641 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4518 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 456 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3375 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 1286 points in source label. mri_label2label --srcsubject fsaverage --srclabel /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject Sub-139 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/developer/Desktop/1st_scan_nii/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = Sub-139 trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/developer/Desktop/1st_scan_nii FREESURFER_HOME /usr/local/freesurfer/7.2.0 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /home/developer/Desktop/1st_scan_nii/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.white Reading target registration /home/developer/Desktop/1st_scan_nii/Sub-139/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 118080 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1111 mri_label2label: Done PIDs (7093 7096 7099 7102 7105 7108 7111 7114) completed and logs appended. Linux developer-VirtualBox 5.4.0-139-generic #156~18.04.1-Ubuntu SMP Wed Jan 25 15:56:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Sub-139 exited with ERRORS at Sat Feb 18 15:00:26 EST 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting