Thu Feb 9 15:12:31 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data /opt/freesurfer/bin/recon-all -subject 31231_T2_3T -i /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT1.ORIG.nii.gz -T2 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all -notal-check subjid 31231_T2_3T setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b Linux cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 25165824 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 1540916 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 376Gi 8.6Gi 144Gi 7.3Gi 223Gi 359Gi Swap: 0B 0B 0B SLURM_JOB_ID 945174 ######################################## program versions used 7.2.0 (freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b) 7.2.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:31-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.2.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 7.2.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.2.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/02/09-21:12:32-GMT BuildTime: Jul 20 2021 22:20:18 BuildStamp: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b User: br74747 Machine: cn06.cluster.local Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 4.9.2 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 /opt/freesurfer/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T mri_convert /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT1.ORIG.nii.gz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/001.mgz mri_convert /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT1.ORIG.nii.gz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/001.mgz reading from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT1.ORIG.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, 1) k_ras = (1, -0, 0) writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Feb 9 15:12:34 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T mri_convert --no_scale 1 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT2.ORIG.nii.gz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz mri_convert --no_scale 1 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT2.ORIG.nii.gz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz reading from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_nii/rawT2.ORIG.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Feb 9 15:12:36 CST 2023 Found 1 runs /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/001.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T mri_convert /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz --conform mri_convert /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz --conform reading from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, 1) k_ras = (1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 5420 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz... mri_add_xform_to_header -c /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/talairach.xfm /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Feb 9 15:12:43 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri /opt/freesurfer/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 cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Thu Feb 9 15:12:43 CST 2023 tmpdir is ./tmp.mri_nu_correct.mni.190256 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.190256/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.190256/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.190256/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.190256/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Thu Feb 9 15:15:04 CST 2023 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Thu Feb 9 15:15:04 CST 2023 Ended at Thu Feb 9 15:15:27 CST 2023 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /opt/freesurfer/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: /opt/freesurfer/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 1.40770 0.01536 -0.14762 5.48192; -2.54691 3.49535 -1.26402 35.68237; 1.09572 -1.13269 2.85396 -75.72906; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Nu Intensity Correction Thu Feb 9 15:15:29 CST 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 /usr/bin/bc /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 nIters 1 mri_nu_correct.mni 7.2.0 Linux cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Thu Feb 9 15:15:29 CST 2023 tmpdir is ./tmp.mri_nu_correct.mni.193348 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.193348/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.193348/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.193348/ones.mgz 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.193348/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.193348/ones.mgz sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 input ./tmp.mri_nu_correct.mni.193348/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.193348/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.193348/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.193348/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.193348/sum.junk --avgwf ./tmp.mri_nu_correct.mni.193348/input.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.193348/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.193348/sum.junk --avgwf ./tmp.mri_nu_correct.mni.193348/input.mean.dat sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.193348/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.193348/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.193348/ones.mgz --i ./tmp.mri_nu_correct.mni.193348/nu0.mgz --sum ./tmp.mri_nu_correct.mni.193348/sum.junk --avgwf ./tmp.mri_nu_correct.mni.193348/output.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.193348/ones.mgz --i ./tmp.mri_nu_correct.mni.193348/nu0.mgz --sum ./tmp.mri_nu_correct.mni.193348/sum.junk --avgwf ./tmp.mri_nu_correct.mni.193348/output.mean.dat sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.193348/ones.mgz Loading ./tmp.mri_nu_correct.mni.193348/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.193348/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.193348/nu0.mgz ./tmp.mri_nu_correct.mni.193348/nu0.mgz mul 1.16509336099585062240 Saving result to './tmp.mri_nu_correct.mni.193348/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.193348/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.193348/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.193348/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 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 5 seconds. mapping (12, 66) to ( 3, 110) Thu Feb 9 15:18:08 CST 2023 mri_nu_correct.mni done mri_add_xform_to_header -c /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Feb 9 15:18:08 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 1.40770 0.01536 -0.14762 5.48192; -2.54691 3.49535 -1.26402 35.68237; 1.09572 -1.13269 2.85396 -75.72906; 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(): error: No such file or directory error: MRIhistogramRegion: input mri nu.mgz is blank error: No such file or directory error: MRIhistogramRegion: input mri nu.mgz is blank MRIsplineNormalize(): npeaks = 7 Starting OpenSpline(): npoints = 7 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 58 (58) csf peak at 36, 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 63 (63), valley at 34 (34) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 20 seconds. #-------------------------------------------- #@# Skull Stripping Thu Feb 9 15:19:28 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_em_register -skull nu.mgz /opt/freesurfer/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 = 12 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/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=41.0 skull bounding box = (52, 43, 26) --> (206, 185, 169) finding center of left hemi white matter using (103, 90, 98) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (84,73,80) --> (121, 107,115) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 8.0 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.713 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.660254 @ (-10.526, 10.526, -10.526) max log p = -4.509140 @ (5.263, -5.263, -15.789) max log p = -4.497379 @ (2.632, -2.632, 2.632) max log p = -4.481826 @ (-1.316, 1.316, -1.316) max log p = -4.463719 @ (0.658, 0.658, -0.658) max log p = -4.451333 @ (0.329, -0.987, 0.329) max log p = -4.451333 @ (0.000, 0.000, 0.000) max log p = -4.451333 @ (0.000, 0.000, 0.000) Found translation: (-3.0, 3.6, -25.3): log p = -4.451 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.030, old_max_log_p =-4.451 (thresh=-4.4) 1.15000 0.00000 0.00000 -22.16998; 0.00000 1.19413 0.31997 -59.44046; 0.00000 -0.29764 1.11081 8.26618; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.030, old_max_log_p =-4.030 (thresh=-4.0) 1.15000 0.00000 0.00000 -22.16998; 0.00000 1.19413 0.31997 -59.44046; 0.00000 -0.29764 1.11081 8.26618; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.949, old_max_log_p =-4.030 (thresh=-4.0) 1.12792 -0.03743 -0.00762 -13.33540; 0.03969 1.23214 0.25093 -60.74823; 0.00000 -0.21070 1.08701 -2.22568; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.948, old_max_log_p =-3.949 (thresh=-3.9) 1.12792 -0.03743 -0.00762 -13.33540; 0.03969 1.23214 0.25093 -60.74823; 0.00000 -0.21465 1.10739 -4.35179; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.929, old_max_log_p =-3.948 (thresh=-3.9) 1.12645 -0.03387 -0.02571 -10.33037; 0.03955 1.22781 0.25004 -60.50327; 0.01839 -0.21447 1.10323 -7.12410; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.923, old_max_log_p =-3.929 (thresh=-3.9) 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.923, old_max_log_p =-3.923 (thresh=-3.9) 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 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 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.923 (old=-4.713) transform before final EM align: 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 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 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 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: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.12792 -0.03758 -0.00770 -12.85018; 0.03970 1.22601 0.25906 -60.99551; -0.00037 -0.22393 1.10142 -2.76225; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 873284 FSRUNTIME@ mri_em_register 0.0259 hours 12 threads registration took 1 minutes and 33 seconds. mri_watershed -T1 -brain_atlas /opt/freesurfer/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=128 y=106 z=130 r=86 first estimation of the main basin volume: 2727806 voxels Looking for seedpoints 2 found in the cerebellum 13 found in the rest of the brain global maximum in x=145, y=98, z=100, Imax=255 CSF=20, 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=1882054789 voxels, voxel volume =1.000 = 1882054789 mmm3 = 1882054.784 cm3 done. PostAnalyze...Basin Prior 71 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=116, z=120, r=9257 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 45954 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 3240 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2916 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 19404 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 20160 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 234 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 3, 30, 64 after analyzing : 3, 21, 30, 31 RIGHT_CER before analyzing : 3, 3, 30, 64 after analyzing : 3, 21, 30, 31 LEFT_CER before analyzing : 3, 3, 30, 64 after analyzing : 3, 21, 30, 31 RIGHT_BRAIN before analyzing : 4, 5, 30, 64 after analyzing : 4, 21, 30, 31 LEFT_BRAIN before analyzing : 3, 3, 30, 63 after analyzing : 3, 21, 30, 31 OTHER before analyzing : 3, 3, 30, 64 after analyzing : 3, 21, 30, 31 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.254, std = 8.339 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.63, sigma = 2.55 after rotation: sse = 1.63, sigma = 2.55 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.64, its var is 2.12 before Erosion-Dilatation 0.01% 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...28 iterations mri_strip_skull: done peeling brain Brain Size = 1484787 voxels, voxel volume = 1.000 mm3 = 1484787 mmm3 = 1484.787 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 30.749813 mri_watershed stimesec 0.435726 mri_watershed ru_maxrss 818056 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 312775 mri_watershed ru_majflt 6 mri_watershed ru_nswap 0 mri_watershed ru_inblock 5576 mri_watershed ru_oublock 2344 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 3038 mri_watershed ru_nivcsw 46 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Feb 9 15:21:14 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/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 = 12 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/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=27.0 skull bounding box = (66, 58, 46) --> (189, 176, 211) finding center of left hemi white matter using (107, 97, 129) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (92,83,109) --> (122, 111,149) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.1 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.292 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.115518 @ (-10.526, 10.526, -10.526) max log p = -3.916986 @ (5.263, -5.263, -5.263) max log p = -3.810478 @ (2.632, 2.632, -2.632) max log p = -3.810478 @ (0.000, 0.000, 0.000) max log p = -3.802593 @ (0.658, -1.974, -0.658) max log p = -3.801558 @ (-0.987, 1.645, -0.329) max log p = -3.801558 @ (0.000, 0.000, 0.000) max log p = -3.801558 @ (0.000, 0.000, 0.000) Found translation: (-3.0, 7.6, -19.4): log p = -3.802 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.626, old_max_log_p =-3.802 (thresh=-3.8) 1.15000 0.00000 0.00000 -22.42493; 0.00000 1.06580 0.14032 -17.30150; 0.00000 -0.13053 0.99144 -3.75700; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.580, old_max_log_p =-3.626 (thresh=-3.6) 1.15000 0.00000 0.00000 -22.42493; 0.00000 1.15425 0.01043 -18.47032; 0.00000 0.00971 1.00128 -20.65178; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.544, old_max_log_p =-3.580 (thresh=-3.6) 1.15000 0.00000 0.00000 -22.42493; 0.00000 1.23157 0.15162 -45.22540; 0.00000 -0.14104 0.99135 -1.59185; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.544, old_max_log_p =-3.544 (thresh=-3.5) 1.15000 0.00000 0.00000 -22.42493; 0.00000 1.23157 0.15162 -45.22540; 0.00000 -0.14104 0.99135 -1.59185; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 8 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.544 (thresh=-3.5) 1.10628 -0.03861 -0.00583 -9.71092; 0.03622 1.17950 0.17819 -45.09188; 0.00000 -0.18312 1.00453 3.55639; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.391, old_max_log_p =-3.401 (thresh=-3.4) 1.10384 -0.07402 -0.04266 -0.74026; 0.07094 1.16491 0.10870 -39.30675; 0.03856 -0.10679 1.01330 -11.38302; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.391, old_max_log_p =-3.391 (thresh=-3.4) 1.10384 -0.07402 -0.04266 -0.74026; 0.07094 1.16491 0.10870 -39.30675; 0.03856 -0.10679 1.01330 -11.38302; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.367, old_max_log_p =-3.391 (thresh=-3.4) 1.10302 -0.07582 -0.02606 -1.97711; 0.07117 1.16263 0.11683 -39.60528; 0.01992 -0.11511 1.01294 -7.49999; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.356, old_max_log_p =-3.367 (thresh=-3.4) 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02888 -0.11559 1.01151 -8.88249; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.351, old_max_log_p =-3.356 (thresh=-3.4) 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 10 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.351, old_max_log_p =-3.351 (thresh=-3.3) 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 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 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.351 (old=-4.292) transform before final EM align: 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 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 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 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: 015: -log(p) = 3.9 tol 0.000000 final transform: 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 860732 FSRUNTIME@ mri_em_register 0.0305 hours 12 threads registration took 1 minutes and 50 seconds. #-------------------------------------- #@# CA Normalize Thu Feb 9 15:23:04 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/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 '/opt/freesurfer/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=27.0 skull bounding box = (66, 58, 46) --> (189, 176, 211) finding center of left hemi white matter using (107, 97, 129) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (92,83,109) --> (122, 111,149) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.1 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246437 sample points... INFO: compute sample coordinates transform 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61459; 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 (125, 58, 45) --> (188, 156, 210) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 143 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 61, 46) --> (129, 161, 211) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 128.0 1 of 92 (1.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (129, 132, 70) --> (175, 171, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 7 (57.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (89, 132, 69) --> (129, 172, 126) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 17 (58.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (114, 126, 106) --> (146, 185, 136) Brain_Stem: limiting intensities to 92.0 --> 132.0 7 of 8 (87.5%) samples deleted using 267 total control points for intensity normalization... bias field = 0.939 +- 0.053 0 of 245 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (125, 58, 45) --> (188, 156, 210) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 204 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 61, 46) --> (129, 161, 211) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 119.0 3 of 186 (1.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (129, 132, 70) --> (175, 171, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 43 of 74 (58.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (89, 132, 69) --> (129, 172, 126) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 80 of 88 (90.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (114, 126, 106) --> (146, 185, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 69 of 71 (97.2%) samples deleted using 623 total control points for intensity normalization... bias field = 1.001 +- 0.059 0 of 418 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (125, 58, 45) --> (188, 156, 210) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 319 (1.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 61, 46) --> (129, 161, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 343 (3.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (129, 132, 70) --> (175, 171, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 102 of 119 (85.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (89, 132, 69) --> (129, 172, 126) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 90 of 99 (90.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (114, 126, 106) --> (146, 185, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 127 of 133 (95.5%) samples deleted using 1013 total control points for intensity normalization... bias field = 1.020 +- 0.061 0 of 670 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 0 seconds. #-------------------------------------- #@# CA Reg Thu Feb 9 15:24:03 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/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 = 12 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/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 0.88944 #FOTS# QuadFit found better minimum quadopt=(dt=223.686,rms=0.808228) vs oldopt=(dt=92.48,rms=0.833927) #GCMRL# 0 dt 223.685932 rms 0.808 9.131% neg 0 invalid 762 tFOTS 3.5080 tGradient 1.9100 tsec 5.7010 #FOTS# QuadFit found better minimum quadopt=(dt=149.213,rms=0.786866) vs oldopt=(dt=92.48,rms=0.790381) #GCMRL# 1 dt 149.212806 rms 0.787 2.643% neg 0 invalid 762 tFOTS 3.8010 tGradient 2.2480 tsec 6.3350 #FOTS# QuadFit found better minimum quadopt=(dt=271.579,rms=0.775803) vs oldopt=(dt=369.92,rms=0.776964) #GCMRL# 2 dt 271.578565 rms 0.776 1.406% neg 0 invalid 762 tFOTS 3.8030 tGradient 1.9150 tsec 6.0050 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.770587) vs oldopt=(dt=92.48,rms=0.770963) #GCMRL# 3 dt 129.472000 rms 0.771 0.672% neg 0 invalid 762 tFOTS 4.0150 tGradient 1.9990 tsec 6.3070 #GCMRL# 4 dt 369.920000 rms 0.766 0.647% neg 0 invalid 762 tFOTS 3.7460 tGradient 1.8930 tsec 5.9290 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.762455) vs oldopt=(dt=92.48,rms=0.762476) #GCMRL# 5 dt 110.976000 rms 0.762 0.411% neg 0 invalid 762 tFOTS 3.9710 tGradient 1.8180 tsec 6.0860 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.758224) vs oldopt=(dt=369.92,rms=0.758888) #GCMRL# 6 dt 517.888000 rms 0.758 0.555% neg 0 invalid 762 tFOTS 3.7540 tGradient 1.9410 tsec 5.9880 #GCMRL# 7 dt 92.480000 rms 0.757 0.000% neg 0 invalid 762 tFOTS 3.9710 tGradient 1.7780 tsec 6.0720 #GCMRL# 8 dt 92.480000 rms 0.756 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8000 tsec 2.0910 #GCMRL# 9 dt 92.480000 rms 0.755 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8680 tsec 2.1710 #GCMRL# 10 dt 92.480000 rms 0.754 0.184% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8680 tsec 2.1630 #GCMRL# 11 dt 92.480000 rms 0.752 0.219% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9120 tsec 2.2020 #GCMRL# 12 dt 92.480000 rms 0.750 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0740 tsec 2.3650 #GCMRL# 13 dt 92.480000 rms 0.749 0.234% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0250 tsec 2.3100 #GCMRL# 14 dt 92.480000 rms 0.747 0.231% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0250 tsec 2.3290 #GCMRL# 15 dt 92.480000 rms 0.745 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7310 tsec 2.0150 #GCMRL# 16 dt 92.480000 rms 0.744 0.212% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6890 tsec 1.9790 #GCMRL# 17 dt 92.480000 rms 0.742 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7620 tsec 2.0460 #GCMRL# 18 dt 92.480000 rms 0.741 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7220 tsec 2.0110 #GCMRL# 19 dt 92.480000 rms 0.740 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8830 tsec 2.1770 #GCMRL# 20 dt 92.480000 rms 0.739 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8580 tsec 2.1510 #GCMRL# 21 dt 92.480000 rms 0.738 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8300 tsec 2.1330 #GCMRL# 22 dt 92.480000 rms 0.737 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7070 tsec 2.0330 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.737279) vs oldopt=(dt=92.48,rms=0.737281) #GCMRL# 23 dt 129.472000 rms 0.737 0.000% neg 0 invalid 762 tFOTS 4.0850 tGradient 1.8030 tsec 6.2290 #GCMRL# 24 dt 129.472000 rms 0.737 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9070 tsec 2.2090 #GCMRL# 25 dt 129.472000 rms 0.737 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8380 tsec 2.1420 #GCMRL# 26 dt 129.472000 rms 0.737 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7630 tsec 2.0600 #GCMRL# 27 dt 129.472000 rms 0.737 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8300 tsec 2.1360 #GCMRL# 28 dt 129.472000 rms 0.737 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9820 tsec 2.2860 #GCAMreg# pass 0 level1 5 level2 1 tsec 102.151 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 0.736993 #GCMRL# 30 dt 92.480000 rms 0.736 0.151% neg 0 invalid 762 tFOTS 3.8220 tGradient 1.8420 tsec 5.9550 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.735841) vs oldopt=(dt=23.12,rms=0.735842) #GCMRL# 31 dt 32.368000 rms 0.736 0.000% neg 0 invalid 762 tFOTS 4.0310 tGradient 2.0020 tsec 6.3700 #GCMRL# 32 dt 32.368000 rms 0.736 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9970 tsec 2.3020 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 0.743709 #FOTS# QuadFit found better minimum quadopt=(dt=86.9014,rms=0.739341) vs oldopt=(dt=103.68,rms=0.739465) #GCMRL# 34 dt 86.901354 rms 0.739 0.587% neg 0 invalid 762 tFOTS 3.8030 tGradient 1.7700 tsec 5.8740 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.729139) vs oldopt=(dt=414.72,rms=0.730625) #GCMRL# 35 dt 331.776000 rms 0.729 1.380% neg 0 invalid 762 tFOTS 3.8080 tGradient 1.7280 tsec 5.8340 #FOTS# QuadFit found better minimum quadopt=(dt=54,rms=0.724106) vs oldopt=(dt=25.92,rms=0.725136) #GCMRL# 36 dt 54.000000 rms 0.724 0.690% neg 0 invalid 762 tFOTS 3.7880 tGradient 1.8470 tsec 5.9300 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.72149) vs oldopt=(dt=103.68,rms=0.721911) #GCMRL# 37 dt 145.152000 rms 0.721 0.361% neg 0 invalid 762 tFOTS 3.8160 tGradient 1.6390 tsec 5.7500 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.720356) vs oldopt=(dt=25.92,rms=0.720576) #GCMRL# 38 dt 36.288000 rms 0.720 0.000% neg 0 invalid 762 tFOTS 3.5510 tGradient 1.6770 tsec 5.5600 #GCMRL# 39 dt 36.288000 rms 0.720 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6640 tsec 1.9680 #GCMRL# 40 dt 36.288000 rms 0.719 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6670 tsec 1.9680 #GCMRL# 41 dt 36.288000 rms 0.718 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7150 tsec 2.0140 #GCMRL# 42 dt 36.288000 rms 0.717 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7100 tsec 2.0120 #GCMRL# 43 dt 36.288000 rms 0.715 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7070 tsec 2.0010 #GCMRL# 44 dt 36.288000 rms 0.714 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7350 tsec 2.0430 #GCMRL# 45 dt 36.288000 rms 0.712 0.209% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5990 tsec 1.8860 #GCMRL# 46 dt 36.288000 rms 0.711 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7160 tsec 2.0170 #GCMRL# 47 dt 36.288000 rms 0.709 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6110 tsec 1.9030 #GCMRL# 48 dt 36.288000 rms 0.708 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6730 tsec 1.9760 #GCMRL# 49 dt 36.288000 rms 0.707 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6580 tsec 1.9540 #GCMRL# 50 dt 36.288000 rms 0.706 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7410 tsec 2.0400 #GCMRL# 51 dt 36.288000 rms 0.705 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7880 tsec 2.0890 #GCMRL# 52 dt 36.288000 rms 0.704 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7280 tsec 2.0470 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.70449) vs oldopt=(dt=25.92,rms=0.704491) #GCMRL# 53 dt 36.288000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 4.2010 tGradient 1.6780 tsec 6.1950 #GCAMreg# pass 0 level1 4 level2 1 tsec 67.521 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 0.705139 #GCMRL# 55 dt 0.000000 rms 0.704 0.092% neg 0 invalid 762 tFOTS 3.7570 tGradient 1.7410 tsec 5.7880 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 0.730142 #GCMRL# 57 dt 0.000000 rms 0.730 0.085% neg 0 invalid 762 tFOTS 3.3130 tGradient 1.6350 tsec 5.2330 #GCAMreg# pass 0 level1 3 level2 1 tsec 12.954 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 0.730142 #GCMRL# 59 dt 0.000000 rms 0.730 0.085% neg 0 invalid 762 tFOTS 3.3690 tGradient 1.6540 tsec 5.3250 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 0.806063 #FOTS# QuadFit found better minimum quadopt=(dt=2.38347,rms=0.782238) vs oldopt=(dt=2.88,rms=0.783242) #GCMRL# 61 dt 2.383469 rms 0.782 2.956% neg 0 invalid 762 tFOTS 3.6440 tGradient 1.6890 tsec 5.6300 #FOTS# QuadFit found better minimum quadopt=(dt=1.32857,rms=0.780446) vs oldopt=(dt=0.72,rms=0.780841) #GCMRL# 62 dt 1.328571 rms 0.780 0.000% neg 0 invalid 762 tFOTS 3.5760 tGradient 1.6020 tsec 5.4990 #GCAMreg# pass 0 level1 2 level2 1 tsec 15.396 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 0.781013 #FOTS# QuadFit found better minimum quadopt=(dt=0.252,rms=0.780413) vs oldopt=(dt=0.18,rms=0.780417) #GCMRL# 64 dt 0.252000 rms 0.780 0.077% neg 0 invalid 762 tFOTS 3.5850 tGradient 1.6240 tsec 5.5050 #FOTS# QuadFit found better minimum quadopt=(dt=0.063,rms=0.7804) vs oldopt=(dt=0.045,rms=0.7804) #GCMRL# 65 dt 0.063000 rms 0.780 0.000% neg 0 invalid 762 tFOTS 3.5470 tGradient 1.6840 tsec 5.5840 #GCMRL# 66 dt 0.063000 rms 0.780 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6130 tsec 1.9110 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 0.842929 #FOTS# QuadFit found better minimum quadopt=(dt=0.464286,rms=0.839238) vs oldopt=(dt=0.32,rms=0.839789) #GCMRL# 68 dt 0.464286 rms 0.839 0.438% neg 0 invalid 762 tFOTS 3.6020 tGradient 1.5580 tsec 5.4510 #FOTS# QuadFit found better minimum quadopt=(dt=0.900081,rms=0.831152) vs oldopt=(dt=1.28,rms=0.832297) #GCMRL# 69 dt 0.900081 rms 0.831 0.963% neg 0 invalid 762 tFOTS 3.5580 tGradient 1.4190 tsec 5.2740 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.829718) vs oldopt=(dt=0.08,rms=0.830013) #GCMRL# 70 dt 0.112000 rms 0.830 0.000% neg 0 invalid 762 tFOTS 3.6190 tGradient 1.5790 tsec 5.5440 #GCMRL# 71 dt 0.112000 rms 0.829 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5300 tsec 1.8230 #GCAMreg# pass 0 level1 1 level2 1 tsec 22.339 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 0.829783 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.828669) vs oldopt=(dt=0.32,rms=0.828748) #GCMRL# 73 dt 0.256000 rms 0.829 0.134% neg 0 invalid 762 tFOTS 3.5720 tGradient 1.5430 tsec 5.4080 #FOTS# QuadFit found better minimum quadopt=(dt=1.05357,rms=0.825335) vs oldopt=(dt=1.28,rms=0.825346) #GCMRL# 74 dt 1.053571 rms 0.825 0.402% neg 0 invalid 762 tFOTS 3.6250 tGradient 1.6370 tsec 5.5650 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.824828) vs oldopt=(dt=0.08,rms=0.824934) #GCMRL# 75 dt 0.112000 rms 0.825 0.000% neg 0 invalid 762 tFOTS 3.5970 tGradient 1.5070 tsec 5.4370 #GCMRL# 76 dt 0.112000 rms 0.825 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5660 tsec 1.8710 #GCMRL# 77 dt 0.112000 rms 0.824 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6230 tsec 1.9380 #GCMRL# 78 dt 0.112000 rms 0.824 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5140 tsec 1.8180 #GCMRL# 79 dt 0.112000 rms 0.823 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5440 tsec 1.8490 #GCMRL# 80 dt 0.112000 rms 0.822 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5100 tsec 1.8110 #GCMRL# 81 dt 0.112000 rms 0.822 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5710 tsec 1.8670 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 0.783071 #FOTS# QuadFit found better minimum quadopt=(dt=0.273526,rms=0.774735) vs oldopt=(dt=0.32,rms=0.774851) #GCMRL# 83 dt 0.273526 rms 0.775 1.064% neg 0 invalid 762 tFOTS 3.5910 tGradient 1.0730 tsec 4.9640 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.774419) vs oldopt=(dt=0.02,rms=0.77443) #GCMRL# 84 dt 0.024000 rms 0.774 0.000% neg 0 invalid 762 tFOTS 3.6640 tGradient 1.1270 tsec 5.1350 #GCAMreg# pass 0 level1 0 level2 1 tsec 13.948 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 0.775048 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.774383) vs oldopt=(dt=0.005,rms=0.77439) #GCMRL# 86 dt 0.007000 rms 0.774 0.086% neg 0 invalid 762 tFOTS 3.6140 tGradient 1.1590 tsec 5.0730 #FOTS# QuadFit found better minimum quadopt=(dt=0.004,rms=0.774377) vs oldopt=(dt=0.005,rms=0.774378) #GCMRL# 87 dt 0.004000 rms 0.774 0.000% neg 0 invalid 762 tFOTS 3.5750 tGradient 1.1380 tsec 5.0430 GCAMregister done in 5.64022 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.19897 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (139 voxels, overlap=0.077) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (139 voxels, peak = 6), gca=6.4 gca peak = 0.17690 (16) mri peak = 0.10404 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (193 voxels, overlap=0.145) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (193 voxels, peak = 6), gca=6.4 gca peak = 0.28275 (96) mri peak = 0.10530 (93) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (664 voxels, overlap=0.700) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (664 voxels, peak = 92), gca=91.7 gca peak = 0.18948 (93) mri peak = 0.10446 (93) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (494 voxels, overlap=0.512) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (494 voxels, peak = 89), gca=88.8 gca peak = 0.20755 (55) mri peak = 0.20568 (51) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (541 voxels, overlap=0.831) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (541 voxels, peak = 50), gca=50.3 gca peak = 0.31831 (58) mri peak = 0.16295 (54) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (656 voxels, overlap=0.473) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (656 voxels, peak = 53), gca=53.1 gca peak = 0.11957 (102) mri peak = 0.10209 (99) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (51715 voxels, overlap=0.849) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (51715 voxels, peak = 104), gca=103.5 gca peak = 0.11429 (102) mri peak = 0.10590 (101) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (53717 voxels, overlap=0.920) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (53717 voxels, peak = 104), gca=103.5 gca peak = 0.14521 (59) mri peak = 0.03498 (53) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11454 voxels, overlap=0.703) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11454 voxels, peak = 60), gca=60.5 gca peak = 0.14336 (58) mri peak = 0.02875 (68) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (10912 voxels, overlap=0.168) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (10912 voxels, peak = 62), gca=62.4 gca peak = 0.13305 (70) mri peak = 0.09946 (67) Right_Caudate (50): linear fit = 0.94 x + 0.0 (668 voxels, overlap=0.723) Right_Caudate (50): linear fit = 0.94 x + 0.0 (668 voxels, peak = 66), gca=66.2 gca peak = 0.15761 (71) mri peak = 0.11908 (67) Left_Caudate (11): linear fit = 0.93 x + 0.0 (904 voxels, overlap=0.407) Left_Caudate (11): linear fit = 0.93 x + 0.0 (904 voxels, peak = 66), gca=65.7 gca peak = 0.13537 (57) mri peak = 0.07144 (57) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (12150 voxels, overlap=0.753) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (12150 voxels, peak = 61), gca=60.7 gca peak = 0.13487 (56) mri peak = 0.04633 (60) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (14749 voxels, overlap=0.957) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (14749 voxels, peak = 59), gca=58.5 gca peak = 0.19040 (84) mri peak = 0.07824 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6452 voxels, overlap=0.899) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6452 voxels, peak = 85), gca=85.3 gca peak = 0.18871 (83) mri peak = 0.07681 (81) Right_Cerebellum_White_Matter (46): linear fit = 0.93 x + 0.0 (6002 voxels, overlap=0.767) Right_Cerebellum_White_Matter (46): linear fit = 0.93 x + 0.0 (6002 voxels, peak = 77), gca=76.8 gca peak = 0.24248 (57) mri peak = 0.10133 (57) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (384 voxels, overlap=0.807) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (384 voxels, peak = 56), gca=56.1 gca peak = 0.35833 (56) mri peak = 0.17669 (51) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (490 voxels, overlap=0.468) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (490 voxels, peak = 51), gca=51.2 gca peak = 0.12897 (85) mri peak = 0.09185 (90) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4552 voxels, overlap=0.563) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (4552 voxels, peak = 91), gca=90.5 gca peak = 0.13127 (83) mri peak = 0.06992 (93) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3638 voxels, overlap=0.774) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3638 voxels, peak = 88), gca=88.4 gca peak = 0.12974 (78) mri peak = 0.08709 (73) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1901 voxels, overlap=0.856) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1901 voxels, peak = 78), gca=77.6 gca peak = 0.17796 (79) mri peak = 0.09450 (75) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1838 voxels, overlap=0.603) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1838 voxels, peak = 76), gca=76.2 gca peak = 0.10999 (80) mri peak = 0.17446 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9933 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9933 voxels, peak = 84), gca=84.4 gca peak = 0.13215 (88) mri peak = 0.09744 (86) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (955 voxels, overlap=0.584) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (955 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.11403 (90) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1172 voxels, overlap=0.544) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1172 voxels, peak = 89), gca=88.6 gca peak = 0.20775 (25) mri peak = 1.00000 (36) gca peak = 0.13297 (21) mri peak = 0.12712 ( 7) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (104 voxels, overlap=0.283) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (104 voxels, peak = 8), gca=8.1 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) 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 0.97 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 2.77227 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 0.776501 #FOTS# QuadFit found better minimum quadopt=(dt=171.609,rms=0.757769) vs oldopt=(dt=92.48,rms=0.762109) #GCMRL# 89 dt 171.608833 rms 0.758 2.412% neg 0 invalid 762 tFOTS 3.7760 tGradient 1.8600 tsec 5.9330 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.750911) vs oldopt=(dt=369.92,rms=0.752568) #GCMRL# 90 dt 221.952000 rms 0.751 0.905% neg 0 invalid 762 tFOTS 3.5240 tGradient 1.9810 tsec 5.7950 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.747629) vs oldopt=(dt=92.48,rms=0.748057) #GCMRL# 91 dt 129.472000 rms 0.748 0.437% neg 0 invalid 762 tFOTS 3.9810 tGradient 1.6820 tsec 5.9490 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.744786) vs oldopt=(dt=369.92,rms=0.744911) #GCMRL# 92 dt 295.936000 rms 0.745 0.380% neg 0 invalid 762 tFOTS 3.8120 tGradient 2.2240 tsec 6.3410 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.742585) vs oldopt=(dt=92.48,rms=0.742738) #GCMRL# 93 dt 129.472000 rms 0.743 0.296% neg 0 invalid 762 tFOTS 4.0590 tGradient 1.7160 tsec 6.0770 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.741358) vs oldopt=(dt=92.48,rms=0.741607) #GCMRL# 94 dt 129.472000 rms 0.741 0.165% neg 0 invalid 762 tFOTS 3.9000 tGradient 2.0950 tsec 6.2980 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.73893) vs oldopt=(dt=369.92,rms=0.739047) #GCMRL# 95 dt 517.888000 rms 0.739 0.328% neg 0 invalid 762 tFOTS 3.8360 tGradient 1.7990 tsec 5.9310 #GCMRL# 96 dt 92.480000 rms 0.737 0.234% neg 0 invalid 762 tFOTS 4.0390 tGradient 2.1140 tsec 6.4540 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.731447) vs oldopt=(dt=1479.68,rms=0.731811) #GCMRL# 97 dt 1775.616000 rms 0.731 0.780% neg 0 invalid 762 tFOTS 3.8640 tGradient 2.2560 tsec 6.4150 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.729647) vs oldopt=(dt=92.48,rms=0.729713) #GCMRL# 98 dt 73.984000 rms 0.730 0.246% neg 0 invalid 762 tFOTS 4.0590 tGradient 2.2340 tsec 6.5840 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.729436) vs oldopt=(dt=92.48,rms=0.729473) #GCMRL# 99 dt 129.472000 rms 0.729 0.000% neg 0 invalid 762 tFOTS 3.9890 tGradient 1.8650 tsec 6.1840 #GCMRL# 100 dt 129.472000 rms 0.729 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6520 tsec 1.9500 #GCMRL# 101 dt 129.472000 rms 0.728 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7460 tsec 2.0430 #GCMRL# 102 dt 129.472000 rms 0.728 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7170 tsec 2.0160 #GCMRL# 103 dt 129.472000 rms 0.727 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2100 tsec 2.5070 #GCMRL# 104 dt 129.472000 rms 0.726 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0280 tsec 2.3180 #GCMRL# 105 dt 129.472000 rms 0.725 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0790 tsec 2.3700 #GCMRL# 106 dt 129.472000 rms 0.724 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0820 tsec 2.3700 #GCMRL# 107 dt 129.472000 rms 0.723 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0760 tsec 2.3730 #GCMRL# 108 dt 129.472000 rms 0.722 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1380 tsec 2.4320 #GCMRL# 109 dt 129.472000 rms 0.722 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1460 tsec 2.4360 #GCMRL# 110 dt 129.472000 rms 0.721 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9120 tsec 2.2080 #GCMRL# 111 dt 129.472000 rms 0.720 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9280 tsec 2.2270 #GCMRL# 112 dt 129.472000 rms 0.719 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9520 tsec 2.2410 #GCMRL# 113 dt 129.472000 rms 0.718 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8290 tsec 2.1190 #GCMRL# 114 dt 129.472000 rms 0.718 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8330 tsec 2.1280 #GCMRL# 115 dt 129.472000 rms 0.717 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7340 tsec 2.0330 #GCMRL# 116 dt 129.472000 rms 0.716 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8240 tsec 2.1130 #GCMRL# 117 dt 129.472000 rms 0.716 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8800 tsec 2.1800 #GCMRL# 118 dt 129.472000 rms 0.715 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7150 tsec 2.0100 #GCMRL# 119 dt 129.472000 rms 0.715 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7750 tsec 2.0650 #GCMRL# 120 dt 129.472000 rms 0.714 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8610 tsec 2.1480 #GCMRL# 121 dt 129.472000 rms 0.714 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8110 tsec 2.1050 #GCMRL# 122 dt 129.472000 rms 0.713 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7750 tsec 2.0650 #GCMRL# 123 dt 129.472000 rms 0.713 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7360 tsec 2.0300 #GCMRL# 124 dt 129.472000 rms 0.712 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9500 tsec 2.2380 #GCMRL# 125 dt 129.472000 rms 0.712 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7090 tsec 2.0000 #GCMRL# 126 dt 129.472000 rms 0.711 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8130 tsec 2.1070 #GCMRL# 127 dt 129.472000 rms 0.711 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6970 tsec 1.9850 #GCMRL# 128 dt 129.472000 rms 0.710 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7830 tsec 2.0750 #GCMRL# 129 dt 129.472000 rms 0.710 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8460 tsec 2.1460 #GCMRL# 130 dt 129.472000 rms 0.710 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8670 tsec 2.1550 #GCMRL# 131 dt 129.472000 rms 0.709 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8450 tsec 2.1380 #GCMRL# 132 dt 129.472000 rms 0.709 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8560 tsec 2.1490 #GCMRL# 133 dt 129.472000 rms 0.709 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9060 tsec 2.2000 #GCMRL# 134 dt 129.472000 rms 0.708 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9090 tsec 2.2080 #GCMRL# 135 dt 129.472000 rms 0.708 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8400 tsec 2.1400 #GCMRL# 136 dt 129.472000 rms 0.708 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8310 tsec 2.1320 #GCMRL# 137 dt 129.472000 rms 0.707 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7610 tsec 2.0570 #GCMRL# 138 dt 129.472000 rms 0.707 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7730 tsec 2.0620 #GCMRL# 139 dt 129.472000 rms 0.707 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8330 tsec 2.1230 #GCMRL# 140 dt 129.472000 rms 0.706 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9330 tsec 2.2300 #GCMRL# 141 dt 129.472000 rms 0.706 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9000 tsec 2.1880 #GCMRL# 142 dt 129.472000 rms 0.706 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8610 tsec 2.1480 #GCMRL# 143 dt 129.472000 rms 0.705 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8870 tsec 2.1850 #GCMRL# 144 dt 129.472000 rms 0.705 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9210 tsec 2.2140 #GCMRL# 145 dt 129.472000 rms 0.705 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9220 tsec 2.2130 #GCMRL# 146 dt 129.472000 rms 0.705 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8700 tsec 2.1650 #GCMRL# 147 dt 129.472000 rms 0.704 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9640 tsec 2.2530 #GCMRL# 148 dt 129.472000 rms 0.704 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9320 tsec 2.2240 #GCMRL# 149 dt 129.472000 rms 0.704 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8950 tsec 2.1890 #GCMRL# 150 dt 129.472000 rms 0.703 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8770 tsec 2.1660 #GCMRL# 151 dt 129.472000 rms 0.703 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8530 tsec 2.1460 #GCMRL# 152 dt 129.472000 rms 0.703 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9050 tsec 2.2000 #GCMRL# 153 dt 129.472000 rms 0.703 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8820 tsec 2.1710 #GCMRL# 154 dt 129.472000 rms 0.703 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8960 tsec 2.1990 #GCMRL# 155 dt 129.472000 rms 0.702 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8880 tsec 2.1800 #GCMRL# 156 dt 129.472000 rms 0.702 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8690 tsec 2.1620 #GCMRL# 157 dt 129.472000 rms 0.702 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9160 tsec 2.2060 #GCMRL# 158 dt 129.472000 rms 0.702 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9390 tsec 2.2320 #GCMRL# 159 dt 129.472000 rms 0.702 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8640 tsec 2.1570 #GCMRL# 160 dt 129.472000 rms 0.701 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9590 tsec 2.2560 #GCMRL# 161 dt 129.472000 rms 0.701 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9010 tsec 2.1880 #GCMRL# 162 dt 129.472000 rms 0.701 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8810 tsec 2.1710 #GCMRL# 163 dt 129.472000 rms 0.701 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0590 tsec 2.3490 #GCMRL# 164 dt 129.472000 rms 0.701 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9760 tsec 2.2620 #GCMRL# 165 dt 129.472000 rms 0.701 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9410 tsec 2.2330 #GCMRL# 166 dt 129.472000 rms 0.700 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9250 tsec 2.2210 #GCMRL# 167 dt 129.472000 rms 0.700 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9220 tsec 2.2200 #GCMRL# 168 dt 129.472000 rms 0.700 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9830 tsec 2.2790 #GCMRL# 169 dt 129.472000 rms 0.700 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9480 tsec 2.2770 #GCMRL# 170 dt 129.472000 rms 0.700 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8950 tsec 2.1840 #GCMRL# 171 dt 129.472000 rms 0.700 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8870 tsec 2.1800 #GCMRL# 172 dt 129.472000 rms 0.699 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9290 tsec 2.2310 #GCMRL# 173 dt 129.472000 rms 0.699 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9310 tsec 2.2550 #GCMRL# 174 dt 1479.680000 rms 0.699 0.000% neg 0 invalid 762 tFOTS 4.0090 tGradient 1.9290 tsec 6.2660 #GCAMreg# pass 0 level1 5 level2 1 tsec 240.445 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 0.699962 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.698696) vs oldopt=(dt=92.48,rms=0.698702) #GCMRL# 176 dt 110.976000 rms 0.699 0.181% neg 0 invalid 762 tFOTS 3.8700 tGradient 1.9850 tsec 6.1530 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.698318) vs oldopt=(dt=369.92,rms=0.698346) #GCMRL# 177 dt 295.936000 rms 0.698 0.054% neg 0 invalid 762 tFOTS 3.8670 tGradient 1.8460 tsec 6.0160 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.697887) vs oldopt=(dt=369.92,rms=0.697888) #GCMRL# 178 dt 295.936000 rms 0.698 0.062% neg 0 invalid 762 tFOTS 4.1380 tGradient 2.0590 tsec 6.5050 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.697726) vs oldopt=(dt=92.48,rms=0.697727) #GCMRL# 179 dt 110.976000 rms 0.698 0.000% neg 0 invalid 762 tFOTS 3.8350 tGradient 2.0550 tsec 6.2190 #GCMRL# 180 dt 110.976000 rms 0.698 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1690 tsec 2.4780 #GCMRL# 181 dt 110.976000 rms 0.697 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9380 tsec 2.2340 #GCMRL# 182 dt 110.976000 rms 0.697 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9470 tsec 2.2440 #GCMRL# 183 dt 110.976000 rms 0.697 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1160 tsec 2.4150 #GCMRL# 184 dt 110.976000 rms 0.697 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0180 tsec 2.3170 #GCMRL# 185 dt 110.976000 rms 0.696 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1580 tsec 2.4620 #GCMRL# 186 dt 110.976000 rms 0.696 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9690 tsec 2.2670 #GCMRL# 187 dt 110.976000 rms 0.696 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9620 tsec 2.2580 #GCMRL# 188 dt 110.976000 rms 0.696 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1150 tsec 2.4100 #GCMRL# 189 dt 110.976000 rms 0.695 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0590 tsec 2.3640 #GCMRL# 190 dt 110.976000 rms 0.695 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2270 tsec 2.5300 #GCMRL# 191 dt 110.976000 rms 0.695 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1550 tsec 2.4530 #GCMRL# 192 dt 110.976000 rms 0.695 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8620 tsec 2.1990 #GCMRL# 193 dt 110.976000 rms 0.695 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0310 tsec 2.3460 #GCMRL# 194 dt 110.976000 rms 0.694 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9570 tsec 2.3210 #GCMRL# 195 dt 110.976000 rms 0.694 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0340 tsec 2.3660 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.694094) vs oldopt=(dt=1479.68,rms=0.694102) #GCMRL# 196 dt 1775.616000 rms 0.694 0.037% neg 0 invalid 762 tFOTS 4.2330 tGradient 1.8940 tsec 6.4500 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.693971) vs oldopt=(dt=92.48,rms=0.693974) #GCMRL# 197 dt 110.976000 rms 0.694 0.000% neg 0 invalid 762 tFOTS 3.9410 tGradient 2.1050 tsec 6.3910 #GCMRL# 198 dt 110.976000 rms 0.694 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0880 tsec 2.4080 #GCMRL# 199 dt 110.976000 rms 0.694 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2440 tsec 2.5510 #GCMRL# 200 dt 110.976000 rms 0.694 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2650 tsec 2.5700 #GCMRL# 201 dt 110.976000 rms 0.694 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2060 tsec 2.5180 #GCMRL# 202 dt 110.976000 rms 0.694 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4630 tsec 2.7810 #GCMRL# 203 dt 110.976000 rms 0.694 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4070 tsec 2.7150 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 0.696065 #FOTS# QuadFit found better minimum quadopt=(dt=87.6812,rms=0.691681) vs oldopt=(dt=103.68,rms=0.691821) #GCMRL# 205 dt 87.681214 rms 0.692 0.630% neg 0 invalid 762 tFOTS 4.0090 tGradient 2.1380 tsec 6.4560 #FOTS# QuadFit found better minimum quadopt=(dt=118.261,rms=0.687075) vs oldopt=(dt=103.68,rms=0.687127) #GCMRL# 206 dt 118.260870 rms 0.687 0.666% neg 0 invalid 762 tFOTS 4.0600 tGradient 1.8900 tsec 6.2600 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.684603) vs oldopt=(dt=25.92,rms=0.684966) #GCMRL# 207 dt 36.288000 rms 0.685 0.360% neg 0 invalid 762 tFOTS 3.8270 tGradient 2.0190 tsec 6.1640 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.675283) vs oldopt=(dt=414.72,rms=0.675523) #GCMRL# 208 dt 497.664000 rms 0.675 1.361% neg 0 invalid 762 tFOTS 3.8100 tGradient 1.8840 tsec 6.0080 #FOTS# QuadFit found better minimum quadopt=(dt=54.5185,rms=0.669642) vs oldopt=(dt=25.92,rms=0.670907) #GCMRL# 209 dt 54.518519 rms 0.670 0.835% neg 0 invalid 762 tFOTS 3.7920 tGradient 2.1540 tsec 6.2580 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.66822) vs oldopt=(dt=25.92,rms=0.668457) #GCMRL# 210 dt 36.288000 rms 0.668 0.212% neg 0 invalid 762 tFOTS 4.0370 tGradient 1.9890 tsec 6.3310 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.658717) vs oldopt=(dt=414.72,rms=0.66037) #GCMRL# 211 dt 580.608000 rms 0.659 1.422% neg 0 invalid 762 tFOTS 3.8560 tGradient 1.9310 tsec 6.0960 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.656147) vs oldopt=(dt=25.92,rms=0.656316) #GCMRL# 212 dt 36.288000 rms 0.656 0.390% neg 0 invalid 762 tFOTS 3.8330 tGradient 2.0010 tsec 6.1500 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.65541) vs oldopt=(dt=103.68,rms=0.655419) #GCMRL# 213 dt 124.416000 rms 0.655 0.112% neg 0 invalid 762 tFOTS 3.8170 tGradient 2.0360 tsec 6.1580 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.654816) vs oldopt=(dt=25.92,rms=0.654893) #GCMRL# 214 dt 36.288000 rms 0.655 0.091% neg 0 invalid 762 tFOTS 3.8910 tGradient 1.9940 tsec 6.1980 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.652831) vs oldopt=(dt=414.72,rms=0.653258) #GCMRL# 215 dt 248.832000 rms 0.653 0.303% neg 0 invalid 762 tFOTS 3.8030 tGradient 1.9050 tsec 6.0240 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.651732) vs oldopt=(dt=25.92,rms=0.651767) #GCMRL# 216 dt 31.104000 rms 0.652 0.168% neg 0 invalid 762 tFOTS 3.8050 tGradient 2.0230 tsec 6.1360 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.649381) vs oldopt=(dt=414.72,rms=0.6494) #GCMRL# 217 dt 497.664000 rms 0.649 0.361% neg 0 invalid 762 tFOTS 3.8800 tGradient 2.0390 tsec 6.2280 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.647351) vs oldopt=(dt=25.92,rms=0.647651) #GCMRL# 218 dt 36.288000 rms 0.647 0.313% neg 0 invalid 762 tFOTS 3.8540 tGradient 2.0180 tsec 6.1910 #GCMRL# 219 dt 103.680000 rms 0.646 0.171% neg 0 invalid 762 tFOTS 3.8440 tGradient 2.0930 tsec 6.2550 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.645699) vs oldopt=(dt=25.92,rms=0.645763) #GCMRL# 220 dt 36.288000 rms 0.646 0.084% neg 0 invalid 762 tFOTS 3.8520 tGradient 2.0800 tsec 6.2440 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.64523) vs oldopt=(dt=103.68,rms=0.645244) #GCMRL# 221 dt 124.416000 rms 0.645 0.073% neg 0 invalid 762 tFOTS 4.1160 tGradient 2.0390 tsec 6.4750 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.644561) vs oldopt=(dt=25.92,rms=0.644669) #GCMRL# 222 dt 36.288000 rms 0.645 0.104% neg 0 invalid 762 tFOTS 3.8520 tGradient 2.0070 tsec 6.1730 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.644244) vs oldopt=(dt=103.68,rms=0.644249) #GCMRL# 223 dt 82.944000 rms 0.644 0.000% neg 0 invalid 762 tFOTS 4.0600 tGradient 2.1110 tsec 6.5220 #GCMRL# 224 dt 82.944000 rms 0.644 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0070 tsec 2.3230 #GCMRL# 225 dt 82.944000 rms 0.643 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0360 tsec 2.3560 #GCMRL# 226 dt 82.944000 rms 0.641 0.327% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1680 tsec 2.4750 #GCMRL# 227 dt 82.944000 rms 0.640 0.237% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1290 tsec 2.4340 #GCMRL# 228 dt 82.944000 rms 0.639 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0700 tsec 2.3910 #GCMRL# 229 dt 82.944000 rms 0.636 0.411% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1220 tsec 2.4300 #GCMRL# 230 dt 82.944000 rms 0.634 0.296% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2170 tsec 2.5280 #GCMRL# 231 dt 82.944000 rms 0.633 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9820 tsec 2.3010 #GCMRL# 232 dt 82.944000 rms 0.631 0.289% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1180 tsec 2.4200 #GCMRL# 233 dt 82.944000 rms 0.629 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0960 tsec 2.4020 #GCMRL# 234 dt 82.944000 rms 0.628 0.284% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2130 tsec 2.5230 #GCMRL# 235 dt 82.944000 rms 0.626 0.208% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1200 tsec 2.4420 #GCMRL# 236 dt 82.944000 rms 0.625 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0350 tsec 2.3440 #GCMRL# 237 dt 82.944000 rms 0.624 0.263% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0040 tsec 2.3070 #GCMRL# 238 dt 82.944000 rms 0.622 0.199% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0130 tsec 2.3320 #GCMRL# 239 dt 82.944000 rms 0.621 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0540 tsec 2.3690 #GCMRL# 240 dt 82.944000 rms 0.620 0.180% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0430 tsec 2.3450 #GCMRL# 241 dt 82.944000 rms 0.619 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9460 tsec 2.2590 #GCMRL# 242 dt 82.944000 rms 0.619 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0140 tsec 2.3300 #GCMRL# 243 dt 82.944000 rms 0.618 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0220 tsec 2.3290 #GCMRL# 244 dt 82.944000 rms 0.617 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9950 tsec 2.3020 #GCMRL# 245 dt 82.944000 rms 0.616 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0610 tsec 2.3760 #GCMRL# 246 dt 82.944000 rms 0.615 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9130 tsec 2.2320 #GCMRL# 247 dt 82.944000 rms 0.615 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9140 tsec 2.2340 #GCMRL# 248 dt 82.944000 rms 0.614 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8540 tsec 2.1600 #GCMRL# 249 dt 82.944000 rms 0.613 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8850 tsec 2.2080 #GCMRL# 250 dt 82.944000 rms 0.613 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9950 tsec 2.4740 #GCMRL# 251 dt 82.944000 rms 0.613 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9010 tsec 2.2160 #GCMRL# 252 dt 82.944000 rms 0.613 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9680 tsec 2.2860 #GCMRL# 253 dt 82.944000 rms 0.612 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7970 tsec 2.1150 #GCMRL# 254 dt 82.944000 rms 0.612 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8330 tsec 2.1460 #GCMRL# 255 dt 82.944000 rms 0.612 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0190 tsec 2.3240 #GCMRL# 256 dt 82.944000 rms 0.611 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8260 tsec 2.1300 #GCMRL# 257 dt 82.944000 rms 0.611 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8720 tsec 2.1860 #GCMRL# 258 dt 82.944000 rms 0.611 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8620 tsec 2.1740 #GCMRL# 259 dt 82.944000 rms 0.610 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8170 tsec 2.1340 #GCMRL# 260 dt 82.944000 rms 0.610 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9150 tsec 2.2250 #GCMRL# 261 dt 82.944000 rms 0.610 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8160 tsec 2.1200 #GCMRL# 262 dt 82.944000 rms 0.609 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8070 tsec 2.1250 #GCMRL# 263 dt 82.944000 rms 0.609 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8600 tsec 2.1680 #GCMRL# 264 dt 82.944000 rms 0.609 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8460 tsec 2.1660 #GCMRL# 265 dt 82.944000 rms 0.608 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8280 tsec 2.1370 #GCMRL# 266 dt 82.944000 rms 0.608 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8670 tsec 2.1880 #GCMRL# 267 dt 82.944000 rms 0.607 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8370 tsec 2.1470 #GCMRL# 268 dt 82.944000 rms 0.607 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8360 tsec 2.1540 #GCMRL# 269 dt 82.944000 rms 0.607 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9750 tsec 2.2810 #GCMRL# 270 dt 82.944000 rms 0.606 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8720 tsec 2.1900 #GCMRL# 271 dt 82.944000 rms 0.606 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7890 tsec 2.1050 #GCMRL# 272 dt 82.944000 rms 0.606 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7600 tsec 2.0960 #GCMRL# 273 dt 82.944000 rms 0.605 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0170 tsec 2.3230 #GCMRL# 274 dt 82.944000 rms 0.605 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8150 tsec 2.1290 #GCMRL# 275 dt 82.944000 rms 0.605 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8310 tsec 2.1410 #GCMRL# 276 dt 82.944000 rms 0.605 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7750 tsec 2.0960 #GCMRL# 277 dt 82.944000 rms 0.604 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8510 tsec 2.1640 #GCMRL# 278 dt 82.944000 rms 0.604 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8020 tsec 2.1250 #GCMRL# 279 dt 82.944000 rms 0.604 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8640 tsec 2.1810 #GCMRL# 280 dt 82.944000 rms 0.603 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8150 tsec 2.1290 #GCMRL# 281 dt 82.944000 rms 0.603 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8630 tsec 2.1690 #GCMRL# 282 dt 82.944000 rms 0.603 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8680 tsec 2.1750 #GCMRL# 283 dt 82.944000 rms 0.603 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8500 tsec 2.1770 #GCMRL# 284 dt 82.944000 rms 0.602 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8880 tsec 2.1940 #GCMRL# 285 dt 82.944000 rms 0.602 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7900 tsec 2.1090 #GCMRL# 286 dt 82.944000 rms 0.602 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8280 tsec 2.1300 #GCMRL# 287 dt 82.944000 rms 0.602 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8260 tsec 2.1310 #GCMRL# 288 dt 82.944000 rms 0.602 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8460 tsec 2.1630 #GCMRL# 289 dt 82.944000 rms 0.601 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8100 tsec 2.1190 #GCMRL# 290 dt 82.944000 rms 0.601 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8480 tsec 2.1870 #GCMRL# 291 dt 82.944000 rms 0.601 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8670 tsec 2.1890 #GCMRL# 292 dt 82.944000 rms 0.601 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8350 tsec 2.1450 #GCMRL# 293 dt 82.944000 rms 0.601 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8670 tsec 2.1780 #GCMRL# 294 dt 82.944000 rms 0.600 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8180 tsec 2.1200 #GCMRL# 295 dt 82.944000 rms 0.600 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8330 tsec 2.1540 #GCMRL# 296 dt 82.944000 rms 0.600 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9220 tsec 2.2440 #GCMRL# 297 dt 82.944000 rms 0.600 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8480 tsec 2.1830 #GCMRL# 298 dt 82.944000 rms 0.600 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8220 tsec 2.1260 #GCMRL# 299 dt 82.944000 rms 0.600 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7510 tsec 2.0970 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.599586) vs oldopt=(dt=103.68,rms=0.599596) #GCMRL# 300 dt 145.152000 rms 0.600 0.000% neg 0 invalid 762 tFOTS 3.9930 tGradient 1.7770 tsec 6.1120 #GCAMreg# pass 0 level1 4 level2 1 tsec 298.88 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 0.600478 #FOTS# QuadFit found better minimum quadopt=(dt=88.6634,rms=0.597935) vs oldopt=(dt=103.68,rms=0.597983) #GCMRL# 302 dt 88.663415 rms 0.598 0.424% neg 0 invalid 762 tFOTS 4.0010 tGradient 1.8730 tsec 6.1920 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.597376) vs oldopt=(dt=25.92,rms=0.597483) #GCMRL# 303 dt 36.288000 rms 0.597 0.093% neg 0 invalid 762 tFOTS 3.9850 tGradient 1.8550 tsec 6.1840 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.596217) vs oldopt=(dt=414.72,rms=0.596544) #GCMRL# 304 dt 248.832000 rms 0.596 0.194% neg 0 invalid 762 tFOTS 3.9820 tGradient 1.8140 tsec 6.1050 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.595895) vs oldopt=(dt=25.92,rms=0.595904) #GCMRL# 305 dt 31.104000 rms 0.596 0.054% neg 0 invalid 762 tFOTS 3.7170 tGradient 2.0110 tsec 6.0310 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.595609) vs oldopt=(dt=103.68,rms=0.595655) #GCMRL# 306 dt 145.152000 rms 0.596 0.000% neg 0 invalid 762 tFOTS 3.9670 tGradient 1.8390 tsec 6.1430 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 0.609435 #FOTS# QuadFit found better minimum quadopt=(dt=23.8882,rms=0.606428) vs oldopt=(dt=32,rms=0.60675) #GCMRL# 308 dt 23.888224 rms 0.606 0.493% neg 0 invalid 762 tFOTS 3.6940 tGradient 1.8280 tsec 5.8220 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.602755) vs oldopt=(dt=32,rms=0.603077) #GCMRL# 309 dt 44.800000 rms 0.603 0.606% neg 0 invalid 762 tFOTS 3.7450 tGradient 1.8350 tsec 5.8870 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.601074) vs oldopt=(dt=8,rms=0.601289) #GCMRL# 310 dt 11.200000 rms 0.601 0.279% neg 0 invalid 762 tFOTS 3.6700 tGradient 1.8260 tsec 5.8030 #GCMRL# 311 dt 128.000000 rms 0.594 1.224% neg 0 invalid 762 tFOTS 3.9440 tGradient 1.9330 tsec 6.1790 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.591461) vs oldopt=(dt=8,rms=0.591935) #GCMRL# 312 dt 11.200000 rms 0.591 0.380% neg 0 invalid 762 tFOTS 3.4640 tGradient 1.7430 tsec 5.5070 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.591168) vs oldopt=(dt=2,rms=0.591244) #GCMRL# 313 dt 2.800000 rms 0.591 0.000% neg 0 invalid 762 tFOTS 3.2680 tGradient 1.8190 tsec 5.4280 #GCMRL# 314 dt 2.800000 rms 0.591 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7340 tsec 2.0360 #GCMRL# 315 dt 0.700000 rms 0.591 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7140 tsec 2.4410 #GCMRL# 316 dt 0.350000 rms 0.591 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6920 tsec 2.3350 #GCMRL# 317 dt 0.125000 rms 0.591 0.000% neg 0 invalid 762 tFOTS 2.7730 tGradient 1.7070 tsec 4.8140 #GCMRL# 318 dt 0.015625 rms 0.591 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7230 tsec 2.5860 #GCMRL# 319 dt 0.003906 rms 0.591 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6890 tsec 2.4190 #GCAMreg# pass 0 level1 3 level2 1 tsec 55.967 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 0.59168 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.586271) vs oldopt=(dt=32,rms=0.586549) #GCMRL# 321 dt 44.800000 rms 0.586 0.914% neg 0 invalid 762 tFOTS 3.9830 tGradient 1.6980 tsec 5.9860 #FOTS# QuadFit found better minimum quadopt=(dt=24.2941,rms=0.58358) vs oldopt=(dt=32,rms=0.583894) #GCMRL# 322 dt 24.294118 rms 0.584 0.459% neg 0 invalid 762 tFOTS 3.7440 tGradient 1.8040 tsec 5.8530 #FOTS# QuadFit found better minimum quadopt=(dt=21.9259,rms=0.582241) vs oldopt=(dt=32,rms=0.582571) #GCMRL# 323 dt 21.925926 rms 0.582 0.230% neg 0 invalid 762 tFOTS 3.8000 tGradient 1.7260 tsec 5.8280 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.58072) vs oldopt=(dt=32,rms=0.580811) #GCMRL# 324 dt 25.600000 rms 0.581 0.261% neg 0 invalid 762 tFOTS 3.7350 tGradient 1.7560 tsec 5.8000 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.579818) vs oldopt=(dt=8,rms=0.579974) #GCMRL# 325 dt 11.200000 rms 0.580 0.155% neg 0 invalid 762 tFOTS 3.7230 tGradient 1.7710 tsec 5.7980 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.577581) vs oldopt=(dt=32,rms=0.578173) #GCMRL# 326 dt 44.800000 rms 0.578 0.386% neg 0 invalid 762 tFOTS 3.5300 tGradient 1.7370 tsec 5.5740 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.576434) vs oldopt=(dt=32,rms=0.576539) #GCMRL# 327 dt 44.800000 rms 0.576 0.199% neg 0 invalid 762 tFOTS 3.9640 tGradient 1.7600 tsec 6.0280 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.575243) vs oldopt=(dt=8,rms=0.575434) #GCMRL# 328 dt 11.200000 rms 0.575 0.207% neg 0 invalid 762 tFOTS 3.5100 tGradient 1.7230 tsec 5.5400 #GCMRL# 329 dt 32.000000 rms 0.574 0.220% neg 0 invalid 762 tFOTS 3.4450 tGradient 1.7010 tsec 5.4490 #FOTS# QuadFit found better minimum quadopt=(dt=102.4,rms=0.571947) vs oldopt=(dt=128,rms=0.572043) #GCMRL# 330 dt 102.400000 rms 0.572 0.354% neg 0 invalid 762 tFOTS 4.0060 tGradient 1.8290 tsec 6.1380 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.570182) vs oldopt=(dt=8,rms=0.570408) #GCMRL# 331 dt 11.200000 rms 0.570 0.309% neg 0 invalid 762 tFOTS 3.4390 tGradient 1.5760 tsec 5.3160 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.569744) vs oldopt=(dt=8,rms=0.569862) #GCMRL# 332 dt 11.200000 rms 0.570 0.077% neg 0 invalid 762 tFOTS 3.4900 tGradient 1.5980 tsec 5.3880 #GCMRL# 333 dt 512.000000 rms 0.562 1.415% neg 0 invalid 762 tFOTS 3.8770 tGradient 1.6420 tsec 5.8280 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.559602) vs oldopt=(dt=8,rms=0.560083) #GCMRL# 334 dt 11.200000 rms 0.560 0.370% neg 0 invalid 762 tFOTS 3.4510 tGradient 2.3260 tsec 6.0740 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.558607) vs oldopt=(dt=8,rms=0.558848) #GCMRL# 335 dt 11.200000 rms 0.559 0.178% neg 0 invalid 762 tFOTS 3.4320 tGradient 1.8050 tsec 5.5430 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.558034) vs oldopt=(dt=8,rms=0.558165) #GCMRL# 336 dt 11.200000 rms 0.558 0.103% neg 0 invalid 762 tFOTS 3.3590 tGradient 1.7170 tsec 5.3730 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.557906) vs oldopt=(dt=2,rms=0.557932) #GCMRL# 337 dt 2.800000 rms 0.558 0.000% neg 0 invalid 762 tFOTS 3.1550 tGradient 1.6750 tsec 5.1600 #GCMRL# 338 dt 2.800000 rms 0.558 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7030 tsec 2.0020 #GCMRL# 339 dt 1.400000 rms 0.558 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6590 tsec 2.2430 #GCMRL# 340 dt 0.700000 rms 0.558 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6460 tsec 2.2650 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.55774) vs oldopt=(dt=0.125,rms=0.557741) 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 0.579761 #GCMRL# 342 dt 0.000000 rms 0.579 0.129% neg 0 invalid 762 tFOTS 3.3730 tGradient 1.6050 tsec 5.2750 #GCMRL# 343 dt 0.150000 rms 0.579 0.000% neg 0 invalid 762 tFOTS 3.3400 tGradient 1.5960 tsec 5.4730 #GCAMreg# pass 0 level1 2 level2 1 tsec 15 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 0.579761 #GCMRL# 345 dt 0.000000 rms 0.579 0.129% neg 0 invalid 762 tFOTS 3.3390 tGradient 1.5560 tsec 5.2040 #GCMRL# 346 dt 0.150000 rms 0.579 0.000% neg 0 invalid 762 tFOTS 3.3230 tGradient 1.5640 tsec 5.4150 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 0.622489 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.617502) vs oldopt=(dt=1.28,rms=0.617625) #GCMRL# 348 dt 1.536000 rms 0.618 0.801% neg 0 invalid 762 tFOTS 3.5760 tGradient 1.5360 tsec 5.4030 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.617236) vs oldopt=(dt=0.32,rms=0.617274) #GCMRL# 349 dt 0.448000 rms 0.617 0.000% neg 0 invalid 762 tFOTS 3.3190 tGradient 1.3690 tsec 5.0140 #GCAMreg# pass 0 level1 1 level2 1 tsec 14.469 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 0.617887 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.615932) vs oldopt=(dt=1.28,rms=0.615944) #GCMRL# 351 dt 1.536000 rms 0.616 0.316% neg 0 invalid 762 tFOTS 3.3400 tGradient 1.3830 tsec 5.0160 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.615915) vs oldopt=(dt=0.08,rms=0.615915) #GCMRL# 352 dt 0.112000 rms 0.616 0.000% neg 0 invalid 762 tFOTS 3.5480 tGradient 1.5260 tsec 5.3940 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 0.568274 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.548661) vs oldopt=(dt=0.32,rms=0.553905) #GCMRL# 354 dt 0.448000 rms 0.549 3.451% neg 0 invalid 762 tFOTS 3.3560 tGradient 1.0120 tsec 4.6600 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.543951) vs oldopt=(dt=0.32,rms=0.545281) #GCMRL# 355 dt 0.448000 rms 0.544 0.858% neg 0 invalid 762 tFOTS 3.3470 tGradient 0.9970 tsec 4.6450 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.540994) vs oldopt=(dt=0.32,rms=0.541821) #GCMRL# 356 dt 0.448000 rms 0.541 0.544% neg 0 invalid 762 tFOTS 3.3520 tGradient 0.9960 tsec 4.6390 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.539656) vs oldopt=(dt=0.32,rms=0.539868) #GCMRL# 357 dt 0.384000 rms 0.540 0.247% neg 0 invalid 762 tFOTS 3.2980 tGradient 0.9850 tsec 4.5710 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.538435) vs oldopt=(dt=0.32,rms=0.538629) #GCMRL# 358 dt 0.384000 rms 0.538 0.226% neg 0 invalid 762 tFOTS 3.3680 tGradient 0.9230 tsec 4.5780 #GCMRL# 359 dt 0.320000 rms 0.538 0.118% neg 0 invalid 762 tFOTS 3.3240 tGradient 0.9260 tsec 4.5440 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.536967) vs oldopt=(dt=0.32,rms=0.537093) #GCMRL# 360 dt 0.384000 rms 0.537 0.155% neg 0 invalid 762 tFOTS 3.3460 tGradient 0.9310 tsec 4.5810 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.536469) vs oldopt=(dt=0.32,rms=0.536535) #GCMRL# 361 dt 0.384000 rms 0.536 0.093% neg 0 invalid 762 tFOTS 3.3380 tGradient 0.9350 tsec 4.5660 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.535896) vs oldopt=(dt=0.32,rms=0.535974) #GCMRL# 362 dt 0.384000 rms 0.536 0.107% neg 0 invalid 762 tFOTS 3.3400 tGradient 0.9290 tsec 4.5670 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.535585) vs oldopt=(dt=0.32,rms=0.535621) #GCMRL# 363 dt 0.384000 rms 0.536 0.058% neg 0 invalid 762 tFOTS 3.3540 tGradient 0.9370 tsec 4.5890 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.535138) vs oldopt=(dt=0.32,rms=0.535192) #GCMRL# 364 dt 0.384000 rms 0.535 0.083% neg 0 invalid 762 tFOTS 3.3160 tGradient 0.9390 tsec 4.5550 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.535042) vs oldopt=(dt=0.08,rms=0.535067) #GCMRL# 365 dt 0.112000 rms 0.535 0.000% neg 0 invalid 762 tFOTS 3.1540 tGradient 0.9390 tsec 4.4200 #GCMRL# 366 dt 0.112000 rms 0.535 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9400 tsec 1.2390 #GCMRL# 367 dt 0.112000 rms 0.535 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9370 tsec 1.2350 #GCMRL# 368 dt 0.112000 rms 0.534 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9440 tsec 1.2400 #GCMRL# 369 dt 0.112000 rms 0.534 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9290 tsec 1.2320 #GCMRL# 370 dt 0.112000 rms 0.534 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9230 tsec 1.2130 #GCMRL# 371 dt 0.112000 rms 0.533 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9340 tsec 1.2290 #GCMRL# 372 dt 0.112000 rms 0.533 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9460 tsec 1.2430 #GCMRL# 373 dt 0.112000 rms 0.533 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9330 tsec 1.2200 #GCMRL# 374 dt 0.112000 rms 0.533 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9480 tsec 1.2400 #GCMRL# 375 dt 0.112000 rms 0.532 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9400 tsec 1.2420 #GCMRL# 376 dt 0.112000 rms 0.532 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9280 tsec 1.2190 #GCMRL# 377 dt 0.112000 rms 0.532 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9410 tsec 1.2360 #GCMRL# 378 dt 0.112000 rms 0.532 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9340 tsec 1.2290 #GCMRL# 379 dt 0.112000 rms 0.531 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9250 tsec 1.2240 #GCMRL# 380 dt 0.112000 rms 0.531 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9240 tsec 1.2220 #GCMRL# 381 dt 0.112000 rms 0.531 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9400 tsec 1.2660 #GCMRL# 382 dt 0.050000 rms 0.531 0.000% neg 0 invalid 762 tFOTS 2.9170 tGradient 0.9360 tsec 4.1830 #GCAMreg# pass 0 level1 0 level2 1 tsec 82.504 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 0.531934 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.529437) vs oldopt=(dt=0.08,rms=0.529926) #GCMRL# 384 dt 0.112000 rms 0.529 0.469% neg 0 invalid 762 tFOTS 3.0970 tGradient 0.9370 tsec 4.3280 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.528079) vs oldopt=(dt=0.08,rms=0.528465) #GCMRL# 385 dt 0.112000 rms 0.528 0.256% neg 0 invalid 762 tFOTS 3.1160 tGradient 0.9420 tsec 4.3550 #FOTS# QuadFit found better minimum quadopt=(dt=0.229167,rms=0.525901) vs oldopt=(dt=0.08,rms=0.527306) #GCMRL# 386 dt 0.229167 rms 0.526 0.412% neg 0 invalid 762 tFOTS 3.0950 tGradient 0.9360 tsec 4.3250 #GCMRL# 387 dt 0.320000 rms 0.524 0.313% neg 0 invalid 762 tFOTS 3.3620 tGradient 0.9420 tsec 4.6090 #GCMRL# 388 dt 0.320000 rms 0.524 0.121% neg 0 invalid 762 tFOTS 3.3030 tGradient 0.9400 tsec 4.5370 #GCMRL# 389 dt 0.320000 rms 0.523 0.000% neg 0 invalid 762 tFOTS 3.3210 tGradient 0.9400 tsec 4.5910 #GCMRL# 390 dt 0.320000 rms 0.523 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9320 tsec 1.2330 #GCMRL# 391 dt 0.320000 rms 0.523 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9460 tsec 1.2530 GCAMregister done in 16.7596 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 0.521196 #FOTS# QuadFit found better minimum quadopt=(dt=0.004335,rms=0.520419) vs oldopt=(dt=0.0036125,rms=0.520419) #GCMRL# 393 dt 0.004335 rms 0.520 0.149% neg 0 invalid 762 tFOTS 5.4100 tGradient 1.6910 tsec 7.4080 #GCAMreg# pass 0 level1 5 level2 1 tsec 15.826 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 0.521196 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.520177) vs oldopt=(dt=92.48,rms=0.520193) #GCMRL# 395 dt 129.472000 rms 0.520 0.196% neg 0 invalid 762 tFOTS 4.0330 tGradient 1.6810 tsec 6.0130 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.51994) vs oldopt=(dt=92.48,rms=0.519944) #GCMRL# 396 dt 110.976000 rms 0.520 0.000% neg 0 invalid 762 tFOTS 3.9940 tGradient 1.6960 tsec 6.0180 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 0.520745 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.519537) vs oldopt=(dt=25.92,rms=0.519546) #GCMRL# 398 dt 31.104000 rms 0.520 0.232% neg 0 invalid 762 tFOTS 4.2510 tGradient 1.5820 tsec 6.1400 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.519262) vs oldopt=(dt=25.92,rms=0.519296) #GCMRL# 399 dt 36.288000 rms 0.519 0.000% neg 0 invalid 762 tFOTS 4.0820 tGradient 1.5650 tsec 5.9700 #GCMRL# 400 dt 36.288000 rms 0.519 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5350 tsec 1.8280 #GCMRL# 401 dt 36.288000 rms 0.519 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5650 tsec 1.8580 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 21.488 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 0.519844 #FOTS# QuadFit found better minimum quadopt=(dt=83.4286,rms=0.516797) vs oldopt=(dt=25.92,rms=0.51745) #GCMRL# 403 dt 83.428571 rms 0.517 0.586% neg 0 invalid 762 tFOTS 4.2400 tGradient 1.5690 tsec 6.1070 #FOTS# QuadFit found better minimum quadopt=(dt=35.8681,rms=0.515004) vs oldopt=(dt=25.92,rms=0.5151) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 404 dt 35.868132 rms 0.515 0.347% neg 0 invalid 762 tFOTS 4.2960 tGradient 1.5820 tsec 6.8060 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.514668) vs oldopt=(dt=25.92,rms=0.514678) #GCMRL# 405 dt 31.104000 rms 0.515 0.000% neg 0 invalid 762 tFOTS 4.0830 tGradient 1.5770 tsec 5.9920 #GCMRL# 406 dt 31.104000 rms 0.514 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5930 tsec 1.8970 #GCMRL# 407 dt 31.104000 rms 0.514 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5660 tsec 1.8590 #GCMRL# 408 dt 31.104000 rms 0.513 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5220 tsec 1.8140 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 409 dt 31.104000 rms 0.513 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5570 tsec 3.2160 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 410 dt 31.104000 rms 0.512 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5570 tsec 2.4170 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 411 dt 31.104000 rms 0.511 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5990 tsec 3.5710 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 0.512412 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.510041) vs oldopt=(dt=8,rms=0.510343) iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 413 dt 11.200000 rms 0.510 0.457% neg 0 invalid 762 tFOTS 4.2790 tGradient 1.4850 tsec 7.6860 #FOTS# QuadFit found better minimum quadopt=(dt=30.8037,rms=0.508607) vs oldopt=(dt=32,rms=0.508619) iter 0, gcam->neg = 16 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 414 dt 30.803738 rms 0.509 0.276% neg 0 invalid 762 tFOTS 4.2390 tGradient 1.4940 tsec 7.9700 #FOTS# QuadFit found better minimum quadopt=(dt=24.306,rms=0.507781) vs oldopt=(dt=32,rms=0.507914) iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 415 dt 24.306011 rms 0.508 0.000% neg 0 invalid 762 tFOTS 4.2330 tGradient 1.4840 tsec 7.4450 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 416 dt 24.306011 rms 0.507 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4920 tsec 3.1750 iter 0, gcam->neg = 22 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 417 dt 24.306011 rms 0.506 0.284% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5040 tsec 3.9640 iter 0, gcam->neg = 35 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 418 dt 24.306011 rms 0.506 -0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4760 tsec 4.1810 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.504997) vs oldopt=(dt=32,rms=0.505048) iter 0, gcam->neg = 27 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 419 dt 44.800000 rms 0.505 0.126% neg 0 invalid 762 tFOTS 4.2730 tGradient 1.4810 tsec 8.0050 #FOTS# QuadFit found better minimum quadopt=(dt=9.6,rms=0.504751) vs oldopt=(dt=8,rms=0.504763) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 51.277 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 0.505563 #FOTS# QuadFit found better minimum quadopt=(dt=36.0979,rms=0.500026) vs oldopt=(dt=32,rms=0.500062) iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 421 dt 36.097928 rms 0.500 1.095% neg 0 invalid 762 tFOTS 4.2420 tGradient 1.4760 tsec 6.5980 #FOTS# QuadFit found better minimum quadopt=(dt=25.1532,rms=0.497904) vs oldopt=(dt=32,rms=0.498108) iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 422 dt 25.153153 rms 0.498 0.424% neg 0 invalid 762 tFOTS 4.2880 tGradient 1.4940 tsec 7.2090 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.497122) vs oldopt=(dt=8,rms=0.497266) iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 423 dt 11.200000 rms 0.497 0.000% neg 0 invalid 762 tFOTS 4.2170 tGradient 1.5020 tsec 8.2310 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 424 dt 11.200000 rms 0.497 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5120 tsec 2.4090 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 425 dt 11.200000 rms 0.496 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5000 tsec 2.9000 #GCMRL# 426 dt 11.200000 rms 0.495 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4940 tsec 1.7970 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 427 dt 11.200000 rms 0.494 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5640 tsec 3.5080 #GCMRL# 428 dt 11.200000 rms 0.493 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4980 tsec 1.7910 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 429 dt 11.200000 rms 0.492 0.185% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4180 tsec 2.8280 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 430 dt 11.200000 rms 0.491 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4230 tsec 3.3660 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 431 dt 11.200000 rms 0.490 0.179% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4220 tsec 3.1670 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 432 dt 11.200000 rms 0.490 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4390 tsec 3.1540 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 433 dt 11.200000 rms 0.489 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4430 tsec 2.5800 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 434 dt 11.200000 rms 0.488 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4850 tsec 2.9400 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 435 dt 11.200000 rms 0.487 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4460 tsec 2.8680 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 436 dt 11.200000 rms 0.487 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4240 tsec 2.8630 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 437 dt 11.200000 rms 0.486 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4250 tsec 2.8980 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.486376) vs oldopt=(dt=32,rms=0.486383) #GCMRL# 438 dt 25.600000 rms 0.486 0.000% neg 0 invalid 762 tFOTS 4.0280 tGradient 1.4280 tsec 5.7960 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 439 dt 25.600000 rms 0.486 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4400 tsec 3.4580 #GCMRL# 440 dt 25.600000 rms 0.486 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4310 tsec 1.7350 #GCMRL# 441 dt 25.600000 rms 0.485 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4270 tsec 1.7310 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 442 dt 25.600000 rms 0.485 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4320 tsec 3.1600 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 443 dt 25.600000 rms 0.485 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4430 tsec 3.4180 iter 0, gcam->neg = 8 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_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 0.48951 #FOTS# QuadFit found better minimum quadopt=(dt=0.432,rms=0.488672) vs oldopt=(dt=0.72,rms=0.488674) #GCMRL# 445 dt 0.432000 rms 0.489 0.171% neg 0 invalid 762 tFOTS 4.2550 tGradient 1.3770 tsec 5.9280 #FOTS# QuadFit found better minimum quadopt=(dt=0.216,rms=0.488669) vs oldopt=(dt=0.18,rms=0.488669) #GCMRL# 446 dt 0.216000 rms 0.489 0.000% neg 0 invalid 762 tFOTS 4.2540 tGradient 1.3660 tsec 5.9410 #GCAMreg# pass 0 level1 2 level2 1 tsec 15.925 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 0.489501 #FOTS# QuadFit found better minimum quadopt=(dt=2.26087,rms=0.488576) vs oldopt=(dt=2.88,rms=0.488587) #GCMRL# 448 dt 2.260870 rms 0.489 0.189% neg 0 invalid 762 tFOTS 4.2860 tGradient 1.3750 tsec 5.9570 #FOTS# QuadFit found better minimum quadopt=(dt=2.66667,rms=0.488477) vs oldopt=(dt=2.88,rms=0.488477) #GCMRL# 449 dt 2.666667 rms 0.488 0.000% neg 0 invalid 762 tFOTS 4.2490 tGradient 1.3600 tsec 5.9460 #GCMRL# 450 dt 2.666667 rms 0.488 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3510 tsec 1.6430 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 0.496726 #GCMRL# 452 dt 0.000000 rms 0.496 0.168% neg 0 invalid 762 tFOTS 4.0670 tGradient 1.3760 tsec 5.7470 #GCAMreg# pass 0 level1 1 level2 1 tsec 13.847 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 0.496726 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.495707) vs oldopt=(dt=0.32,rms=0.495739) #GCMRL# 454 dt 0.448000 rms 0.496 0.205% neg 0 invalid 762 tFOTS 4.3310 tGradient 1.3560 tsec 5.9740 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.495586) vs oldopt=(dt=0.32,rms=0.495603) #GCMRL# 455 dt 0.448000 rms 0.496 0.000% neg 0 invalid 762 tFOTS 4.2600 tGradient 1.3280 tsec 5.9120 #GCMRL# 456 dt 0.448000 rms 0.496 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.3370 tsec 1.6340 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 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 0.486202 #FOTS# QuadFit found better minimum quadopt=(dt=2.02713,rms=0.449602) vs oldopt=(dt=1.28,rms=0.454733) iter 0, gcam->neg = 1479 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 458 dt 2.027130 rms 0.450 7.369% neg 0 invalid 762 tFOTS 4.2370 tGradient 0.8380 tsec 10.3210 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.450392) vs oldopt=(dt=0.005,rms=0.450393) #GCMRL# 459 dt 0.007000 rms 0.450 0.000% neg 0 invalid 762 tFOTS 4.2560 tGradient 0.8530 tsec 5.6360 #GCMRL# 460 dt 0.007000 rms 0.450 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8570 tsec 1.1480 #GCAMreg# pass 0 level1 0 level2 1 tsec 20.634 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 0.451441 #GCMRL# 462 dt 0.080000 rms 0.450 0.298% neg 0 invalid 762 tFOTS 4.2480 tGradient 0.8470 tsec 5.3850 #FOTS# QuadFit found better minimum quadopt=(dt=0.00075,rms=0.450091) vs oldopt=(dt=0.00125,rms=0.450091) #GCMRL# 463 dt 0.000750 rms 0.450 0.000% neg 0 invalid 762 tFOTS 4.2910 tGradient 0.8410 tsec 5.4640 label assignment complete, 0 changed (0.00%) GCAMregister done in 5.45633 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 0.435663 #FOTS# QuadFit found better minimum quadopt=(dt=2.023,rms=0.435662) vs oldopt=(dt=1.445,rms=0.435662) #GCMRL# 465 dt 2.023000 rms 0.436 0.000% neg 0 invalid 762 tFOTS 3.7180 tGradient 1.0630 tsec 5.0480 #GCAMreg# pass 0 level1 5 level2 1 tsec 12.135 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 0.435662 #GCMRL# 467 dt 23.120000 rms 0.436 0.004% neg 0 invalid 762 tFOTS 3.7100 tGradient 1.0680 tsec 5.0410 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 0.435826 #GCAMreg# pass 0 level1 4 level2 1 tsec 6.956 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 0.435826 #GCMRL# 470 dt 25.920000 rms 0.436 0.018% neg 0 invalid 762 tFOTS 3.4770 tGradient 0.9330 tsec 4.6800 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.435686) vs oldopt=(dt=25.92,rms=0.435695) #GCMRL# 471 dt 36.288000 rms 0.436 0.000% neg 0 invalid 762 tFOTS 3.6710 tGradient 0.9310 tsec 4.8990 #GCMRL# 472 dt 36.288000 rms 0.436 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9140 tsec 1.1860 #GCMRL# 473 dt 36.288000 rms 0.436 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.9270 tsec 1.2010 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 0.436325 #FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.436127) vs oldopt=(dt=8,rms=0.436128) #GCMRL# 475 dt 6.400000 rms 0.436 0.045% neg 0 invalid 762 tFOTS 3.7080 tGradient 0.8600 tsec 4.8280 #FOTS# QuadFit found better minimum quadopt=(dt=2.4,rms=0.436112) vs oldopt=(dt=2,rms=0.436113) #GCMRL# 476 dt 2.400000 rms 0.436 0.000% neg 0 invalid 762 tFOTS 3.7030 tGradient 0.8570 tsec 4.8520 #GCAMreg# pass 0 level1 3 level2 1 tsec 13.049 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 0.436112 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.434258) vs oldopt=(dt=32,rms=0.434425) iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 478 dt 44.800000 rms 0.434 0.419% neg 0 invalid 762 tFOTS 3.7260 tGradient 0.8670 tsec 6.3190 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.434022) vs oldopt=(dt=8,rms=0.434046) iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 479 dt 11.200000 rms 0.434 0.000% neg 0 invalid 762 tFOTS 3.6940 tGradient 0.8870 tsec 8.2710 #GCMRL# 480 dt 11.200000 rms 0.434 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8570 tsec 1.1160 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 481 dt 11.200000 rms 0.434 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8620 tsec 2.5790 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 482 dt 11.200000 rms 0.434 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8870 tsec 1.7870 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 483 dt 11.200000 rms 0.434 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8790 tsec 1.7450 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 484 dt 11.200000 rms 0.433 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8600 tsec 3.1130 iter 0, gcam->neg = 14 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 485 dt 11.200000 rms 0.433 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8570 tsec 4.6420 #FOTS# QuadFit found better minimum quadopt=(dt=102.4,rms=0.432221) vs oldopt=(dt=128,rms=0.432359) iter 0, gcam->neg = 28 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 486 dt 102.400000 rms 0.432 0.176% neg 0 invalid 762 tFOTS 3.4520 tGradient 0.8850 tsec 6.7720 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 0.435061 #FOTS# QuadFit found better minimum quadopt=(dt=2.304,rms=0.434946) vs oldopt=(dt=2.88,rms=0.434949) iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 488 dt 2.304000 rms 0.435 0.019% neg 0 invalid 762 tFOTS 3.6720 tGradient 0.8280 tsec 7.1790 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.434959) vs oldopt=(dt=0.72,rms=0.434962) iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 489 dt 1.008000 rms 0.435 0.000% neg 0 invalid 762 tFOTS 3.5160 tGradient 0.8380 tsec 6.8310 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 17.967 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 0.434967 #FOTS# QuadFit found better minimum quadopt=(dt=16.6723,rms=0.433045) vs oldopt=(dt=11.52,rms=0.433224) iter 0, gcam->neg = 14 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 491 dt 16.672269 rms 0.433 0.439% neg 0 invalid 762 tFOTS 3.7090 tGradient 0.8420 tsec 6.7740 iter 0, gcam->neg = 82 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 492 dt 11.520000 rms 0.431 0.448% neg 0 invalid 762 tFOTS 3.6640 tGradient 0.8080 tsec 9.0270 #FOTS# QuadFit found better minimum quadopt=(dt=3.456,rms=0.430863) vs oldopt=(dt=2.88,rms=0.430872) iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 493 dt 3.456000 rms 0.431 0.000% neg 0 invalid 762 tFOTS 3.6620 tGradient 0.8310 tsec 5.7200 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 494 dt 3.456000 rms 0.431 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8120 tsec 1.7610 iter 0, gcam->neg = 8 after 4 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 0.436651 #GCMRL# 496 dt 0.000050 rms 0.437 0.000% neg 0 invalid 762 tFOTS 4.7090 tGradient 0.7970 tsec 5.7790 #GCAMreg# pass 0 level1 1 level2 1 tsec 12.601 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 0.436651 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 0.426801 #FOTS# QuadFit found better minimum quadopt=(dt=0.797203,rms=0.420597) vs oldopt=(dt=0.32,rms=0.422946) iter 0, gcam->neg = 471 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 499 dt 0.797203 rms 0.422 1.137% neg 0 invalid 762 tFOTS 3.7230 tGradient 0.3010 tsec 9.2710 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.421577) vs oldopt=(dt=0.08,rms=0.421641) #GCMRL# 500 dt 0.112000 rms 0.422 0.000% neg 0 invalid 762 tFOTS 3.7330 tGradient 0.3020 tsec 4.3270 #GCMRL# 501 dt 0.112000 rms 0.421 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2970 tsec 0.5530 #GCMRL# 502 dt 0.112000 rms 0.421 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2990 tsec 0.5550 #GCAMreg# pass 0 level1 0 level2 1 tsec 17.501 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 0.420951 #FOTS# QuadFit found better minimum quadopt=(dt=0.820463,rms=0.412955) vs oldopt=(dt=1.28,rms=0.415324) iter 0, gcam->neg = 845 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 504 dt 0.820463 rms 0.419 0.503% neg 0 invalid 762 tFOTS 3.7030 tGradient 0.3090 tsec 8.1860 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.418488) vs oldopt=(dt=0.08,rms=0.418545) #GCMRL# 505 dt 0.112000 rms 0.418 0.000% neg 0 invalid 762 tFOTS 3.6910 tGradient 0.2890 tsec 4.2670 #GCMRL# 506 dt 0.112000 rms 0.418 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2940 tsec 0.5520 #GCMRL# 507 dt 0.112000 rms 0.418 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2930 tsec 0.5530 #GCMRL# 508 dt 0.112000 rms 0.418 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2970 tsec 0.5840 #FOTS# QuadFit found better minimum quadopt=(dt=0.579268,rms=0.415737) vs oldopt=(dt=0.32,rms=0.41636) iter 0, gcam->neg = 43 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 509 dt 0.579268 rms 0.416 0.409% neg 0 invalid 762 tFOTS 3.6910 tGradient 0.2990 tsec 7.8350 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.415655) vs oldopt=(dt=0.32,rms=0.415675) #GCMRL# 510 dt 0.256000 rms 0.416 0.000% neg 0 invalid 762 tFOTS 3.6850 tGradient 0.3050 tsec 4.2750 #GCMRL# 511 dt 0.256000 rms 0.415 0.143% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2950 tsec 0.5610 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 512 dt 0.256000 rms 0.414 0.207% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2950 tsec 1.9310 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 513 dt 0.256000 rms 0.413 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.3050 tsec 1.4110 iter 0, gcam->neg = 20 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 514 dt 0.256000 rms 0.413 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2980 tsec 2.1450 iter 0, gcam->neg = 29 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 515 dt 0.256000 rms 0.413 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2990 tsec 2.4220 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.412732) vs oldopt=(dt=0.08,rms=0.412745) #GCMRL# 516 dt 0.112000 rms 0.413 0.000% neg 0 invalid 762 tFOTS 3.7090 tGradient 0.3040 tsec 4.3030 #GCMRL# 517 dt 0.112000 rms 0.413 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.3040 tsec 0.5740 #GCMRL# 518 dt 0.112000 rms 0.413 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.2970 tsec 0.5590 GCAMregister done in 3.73118 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 3942 tmin = 1.81522 Calls to gcamLabelEnergy 3311 tmin = 1.2031 Calls to gcamJacobianEnergy 3942 tmin = 1.03275 Calls to gcamSmoothnessEnergy 3942 tmin = 3.12065 Calls to gcamLogLikelihoodTerm 520 tmin = 0.51355 Calls to gcamLabelTerm 465 tmin = 5.81052 Calls to gcamJacobianTerm 520 tmin = 0.782967 Calls to gcamSmoothnessTerm 520 tmin = 0.253917 Calls to gcamComputeGradient 520 tmin = 13.8245 Calls to gcamComputeMetricProperties 5623 tmin = 1.9951 mri_ca_register took 0 hours, 34 minutes and 33 seconds. #VMPC# mri_ca_register VmPeak 3026552 FSRUNTIME@ mri_ca_register 0.5759 hours 12 threads #-------------------------------------- #@# SubCort Seg Thu Feb 9 15:58:37 CST 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname cn06.cluster.local machine x86_64 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/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 = 12 == reading 1 input volumes reading classifier array from /opt/freesurfer/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 6.09 Atlas used for the 3D morph was /opt/freesurfer/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 = 0.14720 ( 2) Left_Lateral_Ventricle (4): linear fit = 0.05 x + 0.0 (257 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (257 voxels, peak = 1), gca=8.0 gca peak = 0.20380 (13) mri peak = 0.10273 ( 4) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (225 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (225 voxels, peak = 3), gca=5.2 gca peak = 0.26283 (96) mri peak = 0.11494 (99) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (728 voxels, overlap=0.743) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (728 voxels, peak = 95), gca=94.6 gca peak = 0.15814 (97) mri peak = 0.11043 (97) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (605 voxels, overlap=0.621) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (605 voxels, peak = 99), gca=99.4 gca peak = 0.27624 (56) mri peak = 0.16462 (51) Right_Hippocampus: unreasonable value (49.6/51.0), not in range [50, 90] - rejecting gca peak = 0.28723 (59) mri peak = 0.14614 (54) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (691 voxels, overlap=0.252) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (691 voxels, peak = 55), gca=55.2 gca peak = 0.07623 (103) mri peak = 0.09702 (99) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38504 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38504 voxels, peak = 102), gca=102.5 gca peak = 0.07837 (105) mri peak = 0.10021 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40194 voxels, overlap=0.832) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40194 voxels, peak = 104), gca=104.5 gca peak = 0.10165 (58) mri peak = 0.04056 (53) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11592 voxels, overlap=0.889) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11592 voxels, peak = 59), gca=59.4 gca peak = 0.11113 (58) mri peak = 0.03460 (60) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (9642 voxels, overlap=0.552) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (9642 voxels, peak = 59), gca=59.4 gca peak = 0.27796 (67) mri peak = 0.15516 (67) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1048 voxels, overlap=0.868) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1048 voxels, peak = 66), gca=66.0 gca peak = 0.14473 (69) mri peak = 0.12120 (67) Left_Caudate (11): linear fit = 0.89 x + 0.0 (1120 voxels, overlap=0.534) Left_Caudate (11): linear fit = 0.89 x + 0.0 (1120 voxels, peak = 62), gca=61.8 gca peak = 0.14301 (56) mri peak = 0.07607 (57) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (11986 voxels, overlap=0.645) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (11986 voxels, peak = 60), gca=59.6 gca peak = 0.14610 (55) mri peak = 0.05646 (60) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (14656 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (14656 voxels, peak = 57), gca=57.5 gca peak = 0.16309 (85) mri peak = 0.09530 (84) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4714 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4714 voxels, peak = 84), gca=83.7 gca peak = 0.15172 (84) mri peak = 0.10383 (81) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (5272 voxels, overlap=0.772) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (5272 voxels, peak = 81), gca=81.1 gca peak = 0.30461 (58) mri peak = 0.11864 (57) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (379 voxels, overlap=0.741) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (379 voxels, peak = 56), gca=56.0 gca peak = 0.32293 (57) mri peak = 0.11214 (54) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (395 voxels, overlap=0.976) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (395 voxels, peak = 52), gca=52.2 gca peak = 0.11083 (90) mri peak = 0.09951 (88) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4178 voxels, overlap=0.733) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4178 voxels, peak = 89), gca=88.7 gca peak = 0.11393 (83) mri peak = 0.08202 (88) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3655 voxels, overlap=0.866) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3655 voxels, peak = 88), gca=88.4 gca peak = 0.08575 (81) mri peak = 0.08360 (73) Left_Putamen (12): linear fit = 0.96 x + 0.0 (2022 voxels, overlap=0.852) Left_Putamen (12): linear fit = 0.96 x + 0.0 (2022 voxels, peak = 78), gca=78.2 gca peak = 0.08618 (78) mri peak = 0.08777 (75) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1979 voxels, overlap=0.752) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1979 voxels, peak = 82), gca=81.5 gca peak = 0.08005 (78) mri peak = 0.16230 (80) Brain_Stem (16): linear fit = 1.03 x + 0.0 (9165 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.03 x + 0.0 (9165 voxels, peak = 81), gca=80.7 gca peak = 0.12854 (88) mri peak = 0.07204 (94) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1178 voxels, overlap=0.740) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1178 voxels, peak = 91), gca=91.1 gca peak = 0.15703 (87) mri peak = 0.11443 (90) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1156 voxels, overlap=0.636) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1156 voxels, peak = 89), gca=89.2 gca peak = 0.17522 (25) mri peak = 0.06532 ( 2) gca peak = 0.17113 (14) mri peak = 0.09978 ( 7) Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (87 voxels, overlap=0.263) Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (87 voxels, peak = 5), gca=5.1 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) 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_Hippocampus = 0.27624 (56) 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 setting label Right_Hippocampus based on Left_Hippocampus = 0.94 x + 0: 55 estimating mean gm scale to be 0.97 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 Left_Pallidum too bright - rescaling by 1.010 (from 1.025) to 100.4 (was 99.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31706 ( 7) mri peak = 0.14720 ( 2) Left_Lateral_Ventricle (4): linear fit = 0.14 x + 0.0 (257 voxels, overlap=0.376) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (257 voxels, peak = 1), gca=2.8 gca peak = 0.29334 ( 5) mri peak = 0.10273 ( 4) Right_Lateral_Ventricle (43): linear fit = 0.63 x + 0.0 (225 voxels, overlap=0.925) Right_Lateral_Ventricle (43): linear fit = 0.63 x + 0.0 (225 voxels, peak = 3), gca=3.2 gca peak = 0.21915 (92) mri peak = 0.11494 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (728 voxels, overlap=0.702) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (728 voxels, peak = 92), gca=91.5 gca peak = 0.17574 (98) mri peak = 0.11043 (97) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (605 voxels, overlap=0.876) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (605 voxels, peak = 96), gca=95.6 gca peak = 0.31682 (52) mri peak = 0.16462 (51) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (606 voxels, overlap=0.875) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (606 voxels, peak = 50), gca=50.2 gca peak = 0.33789 (53) mri peak = 0.14614 (54) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (691 voxels, overlap=0.676) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (691 voxels, peak = 53), gca=53.0 gca peak = 0.08109 (103) mri peak = 0.09702 (99) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38504 voxels, overlap=0.809) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38504 voxels, peak = 102), gca=102.5 gca peak = 0.08124 (104) mri peak = 0.10021 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40194 voxels, overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40194 voxels, peak = 103), gca=103.5 gca peak = 0.09372 (59) mri peak = 0.04056 (53) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11592 voxels, overlap=0.891) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11592 voxels, peak = 60), gca=60.5 gca peak = 0.11170 (60) mri peak = 0.03460 (60) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (9642 voxels, overlap=0.538) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (9642 voxels, peak = 62), gca=61.5 gca peak = 0.27794 (66) mri peak = 0.15516 (67) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1048 voxels, overlap=0.783) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1048 voxels, peak = 67), gca=67.0 gca peak = 0.13576 (62) mri peak = 0.12120 (67) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1120 voxels, overlap=0.925) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1120 voxels, peak = 62), gca=62.0 gca peak = 0.12994 (60) mri peak = 0.07607 (57) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (11986 voxels, overlap=0.866) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (11986 voxels, peak = 62), gca=61.5 gca peak = 0.15509 (58) mri peak = 0.05646 (60) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (14656 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (14656 voxels, peak = 59), gca=59.4 gca peak = 0.15882 (83) mri peak = 0.09530 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4714 voxels, overlap=0.878) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4714 voxels, peak = 84), gca=84.2 gca peak = 0.15722 (81) mri peak = 0.10383 (81) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5272 voxels, overlap=0.945) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5272 voxels, peak = 81), gca=81.0 gca peak = 0.30112 (56) mri peak = 0.11864 (57) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (379 voxels, overlap=0.842) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (379 voxels, peak = 56), gca=56.0 gca peak = 0.34721 (52) mri peak = 0.11214 (54) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (395 voxels, overlap=0.958) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (395 voxels, peak = 52), gca=52.0 gca peak = 0.10936 (87) mri peak = 0.09951 (88) Left_Thalamus (10): linear fit = 1.05 x + 0.0 (4178 voxels, overlap=0.721) Left_Thalamus (10): linear fit = 1.05 x + 0.0 (4178 voxels, peak = 92), gca=91.8 gca peak = 0.10519 (86) mri peak = 0.08202 (88) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3655 voxels, overlap=0.861) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3655 voxels, peak = 86), gca=85.6 gca peak = 0.08193 (78) mri peak = 0.08360 (73) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2022 voxels, overlap=0.849) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2022 voxels, peak = 79), gca=79.2 gca peak = 0.11252 (79) mri peak = 0.08777 (75) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1979 voxels, overlap=0.696) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1979 voxels, peak = 78), gca=77.8 gca peak = 0.08677 (81) mri peak = 0.16230 (80) Brain_Stem (16): linear fit = 1.01 x + 0.0 (9165 voxels, overlap=0.631) Brain_Stem (16): linear fit = 1.01 x + 0.0 (9165 voxels, peak = 82), gca=82.2 gca peak = 0.12038 (91) mri peak = 0.07204 (94) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1178 voxels, overlap=0.842) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1178 voxels, peak = 91), gca=90.5 gca peak = 0.17005 (89) mri peak = 0.11443 (90) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1156 voxels, overlap=0.609) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1156 voxels, peak = 89), gca=88.6 gca peak = 0.32031 (10) mri peak = 0.06532 ( 2) gca peak = 0.46125 ( 6) mri peak = 0.09978 ( 7) Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (87 voxels, overlap=0.983) Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (87 voxels, peak = 7), gca=6.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.18938 (26) gca peak Third_Ventricle = 0.32031 (10) gca peak CSF = 0.27810 (15) gca peak Left_Accumbens_area = 0.74940 (56) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89919 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.29930 (22) gca peak Right_Accumbens_area = 0.31657 (64) gca peak Right_vessel = 0.78757 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.92085 (13) gca peak WM_hypointensities = 0.11178 (76) gca peak non_WM_hypointensities = 0.08214 (41) gca peak Optic_Chiasm = 0.51962 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.71 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 76701 voxels changed in iteration 0 of unlikely voxel relabeling 305 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 48098 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 378 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 75782 changed. image ll: -2.111, PF=0.500 pass 2: 21629 changed. image ll: -2.110, PF=0.500 pass 3: 6095 changed. pass 4: 2105 changed. 49498 voxels changed in iteration 0 of unlikely voxel relabeling 361 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7892 voxels changed in iteration 0 of unlikely voxel relabeling 148 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 7001 voxels changed in iteration 0 of unlikely voxel relabeling 60 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6103 voxels changed in iteration 0 of unlikely voxel relabeling 32 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 2 with volume 4174 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 4 with volume 3521 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 7 with volume 101 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 154 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1781.990761 mri_ca_label stimesec 2.687871 mri_ca_label ru_maxrss 2114604 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 2770230 mri_ca_label ru_majflt 5 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1178 mri_ca_label ru_oublock 704 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 1935 mri_ca_label ru_nivcsw 714 auto-labeling took 28 minutes and 16 seconds. #-------------------------------------- #@# CC Seg Thu Feb 9 16:26:53 CST 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/cc_up.lta 31231_T2_3T will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/cc_up.lta reading aseg from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/aseg.auto_noCCseg.mgz reading norm from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/norm.mgz MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 41052 voxels in left wm, 48459 in right wm, xrange [121, 132] searching rotation angles z=[-6 8], y=[-10 4] searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 global minimum found at slice 126.0, rotations (-2.33, 1.18) final transformation (x=126.0, yr=-2.332, zr=1.182): 0.99896 -0.02063 -0.04068 8.81062; 0.02061 0.99979 -0.00084 28.52035; 0.04069 0.00000 0.99917 7.96796; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 min_x_fornix = 152 min_x_fornix = 150 min_x_fornix = 157 min_x_fornix = 140 min_x_fornix = 137 cc center is found at 128 97 115 eigenvectors: -0.00039 -0.00345 0.99999; 0.00858 -0.99996 -0.00345; 0.99996 0.00858 0.00042; MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab error in mid anterior detected - correcting... writing aseg with callosum to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #VMPC# mri_cc VmPeak 523872 mri_cc done #-------------------------------------- #@# Merge ASeg Thu Feb 9 16:27:24 CST 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Feb 9 16:27:24 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 1163 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 109 gm peak at 68 (68), valley at 17 (17) csf peak at 35, setting threshold to 57 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 64 (64), valley at 17 (17) csf peak at 32, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 54 seconds. #-------------------------------------------- #@# Mask BFS Thu Feb 9 16:29:19 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1368763 voxels in mask (pct= 8.16) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Feb 9 16:29:20 CST 2023 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 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 (104.0): 103.6 +- 5.2 [79.0 --> 125.0] CCS GM (72.0) : 71.0 +- 9.3 [30.0 --> 95.0] white_mean 103.587 white_sigma 5.17376 gray_mean 70.996 gray_sigma 9.28679 setting bottom of white matter range wm_low to 80.3 setting top of gray matter range gray_hi to 89.6 wm_low 80.2828 wm_hi 125 gray_low 30 gray_hi 89.5695 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 80.2828 wm_hi 125 gray_low 30 gray_hi 89.5695 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 89.5695, wm_low = 80.2828 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=89.5695, wmlow=80.2828 107719 voxels processed (0.64%) 49115 voxels white (0.29%) 58604 voxels non-white (0.35%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=75.2828, gray_hi=89.5695, wsize=13 187676 voxels tested (1.12%) 42286 voxels changed (0.25%) 40562 multi-scale searches (0.24%) Recovering bright white MRIrecoverBrightWhite() wm_low 80.2828 wm_hi 125 slack 5.17376 pct_thresh 0.33 intensity_thresh 130.174 nvox_thresh 8.58 48 voxels tested (0.00%) 32 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=75.2828, hithr=89.5695 smoothing input volume with sigma = 0.250 72281 voxels tested (0.43%) 15001 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 3107 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2155 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 5009 filled MRIfindBrightNonWM(): 224 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 0.9 minutes writing output to wm.seg.mgz... 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 0.43 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 3677 additional wm voxels added 0 additional wm voxels added SEG EDIT: 43427 voxels turned on, 24502 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 33 found - 33 modified | TOTAL: 55 pass 2 (xy-): 0 found - 33 modified | TOTAL: 55 pass 1 (yz+): 28 found - 28 modified | TOTAL: 83 pass 2 (yz+): 0 found - 28 modified | TOTAL: 83 pass 1 (yz-): 19 found - 19 modified | TOTAL: 102 pass 2 (yz-): 0 found - 19 modified | TOTAL: 102 pass 1 (xz+): 17 found - 17 modified | TOTAL: 119 pass 2 (xz+): 0 found - 17 modified | TOTAL: 119 pass 1 (xz-): 17 found - 17 modified | TOTAL: 136 pass 2 (xz-): 0 found - 17 modified | TOTAL: 136 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 17 found - 17 modified | TOTAL: 30 pass 2 (+++): 0 found - 17 modified | TOTAL: 30 pass 1 (+++): 15 found - 15 modified | TOTAL: 45 pass 2 (+++): 0 found - 15 modified | TOTAL: 45 pass 1 (+++): 10 found - 10 modified | TOTAL: 55 pass 2 (+++): 0 found - 10 modified | TOTAL: 55 Iteration Number : 1 pass 1 (++): 74 found - 74 modified | TOTAL: 74 pass 2 (++): 0 found - 74 modified | TOTAL: 74 pass 1 (+-): 88 found - 88 modified | TOTAL: 162 pass 2 (+-): 0 found - 88 modified | TOTAL: 162 pass 1 (--): 87 found - 87 modified | TOTAL: 249 pass 2 (--): 0 found - 87 modified | TOTAL: 249 pass 1 (-+): 76 found - 76 modified | TOTAL: 325 pass 2 (-+): 0 found - 76 modified | TOTAL: 325 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 4 found - 4 modified | TOTAL: 10 pass 2 (xy-): 0 found - 4 modified | TOTAL: 10 pass 1 (yz+): 6 found - 6 modified | TOTAL: 16 pass 2 (yz+): 0 found - 6 modified | TOTAL: 16 pass 1 (yz-): 4 found - 4 modified | TOTAL: 20 pass 2 (yz-): 0 found - 4 modified | TOTAL: 20 pass 1 (xz+): 5 found - 5 modified | TOTAL: 25 pass 2 (xz+): 0 found - 5 modified | TOTAL: 25 pass 1 (xz-): 2 found - 2 modified | TOTAL: 27 pass 2 (xz-): 0 found - 2 modified | TOTAL: 27 Iteration Number : 2 pass 1 (+++): 5 found - 5 modified | TOTAL: 5 pass 2 (+++): 0 found - 5 modified | TOTAL: 5 pass 1 (+++): 2 found - 2 modified | TOTAL: 7 pass 2 (+++): 0 found - 2 modified | TOTAL: 7 pass 1 (+++): 0 found - 0 modified | TOTAL: 7 pass 1 (+++): 4 found - 4 modified | TOTAL: 11 pass 2 (+++): 0 found - 4 modified | TOTAL: 11 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 5 found - 5 modified | TOTAL: 5 pass 2 (+-): 0 found - 5 modified | TOTAL: 5 pass 1 (--): 4 found - 4 modified | TOTAL: 9 pass 2 (--): 0 found - 4 modified | TOTAL: 9 pass 1 (-+): 1 found - 1 modified | TOTAL: 10 pass 2 (-+): 0 found - 1 modified | TOTAL: 10 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 570 (out of 497771: 0.114510) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Feb 9 16:31:20 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /opt/freesurfer/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 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61458; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.10023 -0.07470 -0.03428 -0.74716; 0.07125 1.16399 0.11696 -39.79147; 0.02882 -0.11532 1.00914 -8.61458; 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] = 1146 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) no need to search using seed (126, 111, 90), TAL = (2.0, -38.0, 17.0) talairach voxel to voxel transform 0.90437 0.06039 0.02372 3.28310; -0.05216 0.84588 -0.09981 32.75983; -0.03179 0.09494 0.97886 12.18651; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 111, 90) --> (2.0, -38.0, 17.0) done. filling took 1.3 minutes talairach cc position changed to (2.00, -38.00, 17.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -38.00, 17.00) SRC: (109.79, 112.04, 107.39) search lh wm seed point around talairach space (-16.00, -38.00, 17.00), SRC: (142.35, 110.16, 106.25) 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... cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Thu Feb 9 16:32:37 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 15 found - 15 modified | TOTAL: 16 pass 2 (yz+): 0 found - 15 modified | TOTAL: 16 pass 1 (yz-): 7 found - 7 modified | TOTAL: 23 pass 2 (yz-): 0 found - 7 modified | TOTAL: 23 pass 1 (xz+): 1 found - 1 modified | TOTAL: 24 pass 2 (xz+): 0 found - 1 modified | TOTAL: 24 pass 1 (xz-): 2 found - 2 modified | TOTAL: 26 pass 2 (xz-): 0 found - 2 modified | TOTAL: 26 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 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 28 (out of 245526: 0.011404) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.2.0 7.2.0 slice 50: 2547 vertices, 2715 faces slice 60: 9010 vertices, 9225 faces slice 70: 16463 vertices, 16761 faces slice 80: 25390 vertices, 25730 faces slice 90: 34756 vertices, 35082 faces slice 100: 44233 vertices, 44554 faces slice 110: 54640 vertices, 54988 faces slice 120: 65073 vertices, 65416 faces slice 130: 74900 vertices, 75244 faces slice 140: 84937 vertices, 85295 faces slice 150: 94062 vertices, 94351 faces slice 160: 101543 vertices, 101761 faces slice 170: 108085 vertices, 108345 faces slice 180: 114593 vertices, 114798 faces slice 190: 119857 vertices, 120068 faces slice 200: 123864 vertices, 123962 faces slice 210: 125468 vertices, 125476 faces slice 220: 125468 vertices, 125476 faces slice 230: 125468 vertices, 125476 faces slice 240: 125468 vertices, 125476 faces slice 250: 125468 vertices, 125476 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; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 125468 voxel in cpt #1: X=-8 [v=125468,e=376428,f=250952] located at (-25.194702, -9.598679, 18.246956) For the whole surface: X=-8 [v=125468,e=376428,f=250952] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Feb 9 16:32:40 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 9 found - 9 modified | TOTAL: 12 pass 2 (yz+): 0 found - 9 modified | TOTAL: 12 pass 1 (yz-): 9 found - 9 modified | TOTAL: 21 pass 2 (yz-): 0 found - 9 modified | TOTAL: 21 pass 1 (xz+): 3 found - 3 modified | TOTAL: 24 pass 2 (xz+): 0 found - 3 modified | TOTAL: 24 pass 1 (xz-): 0 found - 0 modified | TOTAL: 24 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 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 = 26 (out of 245146: 0.010606) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.2.0 7.2.0 slice 50: 1201 vertices, 1298 faces slice 60: 6515 vertices, 6739 faces slice 70: 13632 vertices, 13921 faces slice 80: 21697 vertices, 22023 faces slice 90: 31634 vertices, 31967 faces slice 100: 41055 vertices, 41403 faces slice 110: 51597 vertices, 51958 faces slice 120: 62030 vertices, 62379 faces slice 130: 72045 vertices, 72409 faces slice 140: 82176 vertices, 82499 faces slice 150: 92035 vertices, 92386 faces slice 160: 99839 vertices, 100111 faces slice 170: 106898 vertices, 107168 faces slice 180: 113708 vertices, 113914 faces slice 190: 119852 vertices, 120064 faces slice 200: 124773 vertices, 124922 faces slice 210: 127090 vertices, 127105 faces slice 220: 127112 vertices, 127122 faces slice 230: 127112 vertices, 127122 faces slice 240: 127112 vertices, 127122 faces slice 250: 127112 vertices, 127122 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; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 127112 voxel in cpt #1: X=-10 [v=127112,e=381366,f=254244] located at (27.760353, -5.884181, 17.864229) For the whole surface: X=-10 [v=127112,e=381366,f=254244] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Feb 9 16:32:43 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Thu Feb 9 16:32:43 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 277145 of (277145 277148) to complete... Waiting for PID 277148 of (277145 277148) 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 (277145 277148) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Thu Feb 9 16:32:46 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Thu Feb 9 16:32:46 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 277215 of (277215 277218) to complete... Waiting for PID 277218 of (277215 277218) 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 = 46.8 mm, total surface area = 67858 mm^2 step 000: RMS=0.148 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.080 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.030 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 76.383542 mris_inflate stimesec 1.291861 mris_inflate ru_maxrss 199088 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 467369 mris_inflate ru_majflt 11 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1944 mris_inflate ru_oublock 8848 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 13669 mris_inflate ru_nivcsw 2166 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.4 mm, total surface area = 68656 mm^2 step 000: RMS=0.146 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.030 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 74.800080 mris_inflate stimesec 0.333915 mris_inflate ru_maxrss 202584 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 121544 mris_inflate ru_majflt 7 mris_inflate ru_nswap 0 mris_inflate ru_inblock 38 mris_inflate ru_oublock 8960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 14069 mris_inflate ru_nivcsw 2485 PIDs (277215 277218) completed and logs appended. #-------------------------------------------- #@# QSphere lh Thu Feb 9 16:33:02 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Thu Feb 9 16:33:02 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 277520 of (277520 277523) to complete... Waiting for PID 277523 of (277520 277523) 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: 12 scaling brain by 0.305... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.60 (0.00-->6.06) (max @ vno 46001 --> 46002) face area 0.03 +- 0.03 (-0.07-->0.57) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.429, avgs=0 005/300: dt: 0.9000, rms radial error=177.167, avgs=0 010/300: dt: 0.9000, rms radial error=176.607, avgs=0 015/300: dt: 0.9000, rms radial error=175.871, avgs=0 020/300: dt: 0.9000, rms radial error=175.033, avgs=0 025/300: dt: 0.9000, rms radial error=174.137, avgs=0 030/300: dt: 0.9000, rms radial error=173.208, avgs=0 035/300: dt: 0.9000, rms radial error=172.263, avgs=0 040/300: dt: 0.9000, rms radial error=171.310, avgs=0 045/300: dt: 0.9000, rms radial error=170.355, avgs=0 050/300: dt: 0.9000, rms radial error=169.402, avgs=0 055/300: dt: 0.9000, rms radial error=168.454, avgs=0 060/300: dt: 0.9000, rms radial error=167.509, avgs=0 065/300: dt: 0.9000, rms radial error=166.568, avgs=0 070/300: dt: 0.9000, rms radial error=165.633, avgs=0 075/300: dt: 0.9000, rms radial error=164.702, avgs=0 080/300: dt: 0.9000, rms radial error=163.776, avgs=0 085/300: dt: 0.9000, rms radial error=162.855, avgs=0 090/300: dt: 0.9000, rms radial error=161.939, avgs=0 095/300: dt: 0.9000, rms radial error=161.028, avgs=0 100/300: dt: 0.9000, rms radial error=160.122, avgs=0 105/300: dt: 0.9000, rms radial error=159.221, avgs=0 110/300: dt: 0.9000, rms radial error=158.325, avgs=0 115/300: dt: 0.9000, rms radial error=157.435, avgs=0 120/300: dt: 0.9000, rms radial error=156.550, avgs=0 125/300: dt: 0.9000, rms radial error=155.669, avgs=0 130/300: dt: 0.9000, rms radial error=154.793, avgs=0 135/300: dt: 0.9000, rms radial error=153.922, avgs=0 140/300: dt: 0.9000, rms radial error=153.056, avgs=0 145/300: dt: 0.9000, rms radial error=152.195, avgs=0 150/300: dt: 0.9000, rms radial error=151.338, avgs=0 155/300: dt: 0.9000, rms radial error=150.486, avgs=0 160/300: dt: 0.9000, rms radial error=149.639, avgs=0 165/300: dt: 0.9000, rms radial error=148.796, avgs=0 170/300: dt: 0.9000, rms radial error=147.958, avgs=0 175/300: dt: 0.9000, rms radial error=147.124, avgs=0 180/300: dt: 0.9000, rms radial error=146.295, avgs=0 185/300: dt: 0.9000, rms radial error=145.471, avgs=0 190/300: dt: 0.9000, rms radial error=144.652, avgs=0 195/300: dt: 0.9000, rms radial error=143.838, avgs=0 200/300: dt: 0.9000, rms radial error=143.028, avgs=0 205/300: dt: 0.9000, rms radial error=142.223, avgs=0 210/300: dt: 0.9000, rms radial error=141.422, avgs=0 215/300: dt: 0.9000, rms radial error=140.625, avgs=0 220/300: dt: 0.9000, rms radial error=139.833, avgs=0 225/300: dt: 0.9000, rms radial error=139.046, avgs=0 230/300: dt: 0.9000, rms radial error=138.262, avgs=0 235/300: dt: 0.9000, rms radial error=137.483, avgs=0 240/300: dt: 0.9000, rms radial error=136.709, avgs=0 245/300: dt: 0.9000, rms radial error=135.939, avgs=0 250/300: dt: 0.9000, rms radial error=135.173, avgs=0 255/300: dt: 0.9000, rms radial error=134.411, avgs=0 260/300: dt: 0.9000, rms radial error=133.654, avgs=0 265/300: dt: 0.9000, rms radial error=132.900, avgs=0 270/300: dt: 0.9000, rms radial error=132.151, avgs=0 275/300: dt: 0.9000, rms radial error=131.407, avgs=0 280/300: dt: 0.9000, rms radial error=130.666, avgs=0 285/300: dt: 0.9000, rms radial error=129.930, avgs=0 290/300: dt: 0.9000, rms radial error=129.198, avgs=0 295/300: dt: 0.9000, rms radial error=128.469, avgs=0 300/300: dt: 0.9000, rms radial error=127.745, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14700.63 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00043 epoch 2 (K=40.0), pass 1, starting sse = 2394.70 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00033 epoch 3 (K=160.0), pass 1, starting sse = 228.06 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/19 = 0.01008 epoch 4 (K=640.0), pass 1, starting sse = 7.06 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.26/32 = 0.00810 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0414 hours FSRUNTIME@ mris_sphere 0.0414 hours 12 threads #VMPC# mris_sphere VmPeak 1247944 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: 12 scaling brain by 0.305... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.59 (0.00-->7.22) (max @ vno 90922 --> 90923) face area 0.03 +- 0.03 (-0.11-->0.57) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.204, avgs=0 005/300: dt: 0.9000, rms radial error=176.945, avgs=0 010/300: dt: 0.9000, rms radial error=176.388, avgs=0 015/300: dt: 0.9000, rms radial error=175.657, avgs=0 020/300: dt: 0.9000, rms radial error=174.823, avgs=0 025/300: dt: 0.9000, rms radial error=173.931, avgs=0 030/300: dt: 0.9000, rms radial error=173.006, avgs=0 035/300: dt: 0.9000, rms radial error=172.065, avgs=0 040/300: dt: 0.9000, rms radial error=171.117, avgs=0 045/300: dt: 0.9000, rms radial error=170.167, avgs=0 050/300: dt: 0.9000, rms radial error=169.218, avgs=0 055/300: dt: 0.9000, rms radial error=168.271, avgs=0 060/300: dt: 0.9000, rms radial error=167.329, avgs=0 065/300: dt: 0.9000, rms radial error=166.391, avgs=0 070/300: dt: 0.9000, rms radial error=165.458, avgs=0 075/300: dt: 0.9000, rms radial error=164.530, avgs=0 080/300: dt: 0.9000, rms radial error=163.606, avgs=0 085/300: dt: 0.9000, rms radial error=162.688, avgs=0 090/300: dt: 0.9000, rms radial error=161.774, avgs=0 095/300: dt: 0.9000, rms radial error=160.866, avgs=0 100/300: dt: 0.9000, rms radial error=159.962, avgs=0 105/300: dt: 0.9000, rms radial error=159.064, avgs=0 110/300: dt: 0.9000, rms radial error=158.170, avgs=0 115/300: dt: 0.9000, rms radial error=157.282, avgs=0 120/300: dt: 0.9000, rms radial error=156.398, avgs=0 125/300: dt: 0.9000, rms radial error=155.519, avgs=0 130/300: dt: 0.9000, rms radial error=154.645, avgs=0 135/300: dt: 0.9000, rms radial error=153.776, avgs=0 140/300: dt: 0.9000, rms radial error=152.912, avgs=0 145/300: dt: 0.9000, rms radial error=152.052, avgs=0 150/300: dt: 0.9000, rms radial error=151.197, avgs=0 155/300: dt: 0.9000, rms radial error=150.347, avgs=0 160/300: dt: 0.9000, rms radial error=149.501, avgs=0 165/300: dt: 0.9000, rms radial error=148.660, avgs=0 170/300: dt: 0.9000, rms radial error=147.823, avgs=0 175/300: dt: 0.9000, rms radial error=146.992, avgs=0 180/300: dt: 0.9000, rms radial error=146.164, avgs=0 185/300: dt: 0.9000, rms radial error=145.342, avgs=0 190/300: dt: 0.9000, rms radial error=144.523, avgs=0 195/300: dt: 0.9000, rms radial error=143.710, avgs=0 200/300: dt: 0.9000, rms radial error=142.901, avgs=0 205/300: dt: 0.9000, rms radial error=142.096, avgs=0 210/300: dt: 0.9000, rms radial error=141.296, avgs=0 215/300: dt: 0.9000, rms radial error=140.500, avgs=0 220/300: dt: 0.9000, rms radial error=139.708, avgs=0 225/300: dt: 0.9000, rms radial error=138.921, avgs=0 230/300: dt: 0.9000, rms radial error=138.139, avgs=0 235/300: dt: 0.9000, rms radial error=137.360, avgs=0 240/300: dt: 0.9000, rms radial error=136.586, avgs=0 245/300: dt: 0.9000, rms radial error=135.817, avgs=0 250/300: dt: 0.9000, rms radial error=135.051, avgs=0 255/300: dt: 0.9000, rms radial error=134.290, avgs=0 260/300: dt: 0.9000, rms radial error=133.533, avgs=0 265/300: dt: 0.9000, rms radial error=132.781, avgs=0 270/300: dt: 0.9000, rms radial error=132.032, avgs=0 275/300: dt: 0.9000, rms radial error=131.288, avgs=0 280/300: dt: 0.9000, rms radial error=130.548, avgs=0 285/300: dt: 0.9000, rms radial error=129.812, avgs=0 290/300: dt: 0.9000, rms radial error=129.081, avgs=0 295/300: dt: 0.9000, rms radial error=128.353, avgs=0 300/300: dt: 0.9000, rms radial error=127.629, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14892.58 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00028 epoch 2 (K=40.0), pass 1, starting sse = 2439.62 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00027 epoch 3 (K=160.0), pass 1, starting sse = 225.75 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/18 = 0.00909 epoch 4 (K=640.0), pass 1, starting sse = 6.89 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/23 = 0.00499 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0399 hours FSRUNTIME@ mris_sphere 0.0399 hours 12 threads #VMPC# mris_sphere VmPeak 1250372 mris_sphere done PIDs (277520 277523) completed and logs appended. #@# Fix Topology lh Thu Feb 9 16:35:31 CST 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 31231_T2_3T lh #@# Fix Topology rh Thu Feb 9 16:35:31 CST 2023 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 31231_T2_3T rh Waiting for PID 2004 of (2004 2007) to complete... Waiting for PID 2007 of (2004 2007) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 31231_T2_3T 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=-8 (nv=125468, nf=250952, ne=376428, g=5) 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... 1092 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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: -9.6940 (-4.8470) -vertex loglikelihood: -6.8875 (-3.4437) -normal dot loglikelihood: -3.6220 (-3.6220) -quad curv loglikelihood: -6.1718 (-3.0859) Total Loglikelihood : -26.3754 CORRECTING DEFECT 0 (vertices=66, convex hull=32, v0=52053) After retessellation of defect 0 (v0=52053), euler #=-11 (124785,374065,249269) : difference with theory (-12) = -1 CORRECTING DEFECT 1 (vertices=19, convex hull=41, v0=54359) After retessellation of defect 1 (v0=54359), euler #=-10 (124788,374086,249288) : difference with theory (-11) = -1 CORRECTING DEFECT 2 (vertices=19, convex hull=29, v0=67792) After retessellation of defect 2 (v0=67792), euler #=-9 (124792,374104,249303) : difference with theory (-10) = -1 CORRECTING DEFECT 3 (vertices=5, convex hull=15, v0=67859) After retessellation of defect 3 (v0=67859), euler #=-8 (124793,374110,249309) : difference with theory (-9) = -1 CORRECTING DEFECT 4 (vertices=18, convex hull=29, v0=75508) After retessellation of defect 4 (v0=75508), euler #=-7 (124797,374132,249328) : difference with theory (-8) = -1 CORRECTING DEFECT 5 (vertices=42, convex hull=41, v0=78875) After retessellation of defect 5 (v0=78875), euler #=-6 (124801,374160,249353) : difference with theory (-7) = -1 CORRECTING DEFECT 6 (vertices=31, convex hull=27, v0=82597) After retessellation of defect 6 (v0=82597), euler #=-5 (124808,374192,249379) : difference with theory (-6) = -1 CORRECTING DEFECT 7 (vertices=53, convex hull=34, v0=85662) After retessellation of defect 7 (v0=85662), euler #=-4 (124819,374235,249412) : difference with theory (-5) = -1 CORRECTING DEFECT 8 (vertices=45, convex hull=64, v0=86544) After retessellation of defect 8 (v0=86544), euler #=-3 (124838,374317,249476) : difference with theory (-4) = -1 CORRECTING DEFECT 9 (vertices=27, convex hull=71, v0=86867) After retessellation of defect 9 (v0=86867), euler #=-2 (124852,374390,249536) : difference with theory (-3) = -1 CORRECTING DEFECT 10 (vertices=37, convex hull=35, v0=87736) After retessellation of defect 10 (v0=87736), euler #=-1 (124858,374422,249563) : difference with theory (-2) = -1 CORRECTING DEFECT 11 (vertices=67, convex hull=94, v0=88801) After retessellation of defect 11 (v0=88801), euler #=0 (124891,374564,249673) : difference with theory (-1) = -1 CORRECTING DEFECT 12 (vertices=53, convex hull=38, v0=91717) After retessellation of defect 12 (v0=91717), euler #=1 (124900,374602,249703) : difference with theory (0) = -1 CORRECTING DEFECT 13 (vertices=87, convex hull=56, v0=93897) After retessellation of defect 13 (v0=93897), euler #=2 (124909,374652,249745) : difference with theory (1) = -1 CORRECTING DEFECT 14 (vertices=121, convex hull=125, v0=100848) After retessellation of defect 14 (v0=100848), euler #=2 (124979,374931,249954) : 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-->7.46) (max @ vno 100271 --> 104491) 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-->7.46) (max @ vno 100271 --> 104491) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 61 mutations (40.1%), 91 crossovers (59.9%), 15 vertices were eliminated building final representation... 489 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=124979, nf=249954, ne=374931, g=0) writing corrected surface to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 73 intersecting 001: 10 intersecting 002: 9 intersecting 003: 8 intersecting step 1 with no progress (num=8, old_num=8) 004: 8 intersecting step 2 with no progress (num=8, old_num=8) 005: 8 intersecting step 3 with no progress (num=8, old_num=8) 006: 8 intersecting step 4 with no progress (num=8, old_num=8) 007: 8 intersecting step 5 with no progress (num=8, old_num=8) 008: 8 intersecting step 6 with no progress (num=8, old_num=8) 009: 8 intersecting step 7 with no progress (num=8, old_num=8) 010: 8 intersecting step 8 with no progress (num=8, old_num=8) 011: 8 intersecting step 9 with no progress (num=8, old_num=8) 012: 8 intersecting step 10 with no progress (num=8, old_num=8) 013: 8 intersecting step 11 with no progress (num=8, old_num=8) 014: 8 intersecting step 12 with no progress (num=8, old_num=8) 015: 8 intersecting step 13 with no progress (num=8, old_num=8) 016: 8 intersecting step 14 with no progress (num=8, old_num=8) 017: 8 intersecting step 15 with no progress (num=8, old_num=8) 018: 8 intersecting step 16 with no progress (num=8, old_num=8) terminating search with 8 intersecting topology fixing took 1.5 minutes FSRUNTIME@ mris_fix_topology lh 0.0247 hours 12 threads #VMPC# mris_fix_topology VmPeak 1548292 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 31231_T2_3T 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=-10 (nv=127112, nf=254244, ne=381366, g=6) 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 9 iterations marking ambiguous vertices... 878 ambiguous faces found in tessellation segmenting defects... 14 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 14 defects to be corrected 0 vertices coincident reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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: -9.7103 (-4.8551) -vertex loglikelihood: -6.8063 (-3.4031) -normal dot loglikelihood: -3.6219 (-3.6219) -quad curv loglikelihood: -6.2957 (-3.1478) Total Loglikelihood : -26.4340 CORRECTING DEFECT 0 (vertices=19, convex hull=22, v0=31412) After retessellation of defect 0 (v0=31412), euler #=-11 (126562,379494,252921) : difference with theory (-11) = 0 CORRECTING DEFECT 1 (vertices=15, convex hull=27, v0=34808) After retessellation of defect 1 (v0=34808), euler #=-10 (126568,379522,252944) : difference with theory (-10) = 0 CORRECTING DEFECT 2 (vertices=6, convex hull=12, v0=37466) After retessellation of defect 2 (v0=37466), euler #=-9 (126569,379529,252951) : difference with theory (-9) = 0 CORRECTING DEFECT 3 (vertices=11, convex hull=29, v0=51250) After retessellation of defect 3 (v0=51250), euler #=-8 (126572,379551,252971) : difference with theory (-8) = 0 CORRECTING DEFECT 4 (vertices=83, convex hull=36, v0=52306) After retessellation of defect 4 (v0=52306), euler #=-7 (126581,379590,253002) : difference with theory (-7) = 0 CORRECTING DEFECT 5 (vertices=5, convex hull=21, v0=56930) After retessellation of defect 5 (v0=56930), euler #=-6 (126583,379601,253012) : difference with theory (-6) = 0 CORRECTING DEFECT 6 (vertices=35, convex hull=31, v0=58891) After retessellation of defect 6 (v0=58891), euler #=-5 (126589,379630,253036) : difference with theory (-5) = 0 CORRECTING DEFECT 7 (vertices=48, convex hull=32, v0=67517) After retessellation of defect 7 (v0=67517), euler #=-4 (126596,379662,253062) : difference with theory (-4) = 0 CORRECTING DEFECT 8 (vertices=164, convex hull=105, v0=84794) After retessellation of defect 8 (v0=84794), euler #=-3 (126658,379902,253241) : difference with theory (-3) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=33, v0=89885) After retessellation of defect 9 (v0=89885), euler #=-2 (126661,379921,253258) : difference with theory (-2) = 0 CORRECTING DEFECT 10 (vertices=95, convex hull=93, v0=93720) After retessellation of defect 10 (v0=93720), euler #=-1 (126694,380062,253367) : difference with theory (-1) = 0 CORRECTING DEFECT 11 (vertices=52, convex hull=24, v0=94249) After retessellation of defect 11 (v0=94249), euler #=0 (126699,380082,253383) : difference with theory (0) = 0 CORRECTING DEFECT 12 (vertices=6, convex hull=23, v0=115080) After retessellation of defect 12 (v0=115080), euler #=1 (126701,380094,253394) : difference with theory (1) = 0 CORRECTING DEFECT 13 (vertices=6, convex hull=16, v0=127090) After retessellation of defect 13 (v0=127090), euler #=2 (126701,380097,253398) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.10-->7.28) (max @ vno 92537 --> 96724) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.10-->7.28) (max @ vno 92537 --> 96724) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 32 mutations (39.0%), 50 crossovers (61.0%), 0 vertices were eliminated building final representation... 411 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=126701, nf=253398, ne=380097, g=0) writing corrected surface to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 65 intersecting 001: 4 intersecting terminating search with 0 intersecting topology fixing took 1.1 minutes FSRUNTIME@ mris_fix_topology rh 0.0189 hours 12 threads #VMPC# mris_fix_topology VmPeak 1549920 PIDs (2004 2007) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 124979 - 374931 + 249954 = 2 --> 0 holes F =2V-4: 249954 = 249958-4 (0) 2E=3F: 749862 = 749862 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 126701 - 380097 + 253398 = 2 --> 0 holes F =2V-4: 253398 = 253402-4 (0) 2E=3F: 760194 = 760194 (0) total defect index = 0 Thu Feb 9 16:37:01 CST 2023 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts /opt/freesurfer/bin/defect2seg --s 31231_T2_3T freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b defect2seg 7.2.0 Linux cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux pid 4176 mri_label2vol --defects /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig.nofix /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.defect_labels /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz 1000 0 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/surface.defects.mgz mris_defects_pointset -s /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig.nofix -d /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.defect_labels -o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.defects.pointset Reading in surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig.nofix Reading in defect segmentation /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.defect_labels #VMPC# mris_defects_pointset 1651612 mris_defects_pointset done mri_label2vol --defects /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig.nofix /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.defect_labels /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/surface.defects.mgz 2000 1 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/surface.defects.mgz mris_defects_pointset -s /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig.nofix -d /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.defect_labels -o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.defects.pointset Reading in surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig.nofix Reading in defect segmentation /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.defect_labels #VMPC# mris_defects_pointset 997672 mris_defects_pointset done Started at Thu Feb 9 16:37:01 CST 2023 Ended at Thu Feb 9 16:37:05 CST 2023 Defect2seg-Run-Time-Sec 4 Defect2seg-Run-Time-Min 0.08 Defect2seg-Run-Time-Hours 0.00 tkmeditfv 31231_T2_3T brain.finalsurfs.mgz -defect defect2seg Done mris_remesh --remesh --iters 3 --input /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig.premesh --output /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.710176 remeshing to edge length 0.710176 with 3 iterations avg qual before : 0.892856 after: 0.970977 Removing intersections Remeshed surface quality stats nv0 = 124979 nv = 130564 1.04469 Area 261124 0.30240 0.03380 0.078228 0.4791 Corner 783372 60.00000 8.83104 19.800324 139.8555 Edge 391686 0.84370 0.08269 0.445500 1.2439 Hinge 391686 9.55299 9.99526 0.000002 146.8404 mris_remesh done mris_remesh --remesh --iters 3 --input /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig.premesh --output /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.708895 remeshing to edge length 0.708895 with 3 iterations avg qual before : 0.891377 after: 0.971323 Removing intersections removing intersecting faces 000: 2 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 126701 nv = 132449 1.04537 Area 264894 0.30100 0.03354 0.028644 0.4650 Corner 794682 60.00000 8.78230 13.851017 144.7851 Edge 397341 0.84164 0.08201 0.123978 1.2609 Hinge 397341 9.46288 9.93151 0.000021 139.5066 mris_remesh done /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig rm -f ../surf/lh.inflated /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Thu Feb 9 16:38:10 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 232032 voxels (1.38%) border gray 262669 voxels (1.57%) 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=25802, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 98.5 +- 9.2 [70.0 --> 110.0] CCS GM (70.0) : 69.6 +- 11.3 [30.0 --> 110.0] white_mean = 98.4842 +/- 9.17458, gray_mean = 69.6347 +/- 11.3105 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=249 nbins=250 intensity peaks found at WM=105+-6.1, GM=62+-13.0 white_mode = 105, gray_mode = 62 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 50.7 (was 70.000000) setting MAX_BORDER_WHITE to 114.2 (was 105.000000) setting MIN_BORDER_WHITE to 62.0 (was 85.000000) setting MAX_CSF to 39.4 (was 40.000000) setting MAX_GRAY to 95.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 50.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 28.1 (was 40.000000) When placing the white surface white_border_hi = 114.175; white_border_low = 62; white_outside_low = 50.6895; white_inside_hi = 120; white_outside_hi = 114.175; When placing the pial surface pial_border_hi = 50.6895; pial_border_low = 28.0684; pial_outside_low = 10; pial_inside_hi = 95.8254; pial_outside_hi = 45.0342; #VMPC# mris_autodet_gwstats VmPeak 1032420 mris_autodet_gwstats done #-------------------------------------------- #@# AutoDetGWStats rh Thu Feb 9 16:38:13 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 232032 voxels (1.38%) border gray 262669 voxels (1.57%) 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=25802, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 98.5 +- 9.2 [70.0 --> 110.0] CCS GM (70.0) : 69.6 +- 11.3 [30.0 --> 110.0] white_mean = 98.4842 +/- 9.17458, gray_mean = 69.6347 +/- 11.3105 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=249 nbins=250 intensity peaks found at WM=105+-6.1, GM=62+-13.0 white_mode = 105, gray_mode = 62 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 50.7 (was 70.000000) setting MAX_BORDER_WHITE to 114.2 (was 105.000000) setting MIN_BORDER_WHITE to 62.0 (was 85.000000) setting MAX_CSF to 39.4 (was 40.000000) setting MAX_GRAY to 95.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 50.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 28.1 (was 40.000000) When placing the white surface white_border_hi = 114.175; white_border_low = 62; white_outside_low = 50.6895; white_inside_hi = 120; white_outside_hi = 114.175; When placing the pial surface pial_border_hi = 50.6895; pial_border_low = 28.0684; pial_outside_low = 10; pial_inside_hi = 95.8254; pial_outside_hi = 45.0342; #VMPC# mris_autodet_gwstats VmPeak 1034516 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Thu Feb 9 16:38:16 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 12 --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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 12 --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 261124 0.26741 0.06283 0.003522 0.6185 Corner 783372 60.00000 9.50282 9.221368 134.9251 Edge 391686 0.78972 0.11385 0.064990 1.2681 Hinge 391686 6.41222 6.38644 0.000007 124.9863 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 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 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6252, nmarked2=26, nripped=6252 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 65282: xyz = (-50.596,2.59016,31.1405) oxyz = (-50.596,2.59016,31.1405) wxzy = (-50.596,2.59016,31.1405) pxyz = (0,0,0) CBVO Creating mask 130564 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=6252 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6252, nmarked2=26, nripped=6252 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=2 had to be increased for 185 vertices, nripped=6252 mean border=77.0, 37 (37) missing vertices, mean dist 0.4 [0.6 (%33.9)->0.9 (%66.1))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0181 min Finding expansion regions mean absolute distance = 0.76 +- 0.92 4976 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=cn06., 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=4205253.5, rms=12.784 001: dt: 0.5000, sse=2240481.2, rms=9.195 (28.072%) 002: dt: 0.5000, sse=1379317.1, rms=7.050 (23.333%) 003: dt: 0.5000, sse=929217.6, rms=5.640 (19.999%) 004: dt: 0.5000, sse=717944.4, rms=4.823 (14.490%) 005: dt: 0.5000, sse=608690.1, rms=4.331 (10.197%) 006: dt: 0.5000, sse=563872.3, rms=4.118 (4.913%) 007: dt: 0.5000, sse=534252.6, rms=3.964 (3.734%) rms = 3.9241/3.9643, sse=527449.4/534252.6, time step reduction 1 of 3 to 0.250 0 0 1 008: dt: 0.5000, sse=527449.4, rms=3.924 (1.013%) 009: dt: 0.2500, sse=293318.0, rms=2.420 (38.333%) 010: dt: 0.2500, sse=245792.9, rms=1.983 (18.072%) 011: dt: 0.2500, sse=233920.2, rms=1.850 (6.692%) 012: dt: 0.2500, sse=225942.5, rms=1.761 (4.807%) rms = 1.7154/1.7610, sse=222222.3/225942.5, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=222222.3, rms=1.715 (2.590%) 014: dt: 0.1250, sse=210807.9, rms=1.571 (8.391%) rms = 1.5454/1.5714, sse=208941.1/210807.9, time step reduction 3 of 3 to 0.062 0 0 1 015: dt: 0.1250, sse=208941.1, rms=1.545 (1.657%) maximum number of reductions reached, breaking from loop positioning took 1.1 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=6252 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 1 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 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6544, nmarked2=61, nripped=6544 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=1 had to be increased for 134 vertices, nripped=6544 mean border=81.4, 45 (0) missing vertices, mean dist -0.3 [0.5 (%75.5)->0.3 (%24.5))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0114 min Finding expansion regions mean absolute distance = 0.43 +- 0.66 6012 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=cn06., 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=1160129.6, rms=6.222 016: dt: 0.5000, sse=674605.9, rms=4.379 (29.621%) rms = 4.3321/4.3790, sse=662917.7/674605.9, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=662917.6, rms=4.332 (1.072%) 018: dt: 0.2500, sse=369550.8, rms=2.627 (39.358%) 019: dt: 0.2500, sse=316573.4, rms=2.181 (16.970%) 020: dt: 0.2500, sse=290298.2, rms=1.913 (12.275%) 021: dt: 0.2500, sse=270972.1, rms=1.692 (11.598%) 022: dt: 0.2500, sse=260157.7, rms=1.532 (9.420%) 023: dt: 0.2500, sse=251337.7, rms=1.407 (8.173%) 024: dt: 0.2500, sse=248637.1, rms=1.356 (3.650%) rms = 1.3122/1.3556, sse=247063.5/248637.1, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=247063.5, rms=1.312 (3.205%) 026: dt: 0.1250, sse=240642.2, rms=1.204 (8.211%) rms = 1.1894/1.2044, sse=241431.3/240642.2, time step reduction 3 of 3 to 0.062 0 1 1 027: dt: 0.1250, sse=241431.3, rms=1.189 (1.250%) maximum number of reductions reached, breaking from loop positioning took 0.8 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=6544 removing 4 vertices from ripped group in thread:0 removing 4 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 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=6582, nmarked2=64, nripped=6582 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 241 vertices, nripped=6582 mean border=83.9, 78 (0) missing vertices, mean dist -0.1 [0.3 (%71.6)->0.2 (%28.4))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0065 min Finding expansion regions mean absolute distance = 0.26 +- 0.41 3922 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=cn06., 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=521294.8, rms=3.625 028: dt: 0.5000, sse=465880.7, rms=3.292 (9.183%) rms = 3.7073/3.2921, sse=534052.6/465880.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=301479.0, rms=2.075 (36.963%) 030: dt: 0.2500, sse=249999.2, rms=1.502 (27.605%) 031: dt: 0.2500, sse=235814.2, rms=1.294 (13.889%) 032: dt: 0.2500, sse=233067.3, rms=1.234 (4.582%) rms = 1.2178/1.2344, sse=232072.6/233067.3, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=232072.6, rms=1.218 (1.347%) 034: dt: 0.1250, sse=222616.2, rms=1.064 (12.600%) rms = 1.0499/1.0644, sse=222300.8/222616.2, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=222300.8, rms=1.050 (1.362%) maximum number of reductions reached, breaking from loop positioning took 0.6 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=6582 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=6624, nmarked2=64, nripped=6624 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 274 vertices, nripped=6624 mean border=84.8, 123 (0) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0044 min Finding expansion regions mean absolute distance = 0.21 +- 0.34 3228 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=cn06., 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=257058.0, rms=1.626 rms = 2.0855/1.6263, sse=305439.7/257058.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=220046.8, rms=1.063 (34.641%) 037: dt: 0.2500, sse=209401.2, rms=0.801 (24.636%) rms = 0.7925/0.8011, sse=208148.6/209401.2, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=208148.6, rms=0.793 (1.069%) rms = 0.7712/0.7925, sse=207650.0/208148.6, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=207650.0, rms=0.771 (2.689%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.96 minutes #VMPC# mris_place_surfaces VmPeak 2879244 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Thu Feb 9 16:41:18 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 12 --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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 12 --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 Area 264894 0.26651 0.06205 0.000909 0.5741 Corner 794682 60.00000 9.46176 8.247841 134.6235 Edge 397341 0.78840 0.11280 0.032792 1.2726 Hinge 397341 6.34667 6.35637 0.000002 155.6036 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 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 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6478, nmarked2=118, nripped=6478 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 66225: xyz = (27.7102,5.46847,-16.8024) oxyz = (27.7102,5.46847,-16.8024) wxzy = (27.7102,5.46847,-16.8024) pxyz = (0,0,0) CBVO Creating mask 132449 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=6478 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6478, nmarked2=118, nripped=6478 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=2 had to be increased for 115 vertices, nripped=6478 mean border=77.3, 9 (9) missing vertices, mean dist 0.4 [0.5 (%33.2)->0.9 (%66.8))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0172 min Finding expansion regions mean absolute distance = 0.75 +- 0.91 5016 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=cn06., 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=4012149.0, rms=12.391 001: dt: 0.5000, sse=2105044.8, rms=8.831 (28.730%) 002: dt: 0.5000, sse=1278433.2, rms=6.725 (23.852%) 003: dt: 0.5000, sse=879550.5, rms=5.419 (19.424%) 004: dt: 0.5000, sse=687880.1, rms=4.661 (13.987%) 005: dt: 0.5000, sse=594729.3, rms=4.232 (9.190%) 006: dt: 0.5000, sse=553954.4, rms=4.035 (4.670%) 007: dt: 0.5000, sse=531618.0, rms=3.919 (2.868%) 008: dt: 0.5000, sse=523623.6, rms=3.864 (1.408%) rms = 3.8227/3.8638, sse=516580.0/523623.6, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=516580.0, rms=3.823 (1.064%) 010: dt: 0.2500, sse=289672.0, rms=2.345 (38.650%) 011: dt: 0.2500, sse=246163.0, rms=1.923 (18.007%) 012: dt: 0.2500, sse=232079.7, rms=1.795 (6.637%) 013: dt: 0.2500, sse=225001.9, rms=1.712 (4.641%) rms = 1.6692/1.7120, sse=222404.5/225001.9, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=222404.5, rms=1.669 (2.498%) 015: dt: 0.1250, sse=209888.5, rms=1.514 (9.280%) rms = 1.4903/1.5143, sse=208276.1/209888.5, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=208276.1, rms=1.490 (1.588%) maximum number of reductions reached, breaking from loop positioning took 1.0 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=6478 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 #FML# MRISripMidline(): nmarked=6760, nmarked2=166, nripped=6760 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=1 had to be increased for 104 vertices, nripped=6760 mean border=81.5, 28 (0) missing vertices, mean dist -0.3 [0.5 (%74.9)->0.3 (%25.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0118 min Finding expansion regions mean absolute distance = 0.44 +- 0.67 6218 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=cn06., 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=1146687.6, rms=6.125 017: dt: 0.5000, sse=660544.5, rms=4.264 (30.377%) rms = 4.2163/4.2642, sse=647319.7/660544.5, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=647319.7, rms=4.216 (1.125%) 019: dt: 0.2500, sse=369547.2, rms=2.585 (38.701%) 020: dt: 0.2500, sse=317681.0, rms=2.144 (17.040%) 021: dt: 0.2500, sse=291096.8, rms=1.870 (12.806%) 022: dt: 0.2500, sse=271244.8, rms=1.640 (12.271%) 023: dt: 0.2500, sse=259769.2, rms=1.482 (9.658%) 024: dt: 0.2500, sse=251256.9, rms=1.365 (7.887%) 025: dt: 0.2500, sse=248819.8, rms=1.314 (3.750%) rms = 1.2724/1.3137, sse=246064.2/248819.8, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=246064.2, rms=1.272 (3.145%) 027: dt: 0.1250, sse=240273.2, rms=1.159 (8.909%) rms = 1.1458/1.1590, sse=240657.9/240273.1, time step reduction 3 of 3 to 0.062 0 1 1 028: dt: 0.1250, sse=240657.9, rms=1.146 (1.141%) maximum number of reductions reached, breaking from loop positioning took 0.7 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=6760 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6811, nmarked2=170, nripped=6811 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 370 vertices, nripped=6811 mean border=84.2, 44 (0) missing vertices, mean dist -0.2 [0.3 (%72.1)->0.2 (%27.9))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0065 min Finding expansion regions mean absolute distance = 0.28 +- 0.44 4339 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=cn06., 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=555637.7, rms=3.786 029: dt: 0.5000, sse=475644.1, rms=3.295 (12.960%) rms = 3.6408/3.2954, sse=534152.7/475644.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=314424.2, rms=2.133 (35.276%) 031: dt: 0.2500, sse=261187.7, rms=1.529 (28.317%) 032: dt: 0.2500, sse=246565.7, rms=1.289 (15.714%) 033: dt: 0.2500, sse=236501.9, rms=1.211 (6.057%) rms = 1.1866/1.2106, sse=236213.1/236501.9, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=236213.1, rms=1.187 (1.987%) 035: dt: 0.1250, sse=226134.7, rms=1.036 (12.665%) rms = 1.0189/1.0363, sse=226936.3/226134.7, time step reduction 3 of 3 to 0.062 0 1 1 036: dt: 0.1250, sse=226936.3, rms=1.019 (1.685%) 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=6811 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 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6816, nmarked2=171, nripped=6816 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 386 vertices, nripped=6816 mean border=85.0, 112 (0) missing vertices, mean dist -0.0 [0.2 (%57.6)->0.2 (%42.4))] %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0043 min Finding expansion regions mean absolute distance = 0.22 +- 0.35 3768 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=cn06., 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=263238.3, rms=1.626 rms = 2.0296/1.6259, sse=328299.0/263238.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=226679.0, rms=1.077 (33.771%) 038: dt: 0.2500, sse=216785.9, rms=0.800 (25.705%) rms = 0.7865/0.8000, sse=215763.5/216785.9, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=215763.5, rms=0.786 (1.694%) rms = 0.7663/0.7865, sse=213077.6/215763.5, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=213077.6, rms=0.766 (2.567%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.69 minutes #VMPC# mris_place_surfaces VmPeak 2900484 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Thu Feb 9 16:44:05 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 8 non-cortical segments detected only using segment with 7333 vertices erasing segment 0 (vno[0] = 26250) erasing segment 1 (vno[0] = 28561) erasing segment 3 (vno[0] = 71840) erasing segment 4 (vno[0] = 75891) erasing segment 5 (vno[0] = 76646) erasing segment 6 (vno[0] = 81568) erasing segment 7 (vno[0] = 84323) #-------------------------------------------- #@# CortexLabel+HipAmyg lh Thu Feb 9 16:44:16 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 11 non-cortical segments detected only using segment with 5423 vertices erasing segment 0 (vno[0] = 26250) erasing segment 1 (vno[0] = 28561) erasing segment 3 (vno[0] = 44680) erasing segment 4 (vno[0] = 47333) erasing segment 5 (vno[0] = 51028) erasing segment 6 (vno[0] = 75891) erasing segment 7 (vno[0] = 76646) erasing segment 8 (vno[0] = 81568) erasing segment 9 (vno[0] = 84323) erasing segment 10 (vno[0] = 129955) #-------------------------------------------- #@# CortexLabel rh Thu Feb 9 16:44:28 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 2 non-cortical segments detected only using segment with 7453 vertices erasing segment 1 (vno[0] = 42881) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Thu Feb 9 16:44:40 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 6 non-cortical segments detected only using segment with 5360 vertices erasing segment 1 (vno[0] = 42881) erasing segment 2 (vno[0] = 44934) erasing segment 3 (vno[0] = 65274) erasing segment 4 (vno[0] = 71993) erasing segment 5 (vno[0] = 77136) #-------------------------------------------- #@# Smooth2 lh Thu Feb 9 16:44:52 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Thu Feb 9 16:44:52 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 13133 of (13133 13136) to complete... Waiting for PID 13136 of (13133 13136) 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 (13133 13136) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Thu Feb 9 16:44:54 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Thu Feb 9 16:44:54 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 13202 of (13202 13205) to complete... Waiting for PID 13205 of (13202 13205) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.7 mm, total surface area = 78579 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.084 (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=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 70.103155 mris_inflate stimesec 0.345576 mris_inflate ru_maxrss 202732 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 116876 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10224 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 14025 mris_inflate ru_nivcsw 2179 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.2 mm, total surface area = 79082 mm^2 step 000: RMS=0.166 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.070 (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=0.033 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 71.480556 mris_inflate stimesec 0.308075 mris_inflate ru_maxrss 205524 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 122167 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10376 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 13665 mris_inflate ru_nivcsw 2235 PIDs (13202 13205) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Thu Feb 9 16:45:11 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 Thu Feb 9 16:45:11 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf reconbatchjobs /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 13685 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13688 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13691 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13694 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13697 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13700 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13703 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13706 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13709 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13712 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13715 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... Waiting for PID 13718 of (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 11.645*4pi (146.339) --> -11 handles ICI = 146.4, FI = 1409.4, variation=22478.125 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 233 vertices thresholded to be in k1 ~ [-0.15 0.28], k2 ~ [-0.10 0.05] total integrated curvature = 0.675*4pi (8.485) --> 0 handles ICI = 1.5, FI = 8.8, variation=151.154 129 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 152 vertices thresholded to be in [-0.11 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.021 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 7.721*4pi (97.024) --> -7 handles ICI = 144.6, FI = 1415.0, variation=22549.417 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 231 vertices thresholded to be in k1 ~ [-0.22 0.36], k2 ~ [-0.14 0.04] total integrated curvature = 0.668*4pi (8.394) --> 0 handles ICI = 1.5, FI = 9.4, variation=158.459 136 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 168 vertices thresholded to be in [-0.15 0.17] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 done. PIDs (13685 13688 13691 13694 13697 13700 13703 13706 13709 13712 13715 13718) completed and logs appended. #-------------------------------------------- #@# Sphere lh Thu Feb 9 16:45:51 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Thu Feb 9 16:45:51 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 14406 of (14406 14409) to complete... Waiting for PID 14409 of (14406 14409) 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: 12 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.283... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=cn06., 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 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.34 pass 1: epoch 2 of 3 starting distance error %20.31 unfolding complete - removing small folds... starting distance error %20.25 removing remaining folds... final distance error %20.25 MRISunfold() return, current seed 1234 -01: dt=0.0000, 67 negative triangles VmPeak 1294956 093: dt=0.9900, 67 negative triangles 094: dt=0.9900, 16 negative triangles 095: dt=0.9900, 7 negative triangles 096: dt=0.9900, 3 negative triangles 097: dt=0.9900, 2 negative triangles 098: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0938 hours FSRUNTIME@ mris_sphere 0.0938 hours 12 threads #VMPC# mris_sphere VmPeak 1294956 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: 12 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.282... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=cn06., 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.77 pass 1: epoch 2 of 3 starting distance error %20.75 unfolding complete - removing small folds... starting distance error %20.72 removing remaining folds... final distance error %20.72 MRISunfold() return, current seed 1234 -01: dt=0.0000, 89 negative triangles VmPeak 1649028 081: dt=0.9900, 89 negative triangles 082: dt=0.9900, 31 negative triangles 083: dt=0.9900, 14 negative triangles 084: dt=0.9900, 12 negative triangles 085: dt=0.9900, 10 negative triangles 086: dt=0.9900, 15 negative triangles 087: dt=0.9900, 12 negative triangles 088: dt=0.9900, 7 negative triangles 089: dt=0.9900, 6 negative triangles 090: dt=0.9900, 4 negative triangles 091: dt=0.9900, 5 negative triangles 092: dt=0.9900, 5 negative triangles 093: dt=0.9900, 4 negative triangles 094: dt=0.9900, 1 negative triangles 095: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0890 hours FSRUNTIME@ mris_sphere 0.0890 hours 12 threads #VMPC# mris_sphere VmPeak 1649028 mris_sphere done PIDs (14406 14409) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Thu Feb 9 16:51:29 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_register -curv ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Thu Feb 9 16:51:29 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_register -curv ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 20081 of (20081 20084) to complete... Waiting for PID 20084 of (20081 20084) to complete... mris_register -curv ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts cmdline mris_register -curv ../surf/lh.sphere /opt/freesurfer/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 /opt/freesurfer/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=cn06., 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=cn06., 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=cn06., 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 = 5.372 curvature mean = 0.018, std = 0.817 curvature mean = 0.017, std = 0.861 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (8.00, -3.50, 4.00) sse = 179233.5, elapsed since starting=0.1626 min MRISrigidBodyAlignGlobal() done 0.16 min curvature mean = -0.015, std = 0.834 curvature mean = 0.008, std = 0.948 curvature mean = -0.020, std = 0.844 curvature mean = 0.003, std = 0.980 curvature mean = -0.022, std = 0.846 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.021, std = 0.267 curvature mean = 0.034, std = 0.249 curvature mean = 0.063, std = 0.373 curvature mean = 0.032, std = 0.306 curvature mean = 0.030, std = 0.586 curvature mean = 0.031, std = 0.334 curvature mean = 0.015, std = 0.729 curvature mean = 0.031, std = 0.346 curvature mean = 0.004, std = 0.831 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 1298768 registration took 0.13 hours #VMPC# mris_register VmPeak 1298768 FSRUNTIME@ mris_register 0.1349 hours 12 threads mris_register -curv ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts cmdline mris_register -curv ../surf/rh.sphere /opt/freesurfer/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 /opt/freesurfer/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=cn06., 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=cn06., 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=cn06., 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 = 5.419 curvature mean = 0.019, std = 0.809 curvature mean = 0.018, std = 0.858 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.00, -5.50, 8.50) sse = 189344.5, elapsed since starting=0.1845 min MRISrigidBodyAlignGlobal() done 0.18 min curvature mean = -0.008, std = 0.830 curvature mean = 0.007, std = 0.947 curvature mean = -0.011, std = 0.839 curvature mean = 0.003, std = 0.979 curvature mean = -0.012, std = 0.841 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.021, std = 0.266 curvature mean = 0.033, std = 0.242 curvature mean = 0.060, std = 0.375 curvature mean = 0.029, std = 0.300 curvature mean = 0.027, std = 0.587 curvature mean = 0.028, std = 0.327 curvature mean = 0.013, std = 0.729 curvature mean = 0.028, std = 0.339 curvature mean = 0.002, std = 0.833 MRISregister() return, current seed 0 -01: dt=0.0000, 1 negative triangles VmPeak 1301220 104: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.13 hours #VMPC# mris_register VmPeak 1301220 FSRUNTIME@ mris_register 0.1329 hours 12 threads PIDs (20081 20084) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Thu Feb 9 16:59:35 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Thu Feb 9 16:59:35 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 29478 of (29478 29481) to complete... Waiting for PID 29481 of (29478 29481) 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 (29478 29481) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Thu Feb 9 16:59:36 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Thu Feb 9 16:59:36 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 29548 of (29548 29551) to complete... Waiting for PID 29551 of (29548 29551) to complete... mrisp_paint -a 5 /opt/freesurfer/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 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /opt/freesurfer/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 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (29548 29551) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Thu Feb 9 16:59:37 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Thu Feb 9 16:59:37 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 29617 of (29617 29620) to complete... Waiting for PID 29620 of (29617 29620) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T lh ../surf/lh.sphere.reg /opt/freesurfer/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 /opt/freesurfer/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 1266 labels changed using aseg relabeling using gibbs priors... 000: 2863 changed, 130564 examined... 001: 645 changed, 12246 examined... 002: 153 changed, 3686 examined... 003: 49 changed, 959 examined... 004: 10 changed, 304 examined... 005: 5 changed, 64 examined... 006: 2 changed, 29 examined... 007: 3 changed, 16 examined... 008: 4 changed, 12 examined... 009: 5 changed, 17 examined... 010: 1 changed, 20 examined... 011: 0 changed, 7 examined... 219 labels changed using aseg 000: 108 total segments, 67 labels (185 vertices) changed 001: 41 total segments, 2 labels (7 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1675 vertices marked for relabeling... 1675 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T rh ../surf/rh.sphere.reg /opt/freesurfer/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 /opt/freesurfer/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 1140 labels changed using aseg relabeling using gibbs priors... 000: 2673 changed, 132449 examined... 001: 600 changed, 11541 examined... 002: 125 changed, 3463 examined... 003: 29 changed, 774 examined... 004: 8 changed, 198 examined... 005: 4 changed, 46 examined... 006: 0 changed, 24 examined... 162 labels changed using aseg 000: 81 total segments, 43 labels (144 vertices) changed 001: 39 total segments, 1 labels (1 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1272 vertices marked for relabeling... 1272 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 9 seconds. PIDs (29617 29620) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Thu Feb 9 16:59:46 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 12 --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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 12 --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 261124 0.33116 0.12409 0.000363 3.3132 Corner 783372 60.00000 14.92700 0.130542 179.5541 Edge 391686 0.88648 0.20699 0.013454 3.9027 Hinge 391686 10.93528 12.14858 0.000010 179.9829 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 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 484 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 65282: xyz = (-50.5289,2.80325,31.1252) oxyz = (-50.5289,2.80325,31.1252) wxzy = (-50.5289,2.80325,31.1252) pxyz = (0,0,0) CBVO Creating mask 130564 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=2 had to be increased for 210 vertices, nripped=8051 mean border=76.7, 43 (43) missing vertices, mean dist 0.5 [1.0 (%11.8)->0.7 (%88.2))] %66 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0170 min Finding expansion regions mean absolute distance = 0.71 +- 0.91 3215 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=cn06., 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=2639383.8, rms=10.002 001: dt: 0.5000, sse=1077921.4, rms=6.051 (39.500%) 002: dt: 0.5000, sse=663476.9, rms=4.442 (26.598%) 003: dt: 0.5000, sse=579445.7, rms=4.034 (9.180%) 004: dt: 0.5000, sse=528296.1, rms=3.764 (6.690%) rms = 3.8437/3.7641, sse=543304.5/528296.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=353879.9, rms=2.645 (29.723%) 006: dt: 0.2500, sse=291767.2, rms=2.103 (20.493%) 007: dt: 0.2500, sse=269919.7, rms=1.877 (10.742%) 008: dt: 0.2500, sse=260860.0, rms=1.772 (5.628%) 009: dt: 0.2500, sse=253770.0, rms=1.682 (5.036%) 010: dt: 0.2500, sse=249795.4, rms=1.628 (3.207%) rms = 1.5893/1.6285, sse=247124.0/249795.4, time step reduction 2 of 3 to 0.125 0 0 1 011: dt: 0.2500, sse=247124.0, rms=1.589 (2.406%) 012: dt: 0.1250, sse=241791.1, rms=1.516 (4.593%) rms = 1.5007/1.5163, sse=240865.0/241791.1, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=240865.0, rms=1.501 (1.025%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=1 had to be increased for 158 vertices, nripped=8051 mean border=81.2, 81 (14) missing vertices, mean dist -0.3 [0.5 (%75.8)->0.2 (%24.2))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0117 min Finding expansion regions mean absolute distance = 0.44 +- 0.66 5150 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=cn06., 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=1152529.8, rms=6.216 014: dt: 0.5000, sse=680507.0, rms=4.405 (29.140%) 015: dt: 0.5000, sse=652318.8, rms=4.280 (2.839%) 016: dt: 0.5000, sse=604252.1, rms=4.041 (5.587%) rms = 4.0743/4.0408, sse=613277.3/604252.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=392480.8, rms=2.763 (31.632%) 018: dt: 0.2500, sse=312482.4, rms=2.079 (24.747%) 019: dt: 0.2500, sse=280666.0, rms=1.722 (17.157%) 020: dt: 0.2500, sse=267565.2, rms=1.528 (11.300%) 021: dt: 0.2500, sse=258384.5, rms=1.396 (8.620%) 022: dt: 0.2500, sse=255015.5, rms=1.322 (5.276%) rms = 1.2949/1.3223, sse=252158.4/255015.6, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=252158.4, rms=1.295 (2.078%) 024: dt: 0.1250, sse=246470.0, rms=1.193 (7.853%) rms = 1.1829/1.1932, sse=247398.7/246470.0, time step reduction 3 of 3 to 0.062 0 1 1 025: dt: 0.1250, sse=247398.7, rms=1.183 (0.863%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 252 vertices, nripped=8051 mean border=83.9, 107 (12) missing vertices, mean dist -0.2 [0.3 (%72.2)->0.2 (%27.8))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0068 min Finding expansion regions mean absolute distance = 0.27 +- 0.43 4134 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=cn06., 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=528683.7, rms=3.662 026: dt: 0.5000, sse=478797.3, rms=3.287 (10.240%) rms = 3.6597/3.2872, sse=532750.4/478797.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=314041.0, rms=2.084 (36.609%) 028: dt: 0.2500, sse=262694.2, rms=1.506 (27.711%) 029: dt: 0.2500, sse=247982.7, rms=1.285 (14.672%) 030: dt: 0.2500, sse=245103.1, rms=1.226 (4.608%) rms = 1.2019/1.2261, sse=243247.0/245103.1, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=243247.0, rms=1.202 (1.971%) 032: dt: 0.1250, sse=236131.8, rms=1.059 (11.924%) rms = 1.0435/1.0586, sse=235245.1/236131.8, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=235245.1, rms=1.043 (1.431%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 256 vertices, nripped=8051 mean border=84.8, 180 (8) missing vertices, mean dist -0.1 [0.2 (%57.1)->0.2 (%42.9))] %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0043 min Finding expansion regions mean absolute distance = 0.21 +- 0.34 3387 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=cn06., 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=271691.7, rms=1.655 rms = 2.0965/1.6546, sse=348501.9/271691.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=237328.1, rms=1.107 (33.085%) 035: dt: 0.2500, sse=232127.0, rms=0.850 (23.244%) rms = 0.8385/0.8498, sse=222840.0/232127.0, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=222840.0, rms=0.838 (1.333%) rms = 0.8131/0.8385, sse=222179.1/222840.0, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=222179.1, rms=0.813 (3.026%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 2.76 minutes #VMPC# mris_place_surfaces VmPeak 2861908 mris_place_surface done #-------------------------------------------- #@# WhiteSurfs rh Thu Feb 9 17:02:37 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 12 --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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 12 --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 264894 0.32795 0.12403 0.001085 2.7708 Corner 794682 60.00000 15.44843 0.316515 179.2178 Edge 397341 0.88349 0.20874 0.027786 3.7274 Hinge 397341 11.01982 12.66509 0.000019 179.9721 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 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 427 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 66225: xyz = (28.1535,5.1643,-17.268) oxyz = (28.1535,5.1643,-17.268) wxzy = (28.1535,5.1643,-17.268) pxyz = (0,0,0) CBVO Creating mask 132449 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=2 had to be increased for 221 vertices, nripped=8148 mean border=77.0, 36 (36) missing vertices, mean dist 0.5 [0.9 (%12.4)->0.7 (%87.6))] %66 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0167 min Finding expansion regions mean absolute distance = 0.72 +- 0.91 3613 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=cn06., 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=2663123.8, rms=9.965 001: dt: 0.5000, sse=1094947.2, rms=6.057 (39.221%) 002: dt: 0.5000, sse=680583.3, rms=4.481 (26.011%) 003: dt: 0.5000, sse=593636.1, rms=4.074 (9.095%) 004: dt: 0.5000, sse=536248.9, rms=3.773 (7.394%) rms = 3.8126/3.7725, sse=544080.8/536248.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=365386.8, rms=2.700 (28.431%) 006: dt: 0.2500, sse=299260.6, rms=2.150 (20.363%) 007: dt: 0.2500, sse=274684.7, rms=1.904 (11.444%) 008: dt: 0.2500, sse=264447.5, rms=1.790 (6.017%) 009: dt: 0.2500, sse=256805.8, rms=1.695 (5.273%) 010: dt: 0.2500, sse=252324.7, rms=1.637 (3.417%) rms = 1.5955/1.6373, sse=249368.1/252324.7, time step reduction 2 of 3 to 0.125 0 0 1 011: dt: 0.2500, sse=249368.1, rms=1.595 (2.551%) 012: dt: 0.1250, sse=243650.1, rms=1.518 (4.885%) rms = 1.4987/1.5175, sse=242429.5/243650.1, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=242429.5, rms=1.499 (1.240%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=1 had to be increased for 132 vertices, nripped=8148 mean border=81.4, 47 (5) missing vertices, mean dist -0.3 [0.5 (%75.1)->0.2 (%24.9))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0121 min Finding expansion regions mean absolute distance = 0.45 +- 0.68 6131 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=cn06., 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=1145817.0, rms=6.144 014: dt: 0.5000, sse=668601.6, rms=4.304 (29.949%) 015: dt: 0.5000, sse=652414.6, rms=4.231 (1.690%) 016: dt: 0.5000, sse=606109.1, rms=4.006 (5.324%) rms = 4.0392/4.0062, sse=612366.4/606109.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=399586.3, rms=2.779 (30.645%) 018: dt: 0.2500, sse=320166.5, rms=2.111 (24.017%) 019: dt: 0.2500, sse=286384.4, rms=1.748 (17.198%) 020: dt: 0.2500, sse=270459.1, rms=1.536 (12.155%) 021: dt: 0.2500, sse=261585.3, rms=1.386 (9.775%) 022: dt: 0.2500, sse=255949.1, rms=1.316 (5.023%) rms = 1.2843/1.3159, sse=253899.9/255949.1, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=253899.9, rms=1.284 (2.400%) 024: dt: 0.1250, sse=247224.2, rms=1.167 (9.150%) rms = 1.1524/1.1668, sse=246302.9/247224.2, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=246303.0, rms=1.152 (1.239%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 359 vertices, nripped=8148 mean border=84.1, 65 (5) missing vertices, mean dist -0.2 [0.3 (%72.4)->0.2 (%27.6))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0070 min Finding expansion regions mean absolute distance = 0.29 +- 0.44 4449 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=cn06., 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=557798.2, rms=3.796 026: dt: 0.5000, sse=478438.9, rms=3.286 (13.425%) rms = 3.5992/3.2861, sse=533035.3/478438.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=322347.9, rms=2.142 (34.804%) 028: dt: 0.2500, sse=268212.3, rms=1.535 (28.334%) 029: dt: 0.2500, sse=251002.7, rms=1.294 (15.745%) 030: dt: 0.2500, sse=245776.9, rms=1.211 (6.375%) rms = 1.1802/1.2111, sse=242521.5/245776.9, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=242521.5, rms=1.180 (2.557%) 032: dt: 0.1250, sse=234685.3, rms=1.039 (11.961%) rms = 1.0218/1.0390, sse=234081.0/234685.3, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=234081.0, rms=1.022 (1.660%) 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 = 114.1745760; border_low = 62.0000000; outside_low = 50.6894760; outside_hi = 114.1745760; 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=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 446 vertices, nripped=8148 mean border=85.0, 152 (4) missing vertices, mean dist -0.1 [0.2 (%57.8)->0.2 (%42.2))] %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0044 min Finding expansion regions mean absolute distance = 0.22 +- 0.35 3847 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=cn06., 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=270789.2, rms=1.639 rms = 2.0300/1.6388, sse=323541.0/270789.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=235454.3, rms=1.100 (32.895%) 035: dt: 0.2500, sse=228011.8, rms=0.828 (24.686%) rms = 0.8193/0.8283, sse=228057.6/228011.8, time step reduction 2 of 3 to 0.125 0 1 1 036: dt: 0.2500, sse=228057.6, rms=0.819 (1.079%) rms = 0.7994/0.8193, sse=226262.4/228057.6, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=226262.5, rms=0.799 (2.435%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.62 minutes #VMPC# mris_place_surfaces VmPeak 2866828 mris_place_surface done #-------------------------------------------- #@# T1PialSurf lh Thu Feb 9 17:05:19 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 12 --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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 12 --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 261124 0.33438 0.13958 0.000406 3.3155 Corner 783372 60.00000 16.57416 0.154081 179.6660 Edge 391686 0.89294 0.22971 0.021781 4.1562 Hinge 391686 11.18157 12.82372 0.000010 179.9597 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=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 61.9469 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 65282: xyz = (-50.4889,2.88483,31.0954) oxyz = (-50.4889,2.88483,31.0954) wxzy = (-50.4889,2.88483,31.0954) pxyz = (-50.4889,2.88483,31.0954) CBVO Creating mask 130564 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=2 had to be increased for 363 vertices, nripped=5690 mean border=48.4, 94 (94) missing vertices, mean dist 1.6 [1.6 (%0.0)->2.7 (%100.0))] % 9 local maxima, %49 large gradients and %38 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0136 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=cn06., 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=34508504.0, rms=37.084 001: dt: 0.5000, sse=24243622.0, rms=31.047 (16.280%) 002: dt: 0.5000, sse=17225250.0, rms=26.127 (15.846%) 003: dt: 0.5000, sse=12984873.0, rms=22.642 (13.341%) 004: dt: 0.5000, sse=10488419.0, rms=20.310 (10.296%) 005: dt: 0.5000, sse=8833426.0, rms=18.604 (8.404%) 006: dt: 0.5000, sse=7458465.5, rms=17.055 (8.322%) 007: dt: 0.5000, sse=6112250.0, rms=15.389 (9.770%) 008: dt: 0.5000, sse=4762458.5, rms=13.514 (12.186%) 009: dt: 0.5000, sse=3464175.0, rms=11.423 (15.470%) 010: dt: 0.5000, sse=2366528.5, rms=9.295 (18.627%) 011: dt: 0.5000, sse=1601121.6, rms=7.460 (19.746%) 012: dt: 0.5000, sse=1170761.8, rms=6.192 (16.991%) 013: dt: 0.5000, sse=980693.4, rms=5.539 (10.553%) 014: dt: 0.5000, sse=900843.1, rms=5.238 (5.426%) 015: dt: 0.5000, sse=871070.7, rms=5.119 (2.278%) 016: dt: 0.5000, sse=853536.3, rms=5.046 (1.428%) rms = 5.0082/5.0459, sse=844983.3/853536.3, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=844983.3, rms=5.008 (0.747%) 018: dt: 0.2500, sse=619820.2, rms=3.984 (20.450%) 019: dt: 0.2500, sse=575867.0, rms=3.754 (5.776%) rms = 3.7520/3.7540, sse=576006.4/575867.0, time step reduction 2 of 3 to 0.125 0 1 1 020: dt: 0.2500, sse=576006.4, rms=3.752 (0.052%) 021: dt: 0.1250, sse=516681.2, rms=3.415 (8.978%) 022: dt: 0.1250, sse=508294.5, rms=3.364 (1.487%) rms = 3.3569/3.3644, sse=507178.4/508294.5, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=507178.4, rms=3.357 (0.221%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=1 had to be increased for 9073 vertices, nripped=5690 mean border=47.3, 1490 (6) missing vertices, mean dist 0.1 [0.1 (%61.3)->0.6 (%38.7))] %18 local maxima, %41 large gradients and %36 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0049 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=cn06., 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=660660.7, rms=3.901 rms = 4.6339/3.9015, sse=816446.3/660660.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=595586.2, rms=3.549 (9.042%) 025: dt: 0.2500, sse=583069.2, rms=3.477 (2.025%) rms = 3.5172/3.4768, sse=589816.1/583069.2, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 026: dt: 0.1250, sse=572426.7, rms=3.414 (1.810%) 027: dt: 0.1250, sse=558024.1, rms=3.327 (2.549%) rms = 3.2959/3.3269, sse=552977.9/558024.1, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=552977.9, rms=3.296 (0.931%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; 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=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9558 vertices, nripped=5690 mean border=46.4, 1676 (4) missing vertices, mean dist 0.1 [0.1 (%52.9)->0.4 (%47.1))] %32 local maxima, %27 large gradients and %36 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0029 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=cn06., 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=619668.8, rms=3.670 rms = 4.4298/3.6703, sse=772247.8/619668.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=580899.6, rms=3.450 (5.997%) rms = 3.4106/3.4502, sse=573697.9/580899.6, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=573697.9, rms=3.411 (1.146%) 031: dt: 0.1250, sse=558786.6, rms=3.320 (2.665%) rms = 3.2846/3.3197, sse=552893.8/558786.6, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=552893.8, rms=3.285 (1.058%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; 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=130564 Gdiag_no=-1 vno start=0, stop=130564 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8321 vertices, nripped=5690 mean border=45.6, 3572 (3) missing vertices, mean dist 0.1 [0.1 (%53.4)->0.3 (%46.6))] %36 local maxima, %22 large gradients and %35 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0020 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=cn06., 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=587761.9, rms=3.487 rms = 4.1184/3.4867, sse=705882.8/587762.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=563899.9, rms=3.345 (4.054%) 034: dt: 0.2500, sse=551323.5, rms=3.275 (2.101%) rms = 3.2818/3.2751, sse=551760.7/551323.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 3.2309/3.2751, sse=544279.9/551323.5, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=544279.9, rms=3.231 (1.349%) maximum number of reductions reached, breaking from loop positioning took 0.3 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 2.36 minutes #VMPC# mris_place_surfaces VmPeak 2063912 mris_place_surface done #-------------------------------------------- #@# T1PialSurf rh Thu Feb 9 17:07:46 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 12 --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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 12 --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 264894 0.33086 0.13782 0.000514 2.3165 Corner 794682 60.00000 16.94056 0.337411 178.7056 Edge 397341 0.88952 0.22844 0.010213 3.9945 Hinge 397341 11.28330 13.41565 0.000002 179.9629 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=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 61.9469 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 66225: xyz = (28.1406,5.16566,-17.2798) oxyz = (28.1406,5.16566,-17.2798) wxzy = (28.1406,5.16566,-17.2798) pxyz = (28.1406,5.16566,-17.2798) CBVO Creating mask 132449 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=2 had to be increased for 355 vertices, nripped=5713 mean border=48.5, 79 (79) missing vertices, mean dist 1.6 [0.5 (%0.0)->2.8 (%100.0))] % 8 local maxima, %47 large gradients and %40 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0139 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=cn06., 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=35402340.0, rms=37.284 001: dt: 0.5000, sse=25151806.0, rms=31.392 (15.804%) 002: dt: 0.5000, sse=18148418.0, rms=26.626 (15.182%) 003: dt: 0.5000, sse=13919181.0, rms=23.278 (12.571%) 004: dt: 0.5000, sse=11380948.0, rms=21.014 (9.727%) 005: dt: 0.5000, sse=9636598.0, rms=19.304 (8.139%) 006: dt: 0.5000, sse=8098213.0, rms=17.658 (8.526%) 007: dt: 0.5000, sse=6557910.5, rms=15.840 (10.297%) 008: dt: 0.5000, sse=5056503.0, rms=13.839 (12.629%) 009: dt: 0.5000, sse=3676464.0, rms=11.703 (15.439%) 010: dt: 0.5000, sse=2522910.2, rms=9.556 (18.340%) 011: dt: 0.5000, sse=1692330.0, rms=7.646 (19.993%) 012: dt: 0.5000, sse=1204048.9, rms=6.255 (18.193%) 013: dt: 0.5000, sse=988481.0, rms=5.529 (11.606%) 014: dt: 0.5000, sse=905107.1, rms=5.218 (5.614%) 015: dt: 0.5000, sse=878358.9, rms=5.113 (2.028%) 016: dt: 0.5000, sse=862352.1, rms=5.046 (1.297%) rms = 5.0125/5.0463, sse=854632.4/862352.2, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=854632.4, rms=5.013 (0.669%) 018: dt: 0.2500, sse=619010.4, rms=3.954 (21.115%) 019: dt: 0.2500, sse=572885.9, rms=3.714 (6.070%) rms = 3.7058/3.7141, sse=571879.7/572885.9, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=571879.8, rms=3.706 (0.224%) 021: dt: 0.1250, sse=506109.4, rms=3.331 (10.104%) 022: dt: 0.1250, sse=496213.0, rms=3.271 (1.811%) rms = 3.2580/3.2710, sse=494199.9/496213.0, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=494199.9, rms=3.258 (0.398%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=1 had to be increased for 9054 vertices, nripped=5713 mean border=47.3, 1549 (6) missing vertices, mean dist 0.1 [0.1 (%60.8)->0.6 (%39.2))] %17 local maxima, %40 large gradients and %37 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0047 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=cn06., 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=668567.2, rms=3.940 rms = 4.6077/3.9397, sse=813036.6/668567.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=592159.5, rms=3.533 (10.323%) 025: dt: 0.2500, sse=574766.9, rms=3.434 (2.811%) rms = 3.4619/3.4337, sse=579424.6/574766.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 026: dt: 0.1250, sse=562320.2, rms=3.360 (2.138%) 027: dt: 0.1250, sse=544263.2, rms=3.251 (3.258%) rms = 3.2120/3.2509, sse=537997.9/544263.3, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=537997.9, rms=3.212 (1.196%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; 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=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9446 vertices, nripped=5713 mean border=46.4, 1841 (4) missing vertices, mean dist 0.1 [0.1 (%54.1)->0.4 (%45.9))] %31 local maxima, %26 large gradients and %37 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0027 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=cn06., 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=602231.6, rms=3.578 rms = 4.3520/3.5780, sse=756542.7/602231.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=563299.3, rms=3.355 (6.242%) rms = 3.3112/3.3546, sse=555492.3/563299.3, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=555492.2, rms=3.311 (1.294%) 031: dt: 0.1250, sse=540051.6, rms=3.216 (2.877%) rms = 3.1812/3.2160, sse=534274.7/540051.6, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=534274.7, rms=3.181 (1.082%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.8254240; border_hi = 50.6894760; border_low = 28.0684280; outside_low = 10.0000000; outside_hi = 45.0342140; 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=132449 Gdiag_no=-1 vno start=0, stop=132449 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8293 vertices, nripped=5713 mean border=45.7, 3675 (4) missing vertices, mean dist 0.0 [0.1 (%54.2)->0.3 (%45.8))] %35 local maxima, %22 large gradients and %36 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0021 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=cn06., 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=567955.2, rms=3.379 rms = 4.0027/3.3788, sse=682649.3/567955.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=544931.1, rms=3.241 (4.092%) 034: dt: 0.2500, sse=535170.9, rms=3.186 (1.668%) rms = 3.2097/3.1865, sse=538301.6/535170.9, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 3.1436/3.1865, sse=528422.6/535170.9, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=528422.6, rms=3.144 (1.345%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 36 intersecting 001: 16 intersecting 002: 13 intersecting 003: 3 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.32 minutes #VMPC# mris_place_surfaces VmPeak 2063704 mris_place_surface done #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Feb 9 17:10:10 CST 2023 bbregister --s 31231_T2_3T --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz --lta /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask tmp /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532 Log file is /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.log Thu Feb 9 17:10:10 CST 2023 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts /opt/freesurfer/bin/bbregister --s 31231_T2_3T --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz --lta /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask bbregister 7.2.0 Linux cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_convert /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii mri_convert /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii reading from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii... mri_coreg --s 31231_T2_3T --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --regdat /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.init.dat --reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/mri_coreg.lta --nthreads 12 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts cmdline mri_coreg --s 31231_T2_3T --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --regdat /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.init.dat --reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/mri_coreg.lta --nthreads 12 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii Reading in ref /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/brainmask.mgz Setting cras translation parameters to align volume centers Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Init matrix params -1.0000 1.0000 -1.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial parameters to be opt -1.0000 1.0000 -1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 12 movsat = 1311.0000 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 122.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0366459538 nhits = 166926 out of 16777216, Percent Overlap: 63.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -1.00000; 0.00000 1.00000 0.00000 1.00001; 0.00000 0.00000 1.00000 -1.00000; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -1.00000 0.00000 0.00000 221.00000; 0.00000 0.00000 1.00000 -8.00000; 0.00000 -1.00000 0.00000 247.00000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -1.00000 1.00001 -1.00000 2.00000 0.00000 0.00000 -1.0322631 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -1.000000 1.000008 -1.000000 2.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0366702080 #@# 4 188 -1.00000 1.00001 -1.00000 2.00000 0.00000 0.00000 -1.0366702 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.036670 #@# 4 190 0.00000 1.00001 -1.00000 2.00000 0.00000 0.00000 -1.0370545 #@# 4 195 -0.08973 1.00001 -1.00000 2.00000 0.00000 0.00000 -1.0370605 #@# 4 205 -0.11184 0.38197 -1.00000 2.00000 0.00000 0.00000 -1.0371565 #@# 4 210 -0.11184 0.39197 0.00000 2.00000 0.00000 0.00000 -1.0371946 #@# 4 214 -0.11184 0.39197 -0.38197 2.00000 0.00000 0.00000 -1.0372719 #@# 4 215 -0.11184 0.39197 -0.50183 2.00000 0.00000 0.00000 -1.0372730 #@# 4 216 -0.11184 0.39197 -0.45487 2.00000 0.00000 0.00000 -1.0372740 #@# 4 218 -0.11184 0.39197 -0.43487 2.00000 0.00000 0.00000 -1.0372741 #@# 4 223 -0.11184 0.39197 -0.43487 0.38197 0.00000 0.00000 -1.0374477 #@# 4 224 -0.11184 0.39197 -0.43487 0.71334 0.00000 0.00000 -1.0374836 #@# 4 227 -0.11184 0.39197 -0.43487 0.90106 0.00000 0.00000 -1.0374858 #@# 4 229 -0.11184 0.39197 -0.43487 0.87164 0.00000 0.00000 -1.0374867 #@# 4 250 -0.11184 0.39197 -0.43487 0.88288 0.00000 -0.01000 -1.0374868 powell nthiter 1: fret = -1.037487 #@# 4 269 -0.11184 0.32125 -0.43487 0.88288 0.00000 -0.01000 -1.0374883 #@# 4 278 -0.11184 0.33125 -0.35959 0.88288 0.00000 -0.01000 -1.0374918 #@# 4 287 -0.11184 0.33125 -0.34959 0.82262 0.00000 -0.01000 -1.0374923 #@# 4 288 -0.11184 0.33125 -0.34959 0.83262 0.00000 -0.01000 -1.0374930 Powell done niters total = 1 OptTimeSec 2.5 sec OptTimeMin 0.04 min nEvals 307 Final optimized parameters -0.11184090 0.33124825 -0.34958646 0.83262092 0.01000000 -0.01000000 Final matrix parameters -0.1118 0.3312 -0.3496 0.8326 0.0100 -0.0200 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.037492938329030 --------------------------------- Final RefRAS-to-MovRAS 1.00000 -0.00017 0.00017 -0.11184; 0.00017 0.99989 0.01453 0.33125; -0.00018 -0.01453 0.99989 -0.34959; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -1.00000 -0.00017 -0.00017 221.93144; -0.00017 -0.01453 0.99989 -6.91094; 0.00018 -0.99989 -0.01453 249.49655; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.1118 0.3312 -0.3496 0.8326 0.0100 -0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.1118 0.3312 -0.3496 0.8326 0.0100 -0.0100 nhits = 167015 out of 16777216, Percent Overlap: 63.7 mri_coreg RunTimeSec 56.2 sec To check run: tkregisterfv --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --targ /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/brainmask.mgz --reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/mri_coreg.lta --s 31231_T2_3T --surfs mri_coreg done mri_segreg --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --init-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.init.dat --out-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 7.2.0 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mri_segreg --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --init-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.init.dat --out-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 movvol /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii regfile /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.init.dat subject 31231_T2_3T dof 6 outregfile /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1676385264 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -1.00000 0.00017 -0.00017 0.11322; -0.00018 -0.01453 0.99989 -0.32730; -0.00017 -0.99989 -0.01453 0.80649; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.962041 1 -25.0 -25.0 25.0 0.974565 2 -25.0 25.0 -25.0 0.961789 3 -25.0 25.0 25.0 1.003570 4 25.0 -25.0 -25.0 0.960866 5 25.0 -25.0 25.0 0.949911 6 25.0 25.0 -25.0 0.949865 7 25.0 25.0 25.0 0.947408 REL: 8 0.077898 7.710015 0.963752 rel = 0.0808281 Initial costs ---------------- Number of surface hits 2490 WM Intensity 272.3172 +/- 57.2726 Ctx Intensity 377.7596 +/- 105.4410 Pct Contrast 30.9787 +/- 20.8132 Cost 0.0779 RelCost 0.0808 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9495 0.9495 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9271 0.9271 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9166 0.9166 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8743 0.8743 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8416 0.8416 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8228 0.8228 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.7758 0.7758 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.7758 0.7758 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7680 0.7680 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.7642 0.7642 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6679 0.6679 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6672 0.6672 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6183 0.6183 0.0 361 0.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.5848 0.5848 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5807 0.5807 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0779 0.0779 0.0 Brute Force -------------------------- Min cost was 0.077898 Number of iterations 729 Search time 0.939021 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.077898 17 0.000 -0.618 0.000 0.000 0.000 0.000 0.0671112776 19 0.000 -0.449 0.000 0.000 0.000 0.000 0.0655487906 28 0.000 -0.449 0.382 0.000 0.000 0.000 0.0626084242 31 0.000 -0.449 0.618 0.000 0.000 0.000 0.0603788261 36 0.000 -0.449 0.640 0.000 0.000 0.000 0.0600477893 37 0.000 -0.449 0.642 0.000 0.000 0.000 0.0600272065 39 0.000 -0.449 0.648 0.000 0.000 0.000 0.0600039432 40 0.000 -0.449 0.649 0.000 0.000 0.000 0.0600035984 47 0.000 -0.449 0.649 0.382 0.000 0.000 0.0588237007 48 0.000 -0.449 0.649 0.214 0.000 0.000 0.0579210688 49 0.000 -0.449 0.649 0.230 0.000 0.000 0.0579121892 51 0.000 -0.449 0.649 0.288 0.000 0.000 0.0571375544 53 0.000 -0.449 0.649 0.286 0.000 0.000 0.0571340890 62 0.000 -0.449 0.649 0.286 -0.027 0.000 0.0569897381 64 0.000 -0.449 0.649 0.286 -0.037 0.000 0.0569836278 65 0.000 -0.449 0.649 0.286 -0.035 0.000 0.0569802778 66 0.000 -0.449 0.649 0.286 -0.033 0.000 0.0569791464 75 0.000 -0.449 0.649 0.286 -0.033 0.108 0.0555462060 76 0.000 -0.449 0.649 0.286 -0.033 0.157 0.0551069691 78 0.000 -0.449 0.649 0.286 -0.033 0.168 0.0550574434 80 0.000 -0.449 0.649 0.286 -0.033 0.178 0.0550440939 81 0.000 -0.449 0.649 0.286 -0.033 0.177 0.0550433502 82 0.000 -0.449 0.649 0.286 -0.033 0.176 0.0550432606 powell nthiter 1: fret = 0.055043 91 0.038 -0.449 0.649 0.286 -0.033 0.176 0.0537203042 92 0.132 -0.449 0.649 0.286 -0.033 0.176 0.0527804989 94 0.111 -0.449 0.649 0.286 -0.033 0.176 0.0522687527 95 0.095 -0.449 0.649 0.286 -0.033 0.176 0.0521420475 97 0.096 -0.449 0.649 0.286 -0.033 0.176 0.0521420082 110 0.096 -0.445 0.649 0.286 -0.033 0.176 0.0521331520 112 0.096 -0.446 0.649 0.286 -0.033 0.176 0.0521330424 118 0.096 -0.446 0.031 0.286 -0.033 0.176 0.0514233669 120 0.096 -0.446 0.326 0.286 -0.033 0.176 0.0494743395 123 0.096 -0.446 0.329 0.286 -0.033 0.176 0.0494711872 124 0.096 -0.446 0.333 0.286 -0.033 0.176 0.0494650144 125 0.096 -0.446 0.366 0.286 -0.033 0.176 0.0494508260 126 0.096 -0.446 0.358 0.286 -0.033 0.176 0.0494330502 128 0.096 -0.446 0.356 0.286 -0.033 0.176 0.0494322981 137 0.096 -0.446 0.356 0.313 -0.033 0.176 0.0493639887 139 0.096 -0.446 0.356 0.312 -0.033 0.176 0.0493580254 140 0.096 -0.446 0.356 0.302 -0.033 0.176 0.0493002358 142 0.096 -0.446 0.356 0.301 -0.033 0.176 0.0492971833 150 0.096 -0.446 0.356 0.301 -0.012 0.176 0.0492544142 153 0.096 -0.446 0.356 0.301 -0.011 0.176 0.0492542285 165 0.096 -0.446 0.356 0.301 -0.011 0.169 0.0492373749 166 0.096 -0.446 0.356 0.301 -0.011 0.166 0.0492364337 powell nthiter 2: fret = 0.049236 178 0.089 -0.446 0.356 0.301 -0.011 0.166 0.0492298432 179 0.091 -0.446 0.356 0.301 -0.011 0.166 0.0492290889 191 0.091 -0.439 0.356 0.301 -0.011 0.166 0.0492137326 193 0.091 -0.441 0.356 0.301 -0.011 0.166 0.0492104176 203 0.091 -0.441 0.355 0.301 -0.011 0.166 0.0492083636 204 0.091 -0.441 0.341 0.301 -0.011 0.166 0.0492037543 206 0.091 -0.441 0.347 0.301 -0.011 0.166 0.0492004595 215 0.091 -0.441 0.347 0.319 -0.011 0.166 0.0491633018 217 0.091 -0.441 0.347 0.316 -0.011 0.166 0.0491494618 218 0.091 -0.441 0.347 0.310 -0.011 0.166 0.0491353730 220 0.091 -0.441 0.347 0.311 -0.011 0.166 0.0491351848 228 0.091 -0.441 0.347 0.311 -0.018 0.166 0.0491332248 230 0.091 -0.441 0.347 0.311 -0.016 0.166 0.0491330293 240 0.091 -0.441 0.347 0.311 -0.016 0.167 0.0491315917 241 0.091 -0.441 0.347 0.311 -0.016 0.170 0.0491300170 243 0.091 -0.441 0.347 0.311 -0.016 0.169 0.0491299750 244 0.086 -0.437 0.337 0.322 -0.020 0.172 0.0490798790 247 0.077 -0.429 0.322 0.340 -0.027 0.177 0.0490750244 248 0.081 -0.433 0.329 0.332 -0.024 0.175 0.0490663498 252 0.081 -0.433 0.329 0.332 -0.024 0.175 0.0490662112 254 0.081 -0.432 0.328 0.332 -0.024 0.175 0.0490660326 255 0.081 -0.433 0.328 0.332 -0.024 0.175 0.0490659500 powell nthiter 3: fret = 0.049066 267 0.092 -0.433 0.328 0.332 -0.024 0.175 0.0490364031 268 0.093 -0.433 0.328 0.332 -0.024 0.175 0.0490355739 288 0.093 -0.433 0.286 0.332 -0.024 0.175 0.0488565149 290 0.093 -0.433 0.295 0.332 -0.024 0.175 0.0488317518 291 0.093 -0.433 0.298 0.332 -0.024 0.175 0.0488308762 292 0.093 -0.433 0.297 0.332 -0.024 0.175 0.0488307707 299 0.093 -0.433 0.297 0.332 -0.024 0.207 0.0488204444 300 0.093 -0.433 0.297 0.332 -0.024 0.196 0.0487657237 301 0.093 -0.433 0.297 0.332 -0.024 0.192 0.0487579973 313 0.093 -0.433 0.297 0.332 -0.021 0.192 0.0487562276 321 0.091 -0.431 0.293 0.336 -0.022 0.193 0.0487516556 322 0.092 -0.431 0.294 0.335 -0.022 0.192 0.0487513277 326 0.092 -0.431 0.294 0.335 -0.022 0.192 0.0487511821 327 0.092 -0.431 0.294 0.335 -0.022 0.192 0.0487511293 332 0.092 -0.431 0.294 0.335 -0.022 0.192 0.0487511032 powell nthiter 4: fret = 0.048751 342 0.090 -0.431 0.294 0.335 -0.022 0.192 0.0487502464 354 0.090 -0.422 0.294 0.335 -0.022 0.192 0.0487126867 356 0.090 -0.425 0.294 0.335 -0.022 0.192 0.0487039310 368 0.090 -0.425 0.284 0.335 -0.022 0.192 0.0486990998 369 0.090 -0.425 0.288 0.335 -0.022 0.192 0.0486951477 378 0.090 -0.425 0.288 0.335 -0.022 0.197 0.0486728020 381 0.090 -0.425 0.288 0.335 -0.022 0.204 0.0486622295 394 0.090 -0.425 0.288 0.335 -0.023 0.204 0.0486620097 402 0.089 -0.424 0.287 0.337 -0.024 0.204 0.0486603687 403 0.089 -0.424 0.287 0.337 -0.024 0.204 0.0486603663 405 0.087 -0.417 0.279 0.339 -0.025 0.216 0.0486247132 410 0.085 -0.412 0.275 0.340 -0.026 0.224 0.0486208378 412 0.086 -0.414 0.277 0.339 -0.026 0.221 0.0486189009 413 0.086 -0.414 0.277 0.339 -0.026 0.221 0.0486186219 417 0.086 -0.414 0.277 0.339 -0.026 0.221 0.0486184655 418 0.086 -0.414 0.277 0.339 -0.026 0.221 0.0486184129 powell nthiter 5: fret = 0.048618 429 0.083 -0.414 0.277 0.339 -0.026 0.221 0.0486135727 430 0.081 -0.414 0.277 0.339 -0.026 0.221 0.0486129555 456 0.081 -0.414 0.278 0.339 -0.026 0.221 0.0486115998 457 0.081 -0.414 0.280 0.339 -0.026 0.221 0.0486108231 480 0.081 -0.414 0.280 0.339 -0.024 0.221 0.0486094522 481 0.081 -0.414 0.280 0.339 -0.022 0.221 0.0486093369 489 0.081 -0.413 0.279 0.339 -0.023 0.223 0.0486082166 490 0.081 -0.413 0.279 0.339 -0.023 0.223 0.0486081657 496 0.081 -0.413 0.279 0.339 -0.023 0.223 0.0486080784 powell nthiter 6: fret = 0.048608 517 0.081 -0.413 0.278 0.340 -0.023 0.223 0.0486080655 519 0.081 -0.413 0.278 0.340 -0.023 0.223 0.0486080290 522 0.081 -0.413 0.278 0.340 -0.023 0.223 0.0486080217 534 0.081 -0.413 0.279 0.340 -0.023 0.223 0.0486079904 546 0.081 -0.413 0.279 0.340 -0.023 0.222 0.0486076262 557 0.081 -0.413 0.279 0.340 -0.022 0.222 0.0486076158 558 0.081 -0.413 0.279 0.340 -0.021 0.222 0.0486075581 575 0.081 -0.413 0.279 0.340 -0.021 0.222 0.0486075370 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 0.968104 1 -25.0 -25.0 25.0 0.951368 2 -25.0 25.0 -25.0 0.939250 3 -25.0 25.0 25.0 0.995674 4 25.0 -25.0 -25.0 0.943225 5 25.0 -25.0 25.0 0.953280 6 25.0 25.0 -25.0 0.956256 7 25.0 25.0 25.0 0.965459 REL: 8 0.048608 7.672617 0.959077 rel = 0.0506816 Number of iterations 6 Min cost was 0.048608 Number of FunctionCalls 578 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.742110 sec Parameters at optimum (transmm) 0.08070 -0.41272 0.27940 Parameters at optimum (rotdeg) 0.33962 -0.02069 0.22204 Final costs ---------------- Number of surface hits 2490 WM Intensity 269.9334 +/- 55.1653 Ctx Intensity 375.4230 +/- 93.1796 Pct Contrast 31.6316 +/- 19.5108 Cost 0.0486 RelCost 0.0808 Reg at min cost was -0.99999 0.00057 -0.00405 0.19492; -0.00405 -0.00860 0.99995 -0.74436; -0.00053 -0.99996 -0.00860 1.08397; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat, type = 14 Original Reg -1.00000 0.00017 -0.00017 0.11322; -0.00018 -0.01453 0.99989 -0.32730; -0.00017 -0.99989 -0.01453 0.80649; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 -0.00039 0.00387 -0.08170; 0.00387 -0.00593 -0.00006 0.41706; 0.00036 0.00007 -0.00593 -0.27748; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.594863 Computing change in rh position Surface-RMS-Diff-mm 0.651333 0.196785 1.034671 mri_segreg done mri_segreg --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --init-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat --out-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 7.2.0 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mri_segreg --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii --init-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat --out-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 movvol /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/template.nii regfile /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/tmp.bbregister.41532/bbr.pass1.dat subject 31231_T2_3T dof 6 outregfile /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 1.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1676445934 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 0.00057 -0.00405 0.19492; -0.00405 -0.00860 0.99995 -0.74436; -0.00053 -0.99996 -0.00860 1.08397; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 1.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.984395 1 -25.0 -25.0 25.0 0.968487 2 -25.0 25.0 -25.0 0.959366 3 -25.0 25.0 25.0 0.984293 4 25.0 -25.0 -25.0 0.976010 5 25.0 -25.0 25.0 0.943883 6 25.0 25.0 -25.0 0.950153 7 25.0 25.0 25.0 0.974045 REL: 8 0.046622 7.740632 0.967579 rel = 0.0481838 Initial costs ---------------- Number of surface hits 247725 WM Intensity 267.3166 +/- 52.3476 Ctx Intensity 374.6103 +/- 92.2756 Pct Contrast 32.3264 +/- 18.7308 Cost 0.0466 RelCost 0.0482 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0449 0.0449 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0443 0.0443 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0440 0.0440 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0438 0.0438 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0432 0.0432 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0425 0.0425 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0422 0.0422 0.0 95 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.0422 0.0422 0.0 98 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.1000 0.0415 0.0415 0.0 101 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.1000 0.0415 0.0415 0.0 104 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.0409 0.0409 0.0 183 -0.1000 0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0405 0.0405 0.0 Brute Force -------------------------- Min cost was 0.040475 Number of iterations 729 Search time 0.934602 sec Parameters at best (transmm, rotdeg) -0.100 0.100 -0.100 0.100 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 0.1 2 -0.1 3 0.1 4 0 5 -0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.045041 7 -0.045 0.100 -0.100 0.100 0.000 -0.100 0.0449770559 8 -0.043 0.100 -0.100 0.100 0.000 -0.100 0.0449759466 9 -0.022 0.100 -0.100 0.100 0.000 -0.100 0.0449515434 13 -0.018 0.100 -0.100 0.100 0.000 -0.100 0.0449503354 14 -0.017 0.100 -0.100 0.100 0.000 -0.100 0.0449501811 22 -0.017 0.104 -0.100 0.100 0.000 -0.100 0.0449431056 23 -0.017 0.134 -0.100 0.100 0.000 -0.100 0.0449165957 24 -0.017 0.135 -0.100 0.100 0.000 -0.100 0.0449160489 26 -0.017 0.162 -0.100 0.100 0.000 -0.100 0.0448780940 29 -0.017 0.165 -0.100 0.100 0.000 -0.100 0.0448752190 30 -0.017 0.167 -0.100 0.100 0.000 -0.100 0.0448743694 31 -0.017 0.168 -0.100 0.100 0.000 -0.100 0.0448743166 39 -0.017 0.168 -0.394 0.100 0.000 -0.100 0.0431115369 40 -0.017 0.168 -0.398 0.100 0.000 -0.100 0.0430990260 41 -0.017 0.168 -0.520 0.100 0.000 -0.100 0.0429535149 42 -0.017 0.168 -0.498 0.100 0.000 -0.100 0.0428905090 43 -0.017 0.168 -0.474 0.100 0.000 -0.100 0.0428676959 44 -0.017 0.168 -0.475 0.100 0.000 -0.100 0.0428675184 45 -0.017 0.168 -0.476 0.100 0.000 -0.100 0.0428674227 47 -0.017 0.168 -0.477 0.100 0.000 -0.100 0.0428673736 55 -0.017 0.168 -0.477 0.021 0.000 -0.100 0.0424826417 57 -0.017 0.168 -0.477 -0.017 0.000 -0.100 0.0424578987 59 -0.017 0.168 -0.477 -0.032 0.000 -0.100 0.0424548241 61 -0.017 0.168 -0.477 -0.029 0.000 -0.100 0.0424544953 72 -0.017 0.168 -0.477 -0.029 0.002 -0.100 0.0424544455 73 -0.017 0.168 -0.477 -0.029 0.003 -0.100 0.0424543976 89 -0.017 0.168 -0.477 -0.029 0.003 -0.104 0.0424535656 powell nthiter 1: fret = 0.042454 99 -0.097 0.168 -0.477 -0.029 0.003 -0.104 0.0422957293 100 -0.093 0.168 -0.477 -0.029 0.003 -0.104 0.0422927262 102 -0.089 0.168 -0.477 -0.029 0.003 -0.104 0.0422914085 103 -0.088 0.168 -0.477 -0.029 0.003 -0.104 0.0422913920 111 -0.088 0.071 -0.477 -0.029 0.003 -0.104 0.0419393245 112 -0.088 0.050 -0.477 -0.029 0.003 -0.104 0.0419200152 113 -0.088 0.039 -0.477 -0.029 0.003 -0.104 0.0419141932 115 -0.088 0.025 -0.477 -0.029 0.003 -0.104 0.0419124905 116 -0.088 0.028 -0.477 -0.029 0.003 -0.104 0.0419118084 117 -0.088 0.030 -0.477 -0.029 0.003 -0.104 0.0419116997 126 -0.088 0.030 -0.460 -0.029 0.003 -0.104 0.0418792193 127 -0.088 0.030 -0.447 -0.029 0.003 -0.104 0.0418716668 128 -0.088 0.030 -0.448 -0.029 0.003 -0.104 0.0418714153 129 -0.088 0.030 -0.449 -0.029 0.003 -0.104 0.0418712331 138 -0.088 0.030 -0.449 -0.033 0.003 -0.104 0.0418649559 139 -0.088 0.030 -0.449 -0.062 0.003 -0.104 0.0418364804 141 -0.088 0.030 -0.449 -0.068 0.003 -0.104 0.0418364359 142 -0.088 0.030 -0.449 -0.065 0.003 -0.104 0.0418361598 143 -0.088 0.030 -0.449 -0.064 0.003 -0.104 0.0418361449 150 -0.088 0.030 -0.449 -0.064 -0.001 -0.104 0.0418323775 152 -0.088 0.030 -0.449 -0.064 -0.009 -0.104 0.0418306852 153 -0.088 0.030 -0.449 -0.064 -0.007 -0.104 0.0418300047 154 -0.088 0.030 -0.449 -0.064 -0.006 -0.104 0.0418299836 162 -0.088 0.030 -0.449 -0.064 -0.006 -0.203 0.0417876698 163 -0.088 0.030 -0.449 -0.064 -0.006 -0.174 0.0417822089 165 -0.088 0.030 -0.449 -0.064 -0.006 -0.166 0.0417802876 167 -0.088 0.030 -0.449 -0.064 -0.006 -0.157 0.0417779770 powell nthiter 2: fret = 0.041778 177 -0.100 0.030 -0.449 -0.064 -0.006 -0.157 0.0417690619 178 -0.109 0.030 -0.449 -0.064 -0.006 -0.157 0.0417677963 179 -0.107 0.030 -0.449 -0.064 -0.006 -0.157 0.0417671175 189 -0.107 0.006 -0.449 -0.064 -0.006 -0.157 0.0417620683 190 -0.107 0.013 -0.449 -0.064 -0.006 -0.157 0.0417619722 191 -0.107 0.010 -0.449 -0.064 -0.006 -0.157 0.0417619479 193 -0.107 0.009 -0.449 -0.064 -0.006 -0.157 0.0417619002 202 -0.107 0.009 -0.448 -0.064 -0.006 -0.157 0.0417605563 203 -0.107 0.009 -0.432 -0.064 -0.006 -0.157 0.0417509822 206 -0.107 0.009 -0.431 -0.064 -0.006 -0.157 0.0417509342 217 -0.107 0.009 -0.431 -0.065 -0.006 -0.157 0.0417508687 227 -0.107 0.009 -0.431 -0.065 -0.008 -0.157 0.0417502828 228 -0.107 0.009 -0.431 -0.065 -0.010 -0.157 0.0417502216 231 -0.107 0.009 -0.431 -0.065 -0.009 -0.157 0.0417501685 240 -0.107 0.009 -0.431 -0.065 -0.009 -0.168 0.0417474850 241 -0.107 0.009 -0.431 -0.065 -0.009 -0.171 0.0417474261 242 -0.107 0.009 -0.431 -0.065 -0.009 -0.170 0.0417473720 powell nthiter 3: fret = 0.041747 251 -0.105 0.009 -0.431 -0.065 -0.009 -0.170 0.0417472223 261 -0.105 0.005 -0.431 -0.065 -0.009 -0.170 0.0417469697 263 -0.105 0.006 -0.431 -0.065 -0.009 -0.170 0.0417469240 273 -0.105 0.006 -0.430 -0.065 -0.009 -0.170 0.0417465524 275 -0.105 0.006 -0.428 -0.065 -0.009 -0.170 0.0417463248 285 -0.105 0.006 -0.428 -0.064 -0.009 -0.170 0.0417463097 295 -0.105 0.006 -0.428 -0.064 -0.010 -0.170 0.0417461956 311 -0.105 0.006 -0.428 -0.064 -0.010 -0.169 0.0417461432 powell nthiter 4: fret = 0.041746 319 -0.100 0.006 -0.428 -0.064 -0.010 -0.169 0.0417460239 320 -0.102 0.006 -0.428 -0.064 -0.010 -0.169 0.0417458352 343 -0.102 0.006 -0.429 -0.064 -0.010 -0.169 0.0417458010 353 -0.102 0.006 -0.429 -0.062 -0.010 -0.169 0.0417457888 363 -0.102 0.006 -0.429 -0.062 -0.012 -0.169 0.0417456342 378 -0.099 0.006 -0.430 -0.061 -0.013 -0.169 0.0417450631 381 -0.095 0.006 -0.432 -0.059 -0.016 -0.169 0.0417445700 392 -0.095 0.006 -0.432 -0.059 -0.016 -0.169 0.0417445552 powell nthiter 5: fret = 0.041745 406 -0.095 0.006 -0.432 -0.059 -0.016 -0.168 0.0417444984 429 -0.095 0.006 -0.430 -0.059 -0.016 -0.168 0.0417442106 430 -0.095 0.006 -0.429 -0.059 -0.016 -0.168 0.0417442074 440 -0.095 0.006 -0.429 -0.061 -0.016 -0.168 0.0417438410 450 -0.095 0.006 -0.429 -0.061 -0.017 -0.168 0.0417436076 451 -0.095 0.006 -0.429 -0.061 -0.018 -0.168 0.0417436028 462 -0.094 0.006 -0.429 -0.061 -0.018 -0.168 0.0417435736 466 -0.094 0.006 -0.429 -0.061 -0.018 -0.168 0.0417435565 469 -0.094 0.006 -0.429 -0.061 -0.018 -0.168 0.0417435563 powell nthiter 6: fret = 0.041744 484 -0.094 0.006 -0.429 -0.061 -0.018 -0.169 0.0417435197 508 -0.094 0.006 -0.427 -0.061 -0.018 -0.169 0.0417433080 518 -0.094 0.006 -0.427 -0.062 -0.018 -0.169 0.0417431976 536 -0.094 0.006 -0.427 -0.062 -0.018 -0.169 0.0417431616 539 -0.094 0.006 -0.427 -0.062 -0.018 -0.169 0.0417431575 541 -0.094 0.006 -0.427 -0.062 -0.018 -0.169 0.0417431505 powell nthiter 7: fret = 0.041743 609 -0.094 0.006 -0.427 -0.062 -0.018 -0.169 0.0417431483 610 -0.094 0.006 -0.427 -0.062 -0.018 -0.169 0.0417431440 powell nthiter 8: fret = 0.041743 639 -0.094 0.007 -0.427 -0.062 -0.018 -0.169 0.0417431395 685 -0.094 0.007 -0.427 -0.062 -0.018 -0.169 0.0417431306 powell nthiter 9: fret = 0.041743 Powell done niters = 9 Computing relative cost 0 -25.0 -25.0 -25.0 0.988321 1 -25.0 -25.0 25.0 0.967346 2 -25.0 25.0 -25.0 0.961125 3 -25.0 25.0 25.0 0.981372 4 25.0 -25.0 -25.0 0.974440 5 25.0 -25.0 25.0 0.944111 6 25.0 25.0 -25.0 0.952158 7 25.0 25.0 25.0 0.978224 REL: 8 0.041743 7.747098 0.968387 rel = 0.0431058 Number of iterations 9 Min cost was 0.041743 Number of FunctionCalls 760 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 43.361236 sec Parameters at optimum (transmm) -0.09371 0.00733 -0.42744 Parameters at optimum (rotdeg) -0.06177 -0.01834 -0.16895 Final costs ---------------- Number of surface hits 247725 WM Intensity 268.2657 +/- 53.1385 Ctx Intensity 374.6372 +/- 94.8091 Pct Contrast 31.9488 +/- 18.3027 Cost 0.0417 RelCost 0.0482 Reg at min cost was -1.00000 0.00086 -0.00109 0.09867; -0.00110 -0.00968 0.99995 -0.73643; -0.00085 -0.99995 -0.00968 0.65739; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 0.00057 -0.00405 0.19492; -0.00405 -0.00860 0.99995 -0.74436; -0.00053 -0.99996 -0.00860 1.08397; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 -0.00029 -0.00295 0.09625; -0.00295 0.00108 0.00000 -0.00793; 0.00032 -0.00001 0.00108 0.42658; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.455221 Computing change in rh position Surface-RMS-Diff-mm 0.465864 0.022843 0.525776 mri_segreg done MinCost: 0.041743 268.265712 374.637188 31.948827 tkregister2_cmdl --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz --reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat --noedit --ltaout /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz reg file /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 ---- Input registration matrix -------- -1.00000 0.00086 -0.00109 0.09867; -0.00110 -0.00968 0.99995 -0.73643; -0.00085 -0.99995 -0.00968 0.65739; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 94.00000; 0.00000 0.00000 1.00000 -120.00000; 0.00000 -1.00000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -1.00000 0.00086 -0.00109 0.09867; -0.00110 -0.00968 0.99995 -0.73643; -0.00085 -0.99995 -0.00968 0.65739; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 31231_T2_3T RegMat --------------------------- -1.00000 0.00086 -0.00109 0.09867; -0.00110 -0.00968 0.99995 -0.73643; -0.00085 -0.99995 -0.00968 0.65739; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Thu Feb 9 17:10:10 CST 2023 Ended at Thu Feb 9 17:11:59 CST 2023 BBR-Run-Time-Sec 109 bbregister Done To check results, run: tkregisterfv --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz --reg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.lta --surfs --sd /scratch/g/tmeier/ChronEx/FS7.2/data cp /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.auto.lta /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.lta mri_convert -odt float -at /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.lta -rl /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.prenorm.mgz reading from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) INFO: Reading transformation from file /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz... INFO: Applying transformation from file /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.00000 0.00085 -0.00110 0.08836; -0.00086 0.99995 -0.00968 -0.44263; 0.00109 0.00968 0.99995 0.74805; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from short to float (noscale = 0)... writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.prenorm.mgz... mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/aseg.presurf.mgz -surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white identity.nofile -surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white identity.nofile /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.prenorm.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.norm.mgz setting seed for random number genererator to 1234 using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading mri_src from /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.prenorm.mgz... Copying mri_dst from mri_src computing distance transform computing distance transform min_dist = 1 Erasing Border planes 4 Removing non-wm voxels 48826 non wm control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 MRIapplyBiasCorrectionSameGeometry() writing normalized volume to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 1639392 mri_normalize done mri_mask -transfer 255 -keep_mask_deletion_edits /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.norm.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/brain.finalsurfs.mgz /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/T2.mgz...done. #-------------------------------------------- #@# MMPialSurf lh Thu Feb 9 17:12:38 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 12 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 7.2.0 7.2.0 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 12 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface Area 261124 0.41884 0.31481 0.000384 6.4262 Corner 783372 60.00000 30.52392 0.047450 179.8660 Edge 391686 1.03792 0.46459 0.009736 7.5859 Hinge 391686 19.36499 24.35667 0.000010 179.9998 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=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 61.9469 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 Reading in multimodal volume T2.mgz using multi modal weights vertex 65282: xyz = (-49.2805,3.38477,32.7167) oxyz = (-50.4889,2.88483,31.0954) wxzy = (-50.4889,2.88483,31.0954) pxyz = (-49.2805,3.38477,32.7167) CBVO Creating mask 130564 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 5572 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0157506 Creating white distance volumes t=0.437156 (box.dx, box.dy, box.dz) = (126, 198, 338) (region->dx, region->dy, region->dz) = (126, 198, 338) (region->dx, region->dy, region->dz) = (126, 198, 338) Creating pial distance volumes t=0.794087 (box.dx, box.dy, box.dz) = (140, 212, 346) (region->dx, region->dy, region->dz) = (140, 212, 346) (region->dx, region->dy, region->dz) = (140, 212, 346) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.24201 Starting loop over 130564 vertices vno = 0, t = 1.24201 vno = 20000, t = 2.46708 vno = 40000, t = 3.74086 vno = 60000, t = 4.91693 vno = 80000, t = 6.08661 vno = 100000, t = 7.24765 vno = 120000, t = 8.43909 CPTL: t = 9.06829 72280 surface locations found to contain inconsistent values (12258 in, 60022 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn06., nav=4, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 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=376799.4, rms=0.678 rms = 0.6785/0.6782, sse=345185.7/376799.4, time step reduction 1 of 3 to 0.250 1 0 0 001: dt: 0.5000, sse=345185.7, rms=0.678 (-0.050%) 002: dt: 0.2500, sse=334472.9, rms=0.678 (0.026%) 003: dt: 0.2500, sse=331005.2, rms=0.676 (0.340%) 004: dt: 0.2500, sse=329238.8, rms=0.674 (0.259%) 005: dt: 0.2500, sse=328596.5, rms=0.674 (0.100%) rms = 0.6740/0.6736, sse=327539.7/328596.5, time step reduction 2 of 3 to 0.125 1 0 0 006: dt: 0.2500, sse=327539.7, rms=0.674 (-0.057%) rms = 0.6744/0.6740, sse=326609.7/327539.7, time step reduction 3 of 3 to 0.062 1 0 0 007: dt: 0.1250, sse=326609.7, rms=0.674 (-0.068%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 5572 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0153728 Creating white distance volumes t=0.536769 (box.dx, box.dy, box.dz) = (126, 198, 338) (region->dx, region->dy, region->dz) = (126, 198, 338) (region->dx, region->dy, region->dz) = (126, 198, 338) Creating pial distance volumes t=0.999612 (box.dx, box.dy, box.dz) = (138, 210, 346) (region->dx, region->dy, region->dz) = (138, 210, 346) (region->dx, region->dy, region->dz) = (138, 210, 346) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.57536 Starting loop over 130564 vertices vno = 0, t = 1.57536 vno = 20000, t = 2.78291 vno = 40000, t = 4.02051 vno = 60000, t = 5.18738 vno = 80000, t = 6.3333 vno = 100000, t = 7.47162 vno = 120000, t = 8.65837 CPTL: t = 9.28439 75093 surface locations found to contain inconsistent values (8179 in, 66914 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn06., nav=2, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 mom=0.00, dt=0.50 000: dt: 0.0000, sse=302987.3, rms=0.671 008: dt: 0.5000, sse=303757.6, rms=0.664 (1.087%) 009: dt: 0.5000, sse=302563.3, rms=0.663 (0.093%) rms = 0.6644/0.6629, sse=302183.9/302563.3, time step reduction 1 of 3 to 0.250 1 0 0 010: dt: 0.5000, sse=302183.9, rms=0.664 (-0.228%) rms = 0.6655/0.6644, sse=301606.8/302183.9, time step reduction 2 of 3 to 0.125 1 0 0 011: dt: 0.2500, sse=301606.8, rms=0.665 (-0.155%) rms = 0.6657/0.6655, sse=301326.3/301606.8, time step reduction 3 of 3 to 0.062 1 0 0 012: dt: 0.1250, sse=301326.3, rms=0.666 (-0.034%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Pinning medial wall to white surface removing intersecting faces 000: 3 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T2 #ET# mris_place_surface 19.35 minutes #VMPC# mris_place_surfaces VmPeak 2980340 mris_place_surface done #-------------------------------------------- #@# MMPialSurf rh Thu Feb 9 17:32:05 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 12 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.pial.T1 --o ../surf/rh.pial.T2 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --white-surf ../surf/rh.white --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --mmvol T2.mgz T2 7.2.0 7.2.0 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 12 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.pial.T1 --o ../surf/rh.pial.T2 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --white-surf ../surf/rh.white --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --mmvol T2.mgz T2 Reading in input surface ../surf/rh.pial.T1 Not smoothing input surface Area 264894 0.40750 0.29796 0.000205 6.3746 Corner 794682 60.00000 30.12835 0.050843 179.8559 Edge 397341 1.02302 0.44808 0.004975 7.3639 Hinge 397341 19.04484 24.34817 0.000016 179.9911 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=25802, wmmin=5, clip=110 MRIfindBrightNonWM(): 400 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 61.9469 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 Reading in multimodal volume T2.mgz using multi modal weights vertex 66225: xyz = (30.2069,4.18651,-18.6206) oxyz = (28.1406,5.16566,-17.2798) wxzy = (28.1406,5.16566,-17.2798) pxyz = (30.2069,4.18651,-18.6206) CBVO Creating mask 132449 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 5572 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0156372 Creating white distance volumes t=0.427046 (box.dx, box.dy, box.dz) = (126, 202, 338) (region->dx, region->dy, region->dz) = (126, 202, 338) (region->dx, region->dy, region->dz) = (126, 202, 338) Creating pial distance volumes t=0.772634 (box.dx, box.dy, box.dz) = (136, 214, 344) (region->dx, region->dy, region->dz) = (136, 214, 344) (region->dx, region->dy, region->dz) = (136, 214, 344) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.20064 Starting loop over 132449 vertices vno = 0, t = 1.20064 vno = 20000, t = 2.68684 vno = 40000, t = 3.98591 vno = 60000, t = 5.03635 vno = 80000, t = 6.01925 vno = 100000, t = 6.96373 vno = 120000, t = 8.04338 CPTL: t = 8.74385 75357 surface locations found to contain inconsistent values (13689 in, 61668 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn06., nav=4, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 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=370536.7, rms=0.668 001: dt: 0.5000, sse=339022.3, rms=0.667 (0.284%) 002: dt: 0.5000, sse=328090.6, rms=0.661 (0.757%) 003: dt: 0.5000, sse=323995.0, rms=0.661 (0.067%) 004: dt: 0.5000, sse=321738.8, rms=0.661 (0.017%) rms = 0.6631/0.6609, sse=320706.0/321738.8, time step reduction 1 of 3 to 0.250 1 0 0 005: dt: 0.5000, sse=320706.0, rms=0.663 (-0.330%) rms = 0.6648/0.6631, sse=320144.3/320706.0, time step reduction 2 of 3 to 0.125 1 0 0 006: dt: 0.2500, sse=320144.3, rms=0.665 (-0.262%) rms = 0.6654/0.6648, sse=319818.1/320144.3, time step reduction 3 of 3 to 0.062 1 0 0 007: dt: 0.1250, sse=319818.2, rms=0.665 (-0.087%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 MRIcopyHeader(): source has ctab Changed 5572 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0159006 Creating white distance volumes t=0.441175 (box.dx, box.dy, box.dz) = (126, 202, 338) (region->dx, region->dy, region->dz) = (126, 202, 338) (region->dx, region->dy, region->dz) = (126, 202, 338) Creating pial distance volumes t=0.787434 (box.dx, box.dy, box.dz) = (136, 212, 342) (region->dx, region->dy, region->dz) = (136, 212, 342) (region->dx, region->dy, region->dz) = (136, 212, 342) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.20735 Starting loop over 132449 vertices vno = 0, t = 1.20735 vno = 20000, t = 2.69527 vno = 40000, t = 3.99539 vno = 60000, t = 5.05809 vno = 80000, t = 6.05757 vno = 100000, t = 7.00888 vno = 120000, t = 8.09838 CPTL: t = 8.81145 78569 surface locations found to contain inconsistent values (8120 in, 70449 out) Positioning Surface: tspring = 0.3, nspring = 1, spring = 0, niters = 100 l_repulse = 0.025, l_surf_repulse = 5, checktol = 1 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 1, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn06., nav=2, nbrs=2, l_repulse=0.025, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=1.000, l_location=0.500, l_curv=0.500 mom=0.00, dt=0.50 000: dt: 0.0000, sse=293349.8, rms=0.663 008: dt: 0.5000, sse=294176.2, rms=0.656 (1.122%) 009: dt: 0.5000, sse=293527.7, rms=0.655 (0.186%) rms = 0.6555/0.6546, sse=293115.4/293527.7, time step reduction 1 of 3 to 0.250 1 0 0 010: dt: 0.5000, sse=293115.3, rms=0.655 (-0.128%) rms = 0.6560/0.6555, sse=293104.3/293115.4, time step reduction 2 of 3 to 0.125 1 0 0 011: dt: 0.2500, sse=293104.3, rms=0.656 (-0.080%) rms = 0.6561/0.6560, sse=292535.6/293104.3, time step reduction 3 of 3 to 0.062 1 0 0 012: dt: 0.1250, sse=292535.6, rms=0.656 (-0.010%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 14 intersecting 001: 4 intersecting step 1 with no progress (num=10, old_num=4) 002: 10 intersecting 003: 7 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T2 #ET# mris_place_surface 18.56 minutes #VMPC# mris_place_surfaces VmPeak 2946808 mris_place_surface done #@# white curv lh Thu Feb 9 17:50:44 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 #@# white area lh Thu Feb 9 17:50:46 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area #@# pial curv lh Thu Feb 9 17:50:46 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 #@# pial area lh Thu Feb 9 17:50:48 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial #@# thickness lh Thu Feb 9 17:50:48 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 130564 vertices processed 25000 of 130564 vertices processed 50000 of 130564 vertices processed 75000 of 130564 vertices processed 100000 of 130564 vertices processed 125000 of 130564 vertices processed 0 of 130564 vertices processed 25000 of 130564 vertices processed 50000 of 130564 vertices processed 75000 of 130564 vertices processed 100000 of 130564 vertices processed 125000 of 130564 vertices processed thickness calculation complete, 91:150 truncations. 53267 vertices at 0 distance 112372 vertices at 1 distance 64026 vertices at 2 distance 21214 vertices at 3 distance 7104 vertices at 4 distance 2162 vertices at 5 distance 638 vertices at 6 distance 205 vertices at 7 distance 73 vertices at 8 distance 29 vertices at 9 distance 11 vertices at 10 distance 3 vertices at 11 distance 2 vertices at 12 distance 4 vertices at 13 distance 9 vertices at 14 distance 3 vertices at 15 distance 3 vertices at 16 distance 2 vertices at 17 distance 1 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file ../surf/lh.thickness #@# area and vertex vol lh Thu Feb 9 17:51:11 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T lh /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.volume masking with /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Total face volume 230837 Total vertex volume 230658 (mask=0) #@# 31231_T2_3T lh 230658 vertexvol Done #@# white curv rh Thu Feb 9 17:51:13 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 #@# white area rh Thu Feb 9 17:51:14 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area #@# pial curv rh Thu Feb 9 17:51:15 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 #@# pial area rh Thu Feb 9 17:51:16 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial #@# thickness rh Thu Feb 9 17:51:17 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 132449 vertices processed 25000 of 132449 vertices processed 50000 of 132449 vertices processed 75000 of 132449 vertices processed 100000 of 132449 vertices processed 125000 of 132449 vertices processed 0 of 132449 vertices processed 25000 of 132449 vertices processed 50000 of 132449 vertices processed 75000 of 132449 vertices processed 100000 of 132449 vertices processed 125000 of 132449 vertices processed thickness calculation complete, 245:175 truncations. 55283 vertices at 0 distance 113664 vertices at 1 distance 63500 vertices at 2 distance 21890 vertices at 3 distance 7338 vertices at 4 distance 2242 vertices at 5 distance 639 vertices at 6 distance 180 vertices at 7 distance 51 vertices at 8 distance 21 vertices at 9 distance 20 vertices at 10 distance 17 vertices at 11 distance 5 vertices at 12 distance 15 vertices at 13 distance 6 vertices at 14 distance 9 vertices at 15 distance 8 vertices at 16 distance 6 vertices at 17 distance 2 vertices at 18 distance 0 vertices at 19 distance 2 vertices at 20 distance writing curvature file ../surf/rh.thickness #@# area and vertex vol rh Thu Feb 9 17:51:40 CST 2023 cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T rh /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.volume masking with /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Total face volume 226484 Total vertex volume 226284 (mask=0) #@# 31231_T2_3T rh 226284 vertexvol Done #----------------------------------------- #@# Curvature Stats lh Thu Feb 9 17:51:41 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 31231_T2_3T 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 [ 31231_T2_3T/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 [ 237 ] Gb_filter = 0 #----------------------------------------- #@# Curvature Stats rh Thu Feb 9 17:51:44 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 31231_T2_3T 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 [ 31231_T2_3T/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 [ 228 ] Gb_filter = 0 WARN: S lookup min: -0.035276 WARN: S explicit min: 0.000000 vertex = 1105 #-------------------------------------------- #@# Cortical ribbon mask Thu Feb 9 17:51:46 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T SUBJECTS_DIR is /scratch/g/tmeier/ChronEx/FS7.2/data 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 = 7 MRIcopyHeader(): source has ctab writing volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/ribbon.mgz mris_volmask took 3.87 minutes writing ribbon files MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab #----------------------------------------- #@# Cortical Parc 2 lh Thu Feb 9 17:55:38 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Thu Feb 9 17:55:38 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 90710 of (90710 90713) to complete... Waiting for PID 90713 of (90710 90713) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T lh ../surf/lh.sphere.reg /opt/freesurfer/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 /opt/freesurfer/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 46 labels changed using aseg relabeling using gibbs priors... 000: 8710 changed, 130564 examined... 001: 2018 changed, 33857 examined... 002: 594 changed, 10694 examined... 003: 272 changed, 3387 examined... 004: 123 changed, 1506 examined... 005: 52 changed, 739 examined... 006: 17 changed, 309 examined... 007: 8 changed, 108 examined... 008: 1 changed, 47 examined... 009: 0 changed, 6 examined... 33 labels changed using aseg 000: 224 total segments, 140 labels (1481 vertices) changed 001: 98 total segments, 14 labels (57 vertices) changed 002: 85 total segments, 1 labels (1 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1182 vertices marked for relabeling... 1182 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T rh ../surf/rh.sphere.reg /opt/freesurfer/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 /opt/freesurfer/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 11 labels changed using aseg relabeling using gibbs priors... 000: 8919 changed, 132449 examined... 001: 1991 changed, 34891 examined... 002: 562 changed, 10747 examined... 003: 233 changed, 3274 examined... 004: 101 changed, 1341 examined... 005: 50 changed, 579 examined... 006: 21 changed, 310 examined... 007: 14 changed, 129 examined... 008: 7 changed, 92 examined... 009: 7 changed, 43 examined... 010: 5 changed, 36 examined... 011: 2 changed, 32 examined... 012: 2 changed, 10 examined... 013: 0 changed, 10 examined... 3 labels changed using aseg 000: 224 total segments, 140 labels (2453 vertices) changed 001: 92 total segments, 8 labels (217 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 914 vertices marked for relabeling... 914 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. PIDs (90710 90713) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Thu Feb 9 17:55:50 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Thu Feb 9 17:55:50 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 90971 of (90971 90974) to complete... Waiting for PID 90974 of (90971 90974) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T lh ../surf/lh.sphere.reg /opt/freesurfer/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 /opt/freesurfer/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 1622 labels changed using aseg relabeling using gibbs priors... 000: 1859 changed, 130564 examined... 001: 444 changed, 8757 examined... 002: 129 changed, 2507 examined... 003: 63 changed, 761 examined... 004: 28 changed, 353 examined... 005: 18 changed, 168 examined... 006: 11 changed, 108 examined... 007: 9 changed, 74 examined... 008: 5 changed, 60 examined... 009: 3 changed, 33 examined... 010: 3 changed, 19 examined... 011: 2 changed, 16 examined... 012: 1 changed, 16 examined... 013: 0 changed, 7 examined... 278 labels changed using aseg 000: 54 total segments, 21 labels (99 vertices) changed 001: 33 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... 868 vertices marked for relabeling... 868 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 31231_T2_3T rh ../surf/rh.sphere.reg /opt/freesurfer/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 /opt/freesurfer/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 1697 labels changed using aseg relabeling using gibbs priors... 000: 1917 changed, 132449 examined... 001: 410 changed, 8963 examined... 002: 116 changed, 2367 examined... 003: 48 changed, 683 examined... 004: 25 changed, 285 examined... 005: 13 changed, 144 examined... 006: 13 changed, 86 examined... 007: 13 changed, 69 examined... 008: 6 changed, 57 examined... 009: 1 changed, 35 examined... 010: 1 changed, 8 examined... 011: 1 changed, 7 examined... 012: 3 changed, 7 examined... 013: 5 changed, 13 examined... 014: 2 changed, 21 examined... 015: 4 changed, 13 examined... 016: 3 changed, 14 examined... 017: 5 changed, 18 examined... 018: 5 changed, 24 examined... 019: 4 changed, 19 examined... 020: 4 changed, 18 examined... 021: 5 changed, 24 examined... 022: 2 changed, 25 examined... 023: 1 changed, 9 examined... 024: 1 changed, 7 examined... 025: 1 changed, 6 examined... 026: 1 changed, 8 examined... 027: 0 changed, 8 examined... 287 labels changed using aseg 000: 46 total segments, 13 labels (62 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 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... 756 vertices marked for relabeling... 756 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. PIDs (90971 90974) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Thu Feb 9 17:56:00 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts pctsurfcon --s 31231_T2_3T --lh-only #----------------------------------------- #@# WM/GM Contrast rh Thu Feb 9 17:56:00 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts pctsurfcon --s 31231_T2_3T --rh-only Waiting for PID 91234 of (91234 91237) to complete... Waiting for PID 91237 of (91234 91237) to complete... pctsurfcon --s 31231_T2_3T --lh-only Log file is /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts/pctsurfcon.log Thu Feb 9 17:56:00 CST 2023 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts /opt/freesurfer/bin/pctsurfcon pctsurfcon 7.2.0 Linux cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91234/lh.wm.mgh --regheader 31231_T2_3T --cortex srcvol = /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 INFO: changing type to float Done loading volume Computing registration from header. Using /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Reading surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 = 74576 Masking with /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91234/lh.wm.mgh Dim: 130564 1 1 mri_vol2surf --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91234/lh.gm.mgh --projfrac 0.3 --regheader 31231_T2_3T --cortex srcvol = /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 INFO: changing type to float Done loading volume Computing registration from header. Using /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Reading surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Done reading source surface Reading thickness /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 = 88088 Masking with /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91234/lh.gm.mgh Dim: 130564 1 1 mri_concat /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91234/lh.wm.mgh /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91234/lh.gm.mgh --paired-diff-norm --mul 100 --o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.w-g.pct.mgh mri_segstats --in /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.w-g.pct.mgh --annot 31231_T2_3T lh aparc --sum /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/stats/lh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.w-g.pct.mgh --annot 31231_T2_3T lh aparc --sum /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/stats/lh.w-g.pct.stats --snr sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.annot Seg base 1000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.w-g.pct.mgh Vertex Area is 0.668758 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 31231_T2_3T --rh-only Log file is /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts/pctsurfcon.log Thu Feb 9 17:56:00 CST 2023 setenv SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data cd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/scripts /opt/freesurfer/bin/pctsurfcon pctsurfcon 7.2.0 Linux cn06.cluster.local 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91237/rh.wm.mgh --regheader 31231_T2_3T --cortex srcvol = /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 INFO: changing type to float Done loading volume Computing registration from header. Using /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Reading surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 = 75006 Masking with /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91237/rh.wm.mgh Dim: 132449 1 1 mri_vol2surf --mov /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91237/rh.gm.mgh --projfrac 0.3 --regheader 31231_T2_3T --cortex srcvol = /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 INFO: changing type to float Done loading volume Computing registration from header. Using /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Reading surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Done reading source surface Reading thickness /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 = 88386 Masking with /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Writing to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91237/rh.gm.mgh Dim: 132449 1 1 mri_concat /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91237/rh.wm.mgh /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/tmp.pctsurfcon.91237/rh.gm.mgh --paired-diff-norm --mul 100 --o /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.w-g.pct.mgh mri_segstats --in /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.w-g.pct.mgh --annot 31231_T2_3T rh aparc --sum /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/stats/rh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.w-g.pct.mgh --annot 31231_T2_3T rh aparc --sum /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/stats/rh.w-g.pct.stats --snr sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.annot Seg base 2000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.w-g.pct.mgh Vertex Area is 0.661716 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 (91234 91237) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Thu Feb 9 17:56:03 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 900 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... MRIcopyHeader(): source has ctab 1167 voxels changed to hypointensity... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 2163 hypointense voxels neighboring cortex changed #----------------------------------------- #@# APas-to-ASeg Thu Feb 9 17:56:15 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/ribbon.mgz --threads 12 --lh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label --lh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white --lh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial --rh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label --rh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white --rh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data outvol aseg.mgz 12 avail.processors, using 12 Loading aseg.presurf.hypos.mgz MRIcopyHeader(): source has ctab Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/ribbon.mgz Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Done loading 0 151 235 66 214 22 44 109 193 88 130 172 1 23 45 215 236 194 67 2 24 46 237 195 216 68 3 47 25 196 217 238 173 4 69 48 26 218 197 5 239 70 49 27 198 219 6 240 174 50 71 28 199 220 7 241 51 152 29 89 221 200 72 8 242 110 52 30 201 222 175 9 243 73 53 31 223 202 10 244 54 32 224 203 11 245 176 74 55 33 204 225 12 246 56 131 34 205 226 13 247 75 57 35 177 206 227 153 14 248 111 58 36 228 207 249 15 90 76 59 37 16 250 229 208 178 60 38 17 251 230 209 61 39 18 252 77 210 231 179 62 40 19 253 211 232 63 41 254 20 212 233 78 180 64 154 21 42 255 213 234 112 65 43 181 79 132 91 182 80 183 155 184 113 81 185 186 187 82 188 156 189 92 190 83 191 133 192 84 157 93 114 85 158 134 86 94 87 159 95 135 115 160 96 136 161 97 116 162 98 163 137 117 99 164 165 100 138 166 118 101 167 102 168 139 169 103 119 170 140 171 104 141 120 105 106 142 121 107 143 122 108 144 123 145 124 146 147 148 125 149 150 126 127 128 129 nrelabeled = 197174 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1629892 mri_surf2volseg done mri_brainvol_stats 31231_T2_3T ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1394317.0 #CBVS2 BrainSegVol 1089884.0 #CBVS2 BrainSegVolNotVent 1078275.0 #CBVS2 SupraTentVol 955303.0 #CBVS2 SupraTentVolNotVent 943694.0 #CBVS2 lhCtxGM 231009.3 #CBVS2 rhCtxGM 226429.9 #CBVS2 lhCerebralWM 213870.0 #CBVS2 rhCerebralWM 213516.0 #CBVS2 SubCortGMVol 59284.0 #CBVS2 CerebellumVol 134581.0 #CBVS2 CerebellumGMVol 106942.0 #CBVS2 VentChorVol 9435.0 #CBVS2 3rd4th5thCSF 2174.0 #CBVS2 AllCSF 11609.0 #CBVS2 CCVol 3788.0 #----------------------------------------- #@# AParc-to-ASeg aparc Thu Feb 9 17:56:23 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 12 --lh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.annot 1000 --lh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label --lh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white --lh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial --rh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.annot 2000 --rh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label --rh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white --rh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data outvol aparc+aseg.mgz 12 avail.processors, using 12 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7567 vertices from lh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.annot Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7721 vertices from rh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.annot Done loading 22 0 214 151 193 88 130 44 109 66 235 172 194 45 23 236 195 46 24 215 1 237 2 196 47 25 216 238 3 197 48 26 217 239 4 198 49 27 67 218 240 5 199 50 28 241 219 6 51 29 200 242 220 7 52 30 201 243 221 8 31 53 202 244 222 9 32 54 203 245 223 10 33 55 204 246 224 11 34 56 205 247 225 35 57 12 206 248 226 36 13 58 207 249 227 37 14 59 208 250 228 38 15 60 209 251 68 229 39 16 61 210 252 230 40 17 62 211 253 231 18 41 63 212 254 232 19 42 64 213 255 233 20 43 65 21 234 69 70 110 152 173 71 131 89 72 111 153 174 132 90 112 73 154 175 133 113 91 155 74 176 134 156 114 75 177 92 135 157 115 76 178 136 93 158 116 77 179 159 137 94 78 180 117 138 160 79 95 181 139 118 161 80 96 182 140 81 162 119 183 141 97 184 82 142 185 163 98 186 120 187 188 189 190 191 192 143 83 121 99 144 164 84 145 100 122 85 165 146 101 123 86 147 166 102 124 148 87 103 167 125 149 104 126 168 150 127 105 128 106 169 129 107 170 108 171 nrelabeled = 456985 ndotcheck = 15712 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1614028 mri_surf2volseg done #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Thu Feb 9 17:56:46 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 12 --lh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label --lh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white --lh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial --rh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label --rh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white --rh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data outvol aparc.a2009s+aseg.mgz 12 avail.processors, using 12 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7567 vertices from lh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.a2009s.annot Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7721 vertices from rh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.a2009s.annot Done loading 0 44 109 66 151 172 214 193 235 88 22 130 1 45 194 215 23 236 2 46 195 24 216 237 3 47 196 25 217 238 48 4 197 26 218 239 67 49 27 198 219 5 240 50 28 199 220 241 6 51 29 200 221 242 7 52 30 201 222 243 8 53 31 202 223 244 9 54 32 203 224 245 55 10 33 204 225 246 56 34 11 205 226 247 57 35 227 206 12 248 58 36 228 207 249 13 37 59 229 208 250 14 68 38 60 209 230 251 15 39 61 210 231 252 16 40 62 211 232 253 41 63 17 212 233 254 42 64 18 213 234 255 43 65 19 20 21 69 70 110 152 71 173 131 89 72 111 153 174 132 90 112 73 154 175 133 113 74 91 155 176 134 114 156 75 92 177 135 115 157 76 178 93 136 158 116 77 179 159 137 94 78 117 180 79 160 138 95 118 80 181 139 161 96 81 140 182 119 162 97 141 82 183 120 142 184 98 163 83 185 186 143 187 188 189 190 191 192 121 84 99 144 164 122 85 100 145 165 146 101 86 123 147 102 166 87 124 148 103 125 167 126 104 149 127 168 105 150 128 106 169 129 107 170 108 171 nrelabeled = 456985 ndotcheck = 15712 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1614124 mri_surf2volseg done #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Thu Feb 9 17:57:10 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 12 --lh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label --lh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white --lh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial --rh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label --rh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white --rh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data outvol aparc.DKTatlas+aseg.mgz 12 avail.processors, using 12 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7567 vertices from lh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.DKTatlas.annot Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7721 vertices from rh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.DKTatlas.annot Done loading 0 151 235 88 44 66 172 214 193 130 22 109 1 215 194 236 23 45 2 195 216 237 24 46 3 196 217 238 25 47 197 4 218 239 26 48 67 198 219 240 5 27 49 199 220 241 28 50 6 200 221 242 29 51 7 201 222 243 30 52 8 223 202 31 244 53 9 224 203 32 245 54 10 225 204 33 246 55 11 226 205 34 56 247 227 206 35 12 57 248 228 207 36 13 58 249 229 208 37 59 250 14 68 230 209 38 60 251 15 231 210 39 61 252 16 232 211 40 62 253 17 212 233 41 63 254 18 213 234 42 64 255 19 43 65 20 21 69 70 110 152 173 71 131 89 72 111 153 174 132 90 112 73 154 175 133 113 91 74 155 176 134 114 75 156 92 177 135 115 76 157 178 93 136 158 116 77 179 94 159 137 78 117 180 79 95 138 160 181 118 80 139 96 161 182 81 140 119 97 162 183 82 141 184 98 120 185 142 83 186 163 187 188 189 190 191 192 143 99 121 84 144 164 100 122 85 145 101 123 165 86 146 102 124 147 87 166 103 125 148 104 167 126 149 105 127 168 128 150 106 129 107 169 108 170 171 nrelabeled = 456985 ndotcheck = 15712 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1614028 mri_surf2volseg done #----------------------------------------- #@# WMParc Thu Feb 9 17:57:34 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 12 --lh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.annot 3000 --lh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label --lh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white --lh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial --rh-annot /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.annot 4000 --rh-cortex-mask /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label --rh-white /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white --rh-pial /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data outvol wmparc.mgz 12 avail.processors, using 12 Loading aparc+aseg.mgz MRIcopyHeader(): source has ctab Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 7567 vertices from lh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.aparc.annot Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7721 vertices from rh hemi Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.aparc.annot Done loading 0 235 172 130 109 88 151 193 22 214 66 44 1 236 215 23 194 45 67 2 237 216 195 24 68 46 3 238 217 196 25 47 69 4 239 197 218 26 48 5 240 198 219 27 49 70 6 241 199 220 28 50 7 242 221 200 29 51 8 243 30 222 201 52 9 244 71 31 223 202 53 10 245 32 224 203 54 11 246 33 225 204 55 12 247 34 226 205 56 72 13 248 35 227 206 57 14 249 36 228 207 58 15 250 37 229 208 59 16 251 38 230 209 60 17 252 39 231 210 61 18 253 40 232 211 62 19 254 41 233 212 63 20 255 42 234 213 64 21 43 65 73 173 131 74 89 174 75 132 152 76 175 90 77 133 176 78 110 177 153 134 79 91 178 80 135 179 180 81 92 154 181 136 182 82 111 183 184 185 186 187 188 189 190 191 93 192 83 137 155 84 94 85 112 138 86 156 95 87 113 139 157 96 97 140 158 114 98 159 141 115 160 99 142 116 161 100 117 162 143 101 118 163 144 102 164 119 165 120 103 145 121 166 122 167 123 104 124 168 125 146 126 127 169 128 105 129 170 171 147 106 148 107 149 108 150 nrelabeled = 423598 ndotcheck = 4247 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1614028 mri_surf2volseg done 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 31231_T2_3T --surf-wm-vol --ctab /opt/freesurfer/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 31231_T2_3T --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 158937 mm^3 (det: 12.257028 ) 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 #----------------------------------------- #@# Parcellation Stats lh Thu Feb 9 17:59:55 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T 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 31231_T2_3T lh pial #----------------------------------------- #@# Parcellation Stats rh Thu Feb 9 17:59:55 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T 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 31231_T2_3T rh pial Waiting for PID 95993 of (95993 95997 96000 96003) to complete... Waiting for PID 95997 of (95993 95997 96000 96003) to complete... Waiting for PID 96000 of (95993 95997 96000 96003) to complete... Waiting for PID 96003 of (95993 95997 96000 96003) 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 31231_T2_3T lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 230837 Total vertex volume 230658 (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) = 158937 mm^3 (det: 12.257028 ) 1549 1024 2636 2.783 0.366 0.103 0.021 10 1.2 bankssts 810 562 1504 2.473 0.581 0.125 0.025 11 0.8 caudalanteriorcingulate 3935 2431 7224 2.845 0.495 0.109 0.023 31 3.9 caudalmiddlefrontal 1631 1230 2375 1.941 0.459 0.158 0.038 25 2.5 cuneus 391 268 1012 2.723 0.607 0.099 0.019 3 0.3 entorhinal 4355 3057 9240 2.797 0.515 0.122 0.029 49 4.7 fusiform 6261 4078 11691 2.636 0.476 0.117 0.023 65 5.7 inferiorparietal 4448 3162 8520 2.591 0.519 0.128 0.029 58 5.2 inferiortemporal 1534 1085 2630 2.252 0.831 0.131 0.036 21 1.9 isthmuscingulate 8301 5339 11618 2.091 0.526 0.131 0.034 103 10.9 lateraloccipital 3297 2515 6760 2.560 0.571 0.140 0.034 44 4.8 lateralorbitofrontal 4008 3088 6578 2.159 0.575 0.150 0.039 63 6.6 lingual 2653 1894 4812 2.405 0.602 0.130 0.039 47 4.2 medialorbitofrontal 4871 3278 11300 2.918 0.487 0.109 0.021 51 4.1 middletemporal 1003 635 1853 2.601 0.602 0.085 0.019 6 0.7 parahippocampal 2452 1576 4472 2.622 0.534 0.104 0.022 20 2.2 paracentral 2654 1836 5489 2.730 0.415 0.108 0.022 30 2.3 parsopercularis 946 673 2076 2.665 0.425 0.144 0.029 14 1.1 parsorbitalis 2113 1466 4201 2.597 0.412 0.129 0.027 27 2.2 parstriangularis 1536 1133 1858 1.978 0.526 0.133 0.030 14 2.0 pericalcarine 6372 3869 9447 2.282 0.663 0.106 0.026 56 6.5 postcentral 1784 1248 3154 2.383 0.723 0.129 0.027 23 2.0 posteriorcingulate 7208 4247 12858 2.855 0.591 0.103 0.025 56 7.3 precentral 5510 3923 10188 2.532 0.402 0.125 0.027 65 6.0 precuneus 790 605 1685 2.553 0.553 0.137 0.032 13 0.9 rostralanteriorcingulate 8308 5538 14478 2.401 0.490 0.122 0.024 96 8.2 rostralmiddlefrontal 10417 6946 23014 2.950 0.542 0.112 0.023 86 9.9 superiorfrontal 8354 5457 14358 2.440 0.501 0.121 0.027 93 8.6 superiorparietal 5927 3829 12503 2.976 0.471 0.093 0.020 43 4.5 superiortemporal 4697 3139 9560 2.753 0.531 0.113 0.025 46 4.4 supramarginal 332 227 801 2.624 0.317 0.144 0.029 6 0.5 frontalpole 595 532 2346 3.408 0.538 0.167 0.046 11 1.1 temporalpole 616 413 1230 2.785 0.382 0.135 0.031 7 0.7 transversetemporal 3339 2381 7189 3.044 0.691 0.131 0.040 42 5.4 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 31231_T2_3T lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 230837 Total vertex volume 230658 (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) = 158937 mm^3 (det: 12.257028 ) 1549 865 2636 2.783 0.366 0.090 0.023 28 1.0 bankssts 810 620 1504 2.473 0.581 0.127 0.028 40 0.9 caudalanteriorcingulate 3935 2622 7224 2.845 0.495 0.098 0.021 89 3.1 caudalmiddlefrontal 1631 1309 2375 1.941 0.459 0.132 0.029 43 1.8 cuneus 391 454 1012 2.723 0.607 0.188 0.045 18 1.0 entorhinal 4355 3507 9240 2.797 0.515 0.119 0.024 93 4.0 fusiform 6261 4692 11691 2.636 0.476 0.111 0.020 112 4.7 inferiorparietal 4448 3416 8520 2.591 0.519 0.118 0.028 168 4.2 inferiortemporal 1534 1240 2630 2.252 0.831 0.118 0.031 56 1.7 isthmuscingulate 8301 5824 11618 2.091 0.526 0.111 0.022 219 6.8 lateraloccipital 3297 2651 6760 2.560 0.571 0.115 0.022 52 2.6 lateralorbitofrontal 4008 3203 6578 2.159 0.575 0.109 0.024 77 3.2 lingual 2653 2120 4812 2.405 0.602 0.119 0.025 38 2.2 medialorbitofrontal 4871 4351 11300 2.918 0.487 0.121 0.020 105 3.7 middletemporal 1003 786 1853 2.601 0.602 0.094 0.019 11 0.8 parahippocampal 2452 1794 4472 2.622 0.534 0.096 0.016 28 1.5 paracentral 2654 2191 5489 2.730 0.415 0.113 0.018 35 2.0 parsopercularis 946 876 2076 2.665 0.425 0.131 0.023 10 0.8 parsorbitalis 2113 1760 4201 2.597 0.412 0.129 0.022 43 2.0 parstriangularis 1536 820 1858 1.978 0.526 0.091 0.020 38 1.2 pericalcarine 6372 4402 9447 2.282 0.663 0.092 0.016 70 3.9 postcentral 1784 1353 3154 2.383 0.723 0.115 0.023 101 1.4 posteriorcingulate 7208 4627 12858 2.855 0.591 0.089 0.018 150 4.2 precentral 5510 4081 10188 2.532 0.402 0.115 0.024 104 4.8 precuneus 790 706 1685 2.553 0.553 0.113 0.025 7 0.6 rostralanteriorcingulate 8308 6306 14478 2.401 0.490 0.121 0.023 151 7.5 rostralmiddlefrontal 10417 8303 23014 2.950 0.542 0.112 0.021 174 8.4 superiorfrontal 8354 6099 14358 2.440 0.501 0.108 0.021 130 6.3 superiorparietal 5927 4487 12503 2.976 0.471 0.096 0.016 91 3.5 superiortemporal 4697 3650 9560 2.753 0.531 0.112 0.019 65 3.5 supramarginal 332 387 801 2.624 0.317 0.161 0.018 2 0.3 frontalpole 595 836 2346 3.408 0.538 0.188 0.031 9 0.8 temporalpole 616 472 1230 2.785 0.382 0.099 0.018 6 0.3 transversetemporal 3339 2141 7189 3.044 0.691 0.106 0.028 81 3.0 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 31231_T2_3T rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 226484 Total vertex volume 226284 (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) = 158937 mm^3 (det: 12.257028 ) 1368 887 2129 2.763 0.368 0.092 0.017 7 1.0 bankssts 987 727 1961 2.331 0.718 0.137 0.027 14 1.1 caudalanteriorcingulate 3360 2051 6436 2.846 0.497 0.094 0.018 26 2.4 caudalmiddlefrontal 1987 1423 2626 1.905 0.534 0.138 0.033 24 2.7 cuneus 465 324 1038 2.541 0.661 0.123 0.042 5 1.1 entorhinal 3805 2753 7481 2.667 0.453 0.133 0.031 53 4.9 fusiform 7932 5287 14627 2.602 0.545 0.117 0.026 84 7.8 inferiorparietal 4248 2992 8974 2.734 0.579 0.127 0.032 55 5.5 inferiortemporal 1317 899 2059 2.194 0.834 0.125 0.033 18 1.5 isthmuscingulate 8480 5360 11722 2.153 0.618 0.131 0.034 112 11.1 lateraloccipital 3643 2761 7366 2.621 0.528 0.148 0.039 62 5.6 lateralorbitofrontal 4314 3279 7031 2.186 0.635 0.149 0.038 68 6.8 lingual 2668 1962 4941 2.455 0.583 0.128 0.028 39 3.0 medialorbitofrontal 5084 3332 10647 2.781 0.531 0.105 0.023 54 4.1 middletemporal 852 561 1708 2.762 0.667 0.103 0.022 7 0.7 parahippocampal 2421 1500 4375 2.803 0.513 0.108 0.023 19 2.4 paracentral 2244 1470 4070 2.581 0.378 0.094 0.017 17 1.6 parsopercularis 1178 841 2356 2.516 0.365 0.126 0.024 14 1.2 parsorbitalis 2680 1751 5180 2.700 0.418 0.114 0.020 25 2.4 parstriangularis 1796 1354 2139 1.860 0.513 0.144 0.039 20 3.0 pericalcarine 5716 3433 8194 2.250 0.510 0.097 0.024 43 5.1 postcentral 1643 1142 2879 2.396 0.824 0.128 0.030 21 1.9 posteriorcingulate 8216 4954 14306 2.740 0.555 0.101 0.025 68 8.6 precentral 5644 3989 10109 2.509 0.500 0.122 0.026 65 5.9 precuneus 732 547 1641 2.475 0.821 0.128 0.026 10 0.8 rostralanteriorcingulate 8469 5551 14674 2.479 0.503 0.117 0.025 91 8.4 rostralmiddlefrontal 10011 6545 21074 2.896 0.487 0.109 0.022 87 8.5 superiorfrontal 8176 5164 13045 2.385 0.481 0.119 0.028 100 8.4 superiorparietal 5818 3688 12116 2.954 0.545 0.090 0.020 65 4.6 superiortemporal 5113 3222 9651 2.721 0.480 0.115 0.026 58 5.3 supramarginal 408 297 1013 2.685 0.315 0.141 0.036 7 0.5 frontalpole 594 456 1541 2.791 0.648 0.128 0.035 8 0.8 temporalpole 425 280 901 2.974 0.416 0.119 0.025 4 0.4 transversetemporal 2934 2074 6276 3.060 0.833 0.122 0.030 29 3.9 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 31231_T2_3T rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 226484 Total vertex volume 226284 (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) = 158937 mm^3 (det: 12.257028 ) 1368 635 2129 2.763 0.368 0.082 0.017 25 0.7 bankssts 987 839 1961 2.331 0.718 0.113 0.029 39 0.8 caudalanteriorcingulate 3360 2380 6436 2.846 0.497 0.091 0.015 46 1.9 caudalmiddlefrontal 1987 1420 2626 1.905 0.534 0.110 0.019 102 1.3 cuneus 465 529 1038 2.541 0.661 0.162 0.037 4 0.8 entorhinal 3805 2840 7481 2.667 0.453 0.111 0.024 84 3.1 fusiform 7932 5808 14627 2.602 0.545 0.107 0.020 121 6.1 inferiorparietal 4248 3426 8974 2.734 0.579 0.114 0.024 86 3.4 inferiortemporal 1317 998 2059 2.194 0.834 0.136 0.049 207 0.9 isthmuscingulate 8480 5531 11722 2.153 0.618 0.107 0.025 286 6.8 lateraloccipital 3643 2855 7366 2.621 0.528 0.115 0.024 63 2.9 lateralorbitofrontal 4314 3330 7031 2.186 0.635 0.109 0.020 128 3.0 lingual 2668 2102 4941 2.455 0.583 0.105 0.021 36 1.9 medialorbitofrontal 5084 4249 10647 2.781 0.531 0.112 0.020 110 3.8 middletemporal 852 668 1708 2.762 0.667 0.120 0.023 16 0.8 parahippocampal 2421 1614 4375 2.803 0.513 0.091 0.017 42 1.3 paracentral 2244 1659 4070 2.581 0.378 0.105 0.016 31 1.4 parsopercularis 1178 1031 2356 2.516 0.365 0.115 0.019 14 0.8 parsorbitalis 2680 2059 5180 2.700 0.418 0.104 0.017 31 1.8 parstriangularis 1796 1010 2139 1.860 0.513 0.086 0.022 35 1.1 pericalcarine 5716 3887 8194 2.250 0.510 0.088 0.016 56 3.3 postcentral 1643 1180 2879 2.396 0.824 0.114 0.042 230 2.8 posteriorcingulate 8216 5371 14306 2.740 0.555 0.088 0.016 149 4.9 precentral 5644 4021 10109 2.509 0.500 0.109 0.022 149 4.5 precuneus 732 682 1641 2.475 0.821 0.116 0.027 11 0.5 rostralanteriorcingulate 8469 6014 14674 2.479 0.503 0.107 0.023 212 8.1 rostralmiddlefrontal 10011 7633 21074 2.896 0.487 0.107 0.019 168 6.8 superiorfrontal 8176 5702 13045 2.385 0.481 0.104 0.019 231 5.8 superiorparietal 5818 4382 12116 2.954 0.545 0.092 0.014 54 3.0 superiortemporal 5113 3736 9651 2.721 0.480 0.108 0.020 108 3.9 supramarginal 408 479 1013 2.685 0.315 0.159 0.027 3 0.4 frontalpole 594 674 1541 2.791 0.648 0.140 0.025 4 0.6 temporalpole 425 327 901 2.974 0.416 0.077 0.015 1 0.2 transversetemporal 2934 1884 6276 3.060 0.833 0.115 0.111 63 2.4 insula PIDs (95993 95997 96000 96003) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Feb 9 18:00:10 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T lh white #----------------------------------------- #@# Parcellation Stats 2 rh Thu Feb 9 18:00:10 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T rh white Waiting for PID 96824 of (96824 96827) to complete... Waiting for PID 96827 of (96824 96827) 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 31231_T2_3T lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 230837 Total vertex volume 230658 (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) = 158937 mm^3 (det: 12.257028 ) 1087 768 1662 2.102 0.372 0.123 0.024 15 1.2 G_and_S_frontomargin 2052 1363 3462 2.293 0.551 0.137 0.032 27 2.5 G_and_S_occipital_inf 2028 1207 3489 2.519 0.611 0.112 0.028 23 2.2 G_and_S_paracentral 1357 926 2795 2.910 0.613 0.132 0.032 16 1.6 G_and_S_subcentral 804 521 1598 2.426 0.440 0.143 0.032 14 1.0 G_and_S_transv_frontopol 1760 1327 3373 2.473 0.488 0.124 0.027 20 1.9 G_and_S_cingul-Ant 1156 800 2218 2.764 0.407 0.095 0.019 7 0.9 G_and_S_cingul-Mid-Ant 1353 927 2360 2.571 0.413 0.102 0.022 9 1.2 G_and_S_cingul-Mid-Post 586 438 1523 2.857 0.682 0.153 0.040 11 0.7 G_cingul-Post-dorsal 324 232 680 2.509 0.799 0.166 0.052 6 0.6 G_cingul-Post-ventral 1606 1240 2561 1.880 0.582 0.167 0.041 28 2.7 G_cuneus 1416 986 3535 2.906 0.429 0.123 0.027 24 1.5 G_front_inf-Opercular 479 341 1123 2.630 0.401 0.129 0.030 8 0.6 G_front_inf-Orbital 1244 874 3084 2.797 0.431 0.138 0.033 20 1.5 G_front_inf-Triangul 4977 3123 11171 2.840 0.517 0.126 0.027 66 5.4 G_front_middle 7431 4932 18588 3.100 0.535 0.121 0.027 81 8.4 G_front_sup 641 489 1663 3.266 0.735 0.164 0.059 17 1.6 G_Ins_lg_and_S_cent_ins 720 588 2489 3.472 0.689 0.145 0.044 11 1.2 G_insular_short 2570 1597 4952 2.478 0.652 0.133 0.032 42 3.0 G_occipital_middle 1518 1033 2667 2.292 0.599 0.143 0.036 20 2.1 G_occipital_sup 1892 1281 4409 2.912 0.535 0.118 0.035 25 2.0 G_oc-temp_lat-fusifor 2553 2085 4632 2.088 0.611 0.177 0.050 54 5.4 G_oc-temp_med-Lingual 1033 663 2245 2.629 0.656 0.090 0.021 7 0.8 G_oc-temp_med-Parahip 1980 1580 5244 2.725 0.559 0.154 0.039 39 3.0 G_orbital 2546 1617 5891 2.805 0.490 0.130 0.027 36 2.9 G_pariet_inf-Angular 2190 1477 5540 2.979 0.467 0.113 0.027 27 2.0 G_pariet_inf-Supramar 3440 2185 6590 2.546 0.508 0.123 0.028 46 3.6 G_parietal_sup 2673 1446 4218 2.350 0.651 0.108 0.030 28 3.1 G_postcentral 2762 1385 5895 3.183 0.442 0.095 0.031 25 3.2 G_precentral 2821 2067 6622 2.683 0.430 0.141 0.030 43 3.3 G_precuneus 893 631 1984 2.491 0.589 0.136 0.038 21 1.4 G_rectus 757 516 1384 2.828 0.810 0.138 0.065 12 1.7 G_subcallosal 437 285 1006 2.944 0.359 0.134 0.030 5 0.5 G_temp_sup-G_T_transv 2038 1279 5285 3.108 0.439 0.111 0.028 26 2.0 G_temp_sup-Lateral 740 486 1938 3.301 0.503 0.078 0.020 3 0.6 G_temp_sup-Plan_polar 877 576 1988 3.119 0.401 0.100 0.023 7 0.7 G_temp_sup-Plan_tempo 2312 1665 5440 2.701 0.558 0.134 0.036 39 3.0 G_temporal_inf 2662 1803 7278 3.046 0.455 0.120 0.027 39 2.8 G_temporal_middle 338 232 482 2.373 0.272 0.110 0.019 2 0.2 Lat_Fis-ant-Horizont 389 294 665 2.418 0.262 0.107 0.014 2 0.2 Lat_Fis-ant-Vertical 1064 684 1421 2.620 0.355 0.096 0.018 5 0.8 Lat_Fis-post 2026 1243 2437 1.835 0.521 0.135 0.047 29 3.7 Pole_occipital 1283 1108 4340 3.124 0.458 0.158 0.037 24 1.9 Pole_temporal 2198 1542 2758 2.180 0.581 0.121 0.027 22 2.5 S_calcarine 3093 2055 3689 2.104 0.654 0.102 0.022 16 2.9 S_central 1244 827 1747 2.393 0.341 0.095 0.016 6 0.8 S_cingul-Marginalis 520 349 818 2.776 0.411 0.099 0.020 2 0.4 S_circular_insula_ant 1447 925 2167 2.840 0.582 0.081 0.017 5 1.1 S_circular_insula_inf 1524 972 2074 2.701 0.348 0.100 0.020 7 1.4 S_circular_insula_sup 809 565 1438 2.673 0.470 0.122 0.023 8 0.9 S_collat_transv_ant 597 404 692 2.183 0.363 0.129 0.024 4 0.8 S_collat_transv_post 2769 1813 3795 2.383 0.373 0.105 0.019 18 2.4 S_front_inf 1314 892 1984 2.227 0.560 0.117 0.020 11 1.2 S_front_middle 2887 1909 4465 2.610 0.373 0.093 0.017 13 2.2 S_front_sup 357 245 525 2.582 0.328 0.097 0.018 2 0.2 S_interm_prim-Jensen 2556 1714 3506 2.312 0.372 0.111 0.020 20 2.2 S_intrapariet_and_P_trans 1116 746 1319 2.140 0.427 0.103 0.020 6 0.9 S_oc_middle_and_Lunatus 1180 775 1474 2.185 0.387 0.113 0.022 8 1.1 S_oc_sup_and_transversal 1017 688 1342 2.399 0.354 0.127 0.024 10 1.1 S_occipital_ant 853 646 1465 2.640 0.520 0.140 0.029 9 1.0 S_oc-temp_lat 2115 1446 3190 2.506 0.426 0.096 0.016 11 1.3 S_oc-temp_med_and_Lingual 429 310 632 2.332 0.390 0.135 0.026 5 0.5 S_orbital_lateral 546 387 756 2.109 0.523 0.115 0.024 4 0.6 S_orbital_med-olfact 1196 895 2121 2.449 0.488 0.138 0.030 11 1.7 S_orbital-H_Shaped 1813 1249 2743 2.463 0.394 0.115 0.026 15 1.9 S_parieto_occipital 1253 809 1069 1.568 0.483 0.133 0.027 23 1.3 S_pericallosal 2922 1930 4015 2.328 0.410 0.104 0.019 18 2.4 S_postcentral 1659 1074 2353 2.572 0.432 0.103 0.017 10 1.3 S_precentral-inf-part 1283 835 1811 2.622 0.344 0.097 0.016 6 1.0 S_precentral-sup-part 615 458 912 2.258 0.418 0.139 0.027 7 0.7 S_suborbital 1064 721 1531 2.405 0.330 0.108 0.020 6 0.9 S_subparietal 1730 1188 2330 2.372 0.409 0.113 0.016 12 1.5 S_temporal_inf 5726 3781 9360 2.692 0.396 0.096 0.017 30 4.1 S_temporal_sup 350 238 644 3.056 0.504 0.103 0.019 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 31231_T2_3T rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 226484 Total vertex volume 226284 (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) = 158937 mm^3 (det: 12.257028 ) 757 553 1442 2.408 0.463 0.146 0.032 12 1.0 G_and_S_frontomargin 1459 1001 2848 2.634 0.593 0.135 0.032 18 1.8 G_and_S_occipital_inf 1660 921 2739 2.566 0.671 0.111 0.032 16 2.2 G_and_S_paracentral 1231 817 2293 2.572 0.518 0.131 0.041 15 1.8 G_and_S_subcentral 1280 796 2531 2.662 0.388 0.118 0.026 15 1.3 G_and_S_transv_frontopol 2617 1896 5094 2.539 0.562 0.117 0.022 24 2.5 G_and_S_cingul-Ant 1372 950 2650 2.775 0.421 0.109 0.022 12 1.2 G_and_S_cingul-Mid-Ant 1258 879 2299 2.727 0.529 0.119 0.027 11 1.5 G_and_S_cingul-Mid-Post 490 360 1223 2.790 0.760 0.145 0.039 8 0.7 G_cingul-Post-dorsal 293 205 598 2.325 0.767 0.141 0.041 5 0.4 G_cingul-Post-ventral 1927 1414 2616 1.802 0.521 0.148 0.040 28 3.1 G_cuneus 1504 1018 3727 2.850 0.302 0.105 0.020 17 1.2 G_front_inf-Opercular 429 286 1043 2.756 0.254 0.113 0.022 5 0.4 G_front_inf-Orbital 1270 815 2951 2.903 0.396 0.125 0.023 16 1.2 G_front_inf-Triangul 3935 2368 8544 2.820 0.520 0.115 0.029 55 4.2 G_front_middle 6625 4365 15984 3.041 0.473 0.120 0.026 75 6.7 G_front_sup 576 458 1489 3.251 1.151 0.140 0.043 9 0.9 G_Ins_lg_and_S_cent_ins 677 518 2225 3.510 0.832 0.145 0.038 11 1.2 G_insular_short 2936 1830 5164 2.369 0.727 0.127 0.036 41 4.1 G_occipital_middle 1835 1123 2999 2.301 0.534 0.136 0.040 33 2.6 G_occipital_sup 1622 1187 3825 2.724 0.537 0.151 0.041 33 2.6 G_oc-temp_lat-fusifor 2559 2065 4906 2.237 0.673 0.164 0.046 50 4.7 G_oc-temp_med-Lingual 887 580 1974 2.667 0.712 0.112 0.035 9 1.2 G_oc-temp_med-Parahip 2323 1848 5925 2.725 0.577 0.149 0.038 47 3.2 G_orbital 3419 2203 7469 2.709 0.620 0.128 0.035 57 4.1 G_pariet_inf-Angular 2587 1594 5363 2.793 0.459 0.127 0.032 53 3.3 G_pariet_inf-Supramar 2942 1799 5302 2.473 0.536 0.123 0.033 42 3.2 G_parietal_sup 2070 1102 3119 2.274 0.516 0.095 0.027 20 2.1 G_postcentral 3154 1640 6078 2.890 0.635 0.106 0.033 35 4.1 G_precentral 2332 1660 5079 2.598 0.531 0.133 0.031 36 2.9 G_precuneus 732 574 1646 2.386 0.534 0.147 0.030 13 0.8 G_rectus 555 379 1031 2.839 0.826 0.145 0.055 10 1.1 G_subcallosal 342 222 817 3.031 0.316 0.108 0.024 3 0.3 G_temp_sup-G_T_transv 2037 1275 5220 3.183 0.526 0.109 0.030 29 2.0 G_temp_sup-Lateral 867 569 1946 3.203 0.521 0.082 0.020 3 0.8 G_temp_sup-Plan_polar 744 489 1625 2.995 0.425 0.092 0.019 4 0.4 G_temp_sup-Plan_tempo 2315 1617 5723 2.870 0.591 0.131 0.037 39 3.2 G_temporal_inf 2889 1887 7187 2.922 0.506 0.117 0.029 43 2.6 G_temporal_middle 379 252 518 2.463 0.245 0.093 0.013 1 0.2 Lat_Fis-ant-Horizont 334 224 463 2.477 0.356 0.081 0.012 1 0.1 Lat_Fis-ant-Vertical 1346 881 1866 2.611 0.367 0.102 0.018 7 1.1 Lat_Fis-post 3532 2278 3953 1.760 0.543 0.148 0.041 57 5.7 Pole_occipital 1571 1264 4079 2.739 0.513 0.141 0.034 24 2.2 Pole_temporal 2182 1495 2910 2.267 0.671 0.119 0.027 17 2.5 S_calcarine 2909 1909 3652 2.273 0.579 0.091 0.016 12 2.1 S_central 1271 878 2004 2.597 0.343 0.114 0.020 12 1.1 S_cingul-Marginalis 542 370 838 2.527 0.454 0.088 0.018 2 0.4 S_circular_insula_ant 1069 658 1519 2.802 0.575 0.073 0.012 4 0.6 S_circular_insula_inf 1186 756 1578 2.658 0.381 0.103 0.020 5 1.1 S_circular_insula_sup 779 576 1496 2.793 0.493 0.118 0.025 7 0.9 S_collat_transv_ant 755 498 930 2.322 0.335 0.126 0.029 6 0.9 S_collat_transv_post 2401 1561 3295 2.314 0.356 0.089 0.016 13 1.6 S_front_inf 2160 1452 3330 2.377 0.483 0.109 0.020 17 1.8 S_front_middle 2812 1814 4727 2.693 0.432 0.091 0.016 15 2.0 S_front_sup 270 188 418 2.263 0.568 0.108 0.014 2 0.2 S_interm_prim-Jensen 2597 1752 3539 2.283 0.387 0.110 0.019 22 2.2 S_intrapariet_and_P_trans 972 639 1156 2.343 0.468 0.113 0.019 7 0.8 S_oc_middle_and_Lunatus 1360 889 1713 2.268 0.308 0.109 0.022 9 1.3 S_oc_sup_and_transversal 597 417 775 2.318 0.362 0.132 0.030 5 0.9 S_occipital_ant 1031 711 1464 2.511 0.361 0.123 0.024 9 1.1 S_oc-temp_lat 1878 1320 2977 2.617 0.453 0.114 0.021 13 1.7 S_oc-temp_med_and_Lingual 608 416 766 2.237 0.327 0.137 0.026 6 0.7 S_orbital_lateral 636 455 1018 2.406 0.565 0.128 0.027 6 0.7 S_orbital_med-olfact 1462 1053 2443 2.597 0.465 0.143 0.031 19 2.1 S_orbital-H_Shaped 2411 1675 3366 2.339 0.461 0.116 0.023 22 2.2 S_parieto_occipital 1423 910 1074 1.499 0.347 0.117 0.024 19 1.2 S_pericallosal 2402 1526 3191 2.420 0.388 0.091 0.015 12 1.5 S_postcentral 2357 1533 3577 2.477 0.414 0.099 0.017 16 1.7 S_precentral-inf-part 1358 885 2085 2.733 0.444 0.084 0.012 5 0.7 S_precentral-sup-part 285 220 482 2.469 0.432 0.143 0.029 3 0.4 S_suborbital 1078 765 1815 2.566 0.372 0.107 0.022 6 0.9 S_subparietal 1352 899 1781 2.332 0.455 0.101 0.016 8 1.0 S_temporal_inf 6650 4286 10256 2.644 0.401 0.089 0.015 34 4.4 S_temporal_sup 266 184 539 3.200 0.501 0.102 0.016 1 0.2 S_temporal_transverse PIDs (96824 96827) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Feb 9 18:00:24 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T lh white #----------------------------------------- #@# Parcellation Stats 3 rh Thu Feb 9 18:00:24 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 31231_T2_3T rh white Waiting for PID 97253 of (97253 97256) to complete... Waiting for PID 97256 of (97253 97256) 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 31231_T2_3T lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 230837 Total vertex volume 230658 (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) = 158937 mm^3 (det: 12.257028 ) 1342 924 2404 2.527 0.526 0.117 0.023 16 1.3 caudalanteriorcingulate 4227 2618 7758 2.847 0.501 0.108 0.023 33 4.2 caudalmiddlefrontal 2365 1723 3668 2.085 0.532 0.148 0.035 32 3.4 cuneus 368 247 933 2.721 0.608 0.093 0.019 3 0.3 entorhinal 4218 2895 8630 2.788 0.519 0.121 0.029 45 4.6 fusiform 6132 3979 11636 2.646 0.487 0.117 0.023 64 5.6 inferiorparietal 4232 3104 8780 2.609 0.535 0.130 0.030 60 4.9 inferiortemporal 1519 1072 2575 2.245 0.826 0.132 0.035 21 1.9 isthmuscingulate 8314 5356 11604 2.085 0.521 0.131 0.034 105 10.8 lateraloccipital 3704 2837 7855 2.564 0.619 0.148 0.039 61 6.3 lateralorbitofrontal 4080 3145 6635 2.141 0.571 0.149 0.038 63 6.6 lingual 2165 1549 4214 2.411 0.598 0.125 0.035 38 3.1 medialorbitofrontal 6509 4375 13938 2.854 0.477 0.110 0.022 64 5.7 middletemporal 1034 659 1910 2.607 0.605 0.087 0.020 7 0.8 parahippocampal 2802 1803 5343 2.696 0.552 0.104 0.022 22 2.6 paracentral 2441 1659 4972 2.729 0.417 0.109 0.022 29 2.1 parsopercularis 1021 722 1975 2.527 0.462 0.124 0.025 13 1.0 parsorbitalis 2708 1870 5101 2.559 0.417 0.124 0.025 32 2.7 parstriangularis 1507 1098 1795 1.983 0.527 0.132 0.030 14 1.9 pericalcarine 7214 4420 10836 2.311 0.666 0.107 0.026 69 7.2 postcentral 1908 1325 3320 2.407 0.700 0.126 0.027 24 2.1 posteriorcingulate 7117 4195 12741 2.863 0.587 0.103 0.026 55 7.3 precentral 5524 3942 10361 2.528 0.419 0.126 0.027 66 6.1 precuneus 1179 878 2231 2.492 0.559 0.139 0.034 18 1.5 rostralanteriorcingulate 5916 3943 10668 2.442 0.490 0.123 0.025 66 6.1 rostralmiddlefrontal 11471 7657 24581 2.858 0.580 0.116 0.024 106 11.2 superiorfrontal 6734 4373 11654 2.478 0.475 0.119 0.026 69 6.8 superiorparietal 7501 4987 16459 2.984 0.489 0.101 0.022 61 6.6 superiortemporal 4341 2895 8525 2.714 0.520 0.111 0.024 41 3.9 supramarginal 597 401 1191 2.772 0.388 0.136 0.031 7 0.7 transversetemporal 2807 2033 6365 3.096 0.673 0.125 0.035 33 4.2 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 31231_T2_3T rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 226484 Total vertex volume 226284 (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) = 158937 mm^3 (det: 12.257028 ) 1111 814 2211 2.330 0.725 0.136 0.027 15 1.3 caudalanteriorcingulate 3526 2133 6720 2.855 0.485 0.095 0.019 28 2.6 caudalmiddlefrontal 2525 1768 3414 1.983 0.540 0.138 0.035 33 3.5 cuneus 405 275 894 2.512 0.676 0.113 0.042 4 0.9 entorhinal 3442 2478 6761 2.679 0.460 0.134 0.032 47 4.4 fusiform 7864 5241 14404 2.595 0.543 0.118 0.026 83 7.9 inferiorparietal 4621 3285 9722 2.722 0.562 0.128 0.032 62 6.0 inferiortemporal 1308 892 2029 2.194 0.832 0.124 0.033 18 1.5 isthmuscingulate 8419 5319 11652 2.137 0.617 0.131 0.034 111 11.1 lateraloccipital 3852 2949 8252 2.657 0.547 0.152 0.039 69 5.8 lateralorbitofrontal 4264 3237 6922 2.187 0.621 0.149 0.038 67 6.7 lingual 1997 1510 3967 2.491 0.615 0.135 0.032 31 2.5 medialorbitofrontal 6087 3981 12271 2.778 0.523 0.105 0.022 60 4.9 middletemporal 900 593 1833 2.791 0.645 0.104 0.022 7 0.7 parahippocampal 2511 1556 4558 2.808 0.514 0.108 0.024 20 2.4 paracentral 2623 1707 4677 2.571 0.380 0.095 0.018 21 1.9 parsopercularis 1074 747 2053 2.489 0.321 0.107 0.019 10 0.9 parsorbitalis 2603 1694 4867 2.674 0.430 0.120 0.023 26 2.5 parstriangularis 1755 1335 2114 1.858 0.519 0.139 0.037 18 2.7 pericalcarine 6423 3837 9230 2.278 0.523 0.098 0.023 51 5.9 postcentral 1706 1183 2963 2.429 0.807 0.128 0.030 22 2.0 posteriorcingulate 7877 4749 13635 2.730 0.559 0.102 0.025 65 8.4 precentral 5827 4128 10437 2.484 0.511 0.125 0.027 71 6.1 precuneus 1005 752 2148 2.486 0.775 0.134 0.029 17 1.2 rostralanteriorcingulate 6221 4083 10612 2.439 0.506 0.115 0.025 66 6.1 rostralmiddlefrontal 12631 8274 25800 2.826 0.496 0.110 0.022 111 10.9 superiorfrontal 6643 4197 10708 2.403 0.474 0.119 0.028 79 6.7 superiorparietal 7370 4791 15167 2.903 0.552 0.096 0.022 80 6.2 superiortemporal 4909 3091 9272 2.725 0.478 0.114 0.027 55 5.3 supramarginal 421 277 896 2.970 0.407 0.121 0.025 4 0.4 transversetemporal 2808 1977 6095 3.091 0.811 0.116 0.027 25 3.3 insula PIDs (97253 97256) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Thu Feb 9 18:00:38 CST 2023 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T 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 /opt/freesurfer/ASegStatsLUT.txt --subject 31231_T2_3T 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 /opt/freesurfer/ASegStatsLUT.txt --subject 31231_T2_3T sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 158937 mm^3 (det: 12.257028 ) Computing euler number orig.nofix lheno = -8, rheno = -10 orig.nofix lhholes = 5, rhholes = 6 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 /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Feb 9 18:00:58 CST 2023 mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 97982 of (97982 97985 97989 97993 97996) to complete... Waiting for PID 97985 of (97982 97985 97989 97993 97996) to complete... Waiting for PID 97989 of (97982 97985 97989 97993 97996) to complete... Waiting for PID 97993 of (97982 97985 97989 97993 97996) to complete... Waiting for PID 97996 of (97982 97985 97989 97993 97996) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4373 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 358 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8267 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6050 mri_label2label: Done PIDs (97982 97985 97989 97993 97996) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA6_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA44_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA45_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 98103 of (98103 98106 98109 98112) to complete... Waiting for PID 98106 of (98103 98106 98109 98112) to complete... Waiting for PID 98109 of (98103 98106 98109 98112) to complete... Waiting for PID 98112 of (98103 98106 98109 98112) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4170 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA6_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 962 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA44_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 389 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4570 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA45_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 830 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4252 mri_label2label: Done PIDs (98103 98106 98109 98112) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.MT_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 98428 of (98428 98431 98434 98437 98440) to complete... Waiting for PID 98431 of (98428 98431 98434 98437 98440) to complete... Waiting for PID 98434 of (98428 98431 98434 98437 98440) to complete... Waiting for PID 98437 of (98428 98431 98434 98437 98440) to complete... Waiting for PID 98440 of (98428 98431 98434 98437 98440) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 520 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5161 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 1833 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9947 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.MT_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 596 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2614 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 2 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1201 mri_label2label: Done PIDs (98428 98431 98434 98437 98440) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 98580 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98586 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98589 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98596 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98599 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98602 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98608 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... Waiting for PID 98619 of (98580 98586 98589 98596 98599 98602 98608 98619) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 556 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 286 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 989 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1977 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2408 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4205 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 698 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3617 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 490 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1776 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T 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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/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 130564 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1359 mri_label2label: Done PIDs (98580 98586 98589 98596 98599 98602 98608 98619) completed and logs appended. mris_label2annot --s 31231_T2_3T --ctab /opt/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /opt/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label cmdline mris_label2annot --s 31231_T2_3T --ctab /opt/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 subject 31231_T2_3T hemi lh SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data ColorTable /opt/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 115737 unhit vertices Writing annot to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.mpm.vpnl.annot mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 98916 of (98916 98920 98924 98927 98930) to complete... Waiting for PID 98920 of (98916 98920 98924 98927 98930) to complete... Waiting for PID 98924 of (98916 98920 98924 98927 98930) to complete... Waiting for PID 98927 of (98916 98920 98924 98927 98930) to complete... Waiting for PID 98930 of (98916 98920 98924 98927 98930) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA1_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1064 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA2_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 171 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2263 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA3a_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1519 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA3b_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2043 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA4a_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2454 mri_label2label: Done PIDs (98916 98920 98924 98927 98930) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 99207 of (99207 99210 99213 99216) to complete... Waiting for PID 99210 of (99207 99210 99213 99216) to complete... Waiting for PID 99213 of (99207 99210 99213 99216) to complete... Waiting for PID 99216 of (99207 99210 99213 99216) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA4p_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1575 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA6_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7363 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA44_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2050 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.BA45_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 421 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1572 mri_label2label: Done PIDs (99207 99210 99213 99216) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 99294 of (99294 99297 99300 99303 99306) to complete... Waiting for PID 99297 of (99294 99297 99300 99303 99306) to complete... Waiting for PID 99300 of (99294 99297 99300 99303 99306) to complete... Waiting for PID 99303 of (99294 99297 99300 99303 99306) to complete... Waiting for PID 99306 of (99294 99297 99300 99303 99306) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.V1_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 274 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3679 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.V2_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 815 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4149 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.MT_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 169 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 682 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.entorhinal_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 473 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./lh.perirhinal_exvivo.thresh.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 /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 130564 Number of reverse mapping hits = 1 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 451 mri_label2label: Done PIDs (99294 99297 99300 99303 99306) completed and logs appended. mris_label2annot --s 31231_T2_3T --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label cmdline mris_label2annot --s 31231_T2_3T --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 subject 31231_T2_3T hemi lh SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89799 unhit vertices Writing annot to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.BA_exvivo.annot mris_label2annot --s 31231_T2_3T --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label cmdline mris_label2annot --s 31231_T2_3T --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 subject 31231_T2_3T hemi lh SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 106899 unhit vertices Writing annot to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 31231_T2_3T lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 230837 Total vertex volume 230658 (mask=0) Saving annotation colortable ./BA_exvivo.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) = 158937 mm^3 (det: 12.257028 ) 1202 633 1806 2.273 0.644 0.121 0.035 14 1.6 BA1_exvivo 3942 2499 6336 2.497 0.490 0.106 0.023 32 3.5 BA2_exvivo 1042 693 941 1.826 0.369 0.136 0.029 9 1.3 BA3a_exvivo 2340 1472 3227 1.966 0.599 0.104 0.027 21 2.3 BA3b_exvivo 1783 984 3525 3.031 0.497 0.090 0.023 13 1.5 BA4a_exvivo 1301 840 2072 2.747 0.657 0.104 0.031 9 1.6 BA4p_exvivo 9447 5754 20465 3.047 0.495 0.102 0.022 73 8.6 BA6_exvivo 2326 1537 4556 2.764 0.416 0.110 0.022 23 2.2 BA44_exvivo 3457 2398 6783 2.560 0.450 0.121 0.025 42 3.3 BA45_exvivo 2806 2106 3628 1.893 0.549 0.150 0.042 39 5.3 V1_exvivo 7686 5392 10655 1.958 0.500 0.146 0.039 116 11.9 V2_exvivo 2401 1581 3890 2.432 0.442 0.125 0.026 26 2.6 MT_exvivo 517 364 1043 2.595 0.536 0.100 0.017 4 0.4 perirhinal_exvivo 515 361 1237 2.355 1.190 0.132 0.053 10 1.1 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 31231_T2_3T lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 230837 Total vertex volume 230658 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.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) = 158937 mm^3 (det: 12.257028 ) 784 389 1124 2.241 0.622 0.119 0.033 10 1.0 BA1_exvivo 1673 1016 2990 2.700 0.433 0.098 0.023 14 1.4 BA2_exvivo 877 582 752 1.765 0.341 0.134 0.030 8 1.1 BA3a_exvivo 1445 925 1638 1.727 0.373 0.091 0.021 8 1.2 BA3b_exvivo 1735 958 3244 3.011 0.530 0.088 0.025 10 1.6 BA4a_exvivo 1020 674 1592 2.692 0.636 0.111 0.030 8 1.3 BA4p_exvivo 5130 3036 11181 3.110 0.483 0.098 0.023 35 4.8 BA6_exvivo 1554 1036 2999 2.718 0.379 0.111 0.023 18 1.4 BA44_exvivo 1531 1078 3636 2.788 0.456 0.137 0.032 25 1.8 BA45_exvivo 2997 2270 3961 1.896 0.538 0.150 0.041 42 5.5 V1_exvivo 3761 2711 4935 1.847 0.471 0.163 0.047 70 7.1 V2_exvivo 653 439 1155 2.612 0.485 0.142 0.033 8 0.9 MT_exvivo 204 134 376 2.689 0.312 0.084 0.014 2 0.1 perirhinal_exvivo 301 212 894 2.861 0.634 0.090 0.018 1 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Thu Feb 9 18:01:48 CST 2023 mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 99767 of (99767 99770 99773 99776 99779) to complete... Waiting for PID 99770 of (99767 99770 99773 99776 99779) to complete... Waiting for PID 99773 of (99767 99770 99773 99776 99779) to complete... Waiting for PID 99776 of (99767 99770 99773 99776 99779) to complete... Waiting for PID 99779 of (99767 99770 99773 99776 99779) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6808 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4003 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4596 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5927 mri_label2label: Done PIDs (99767 99770 99773 99776 99779) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA6_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA44_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA45_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 100084 of (100084 100087 100090 100093) to complete... Waiting for PID 100087 of (100084 100087 100090 100093) to complete... Waiting for PID 100090 of (100084 100087 100090 100093) to complete... Waiting for PID 100093 of (100084 100087 100090 100093) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4531 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA6_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 800 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13056 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA44_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 996 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7908 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA45_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 1062 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6417 mri_label2label: Done PIDs (100084 100087 100090 100093) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.MT_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 100171 of (100171 100174 100177 100180 100183) to complete... Waiting for PID 100174 of (100171 100174 100177 100180 100183) to complete... Waiting for PID 100177 of (100171 100174 100177 100180 100183) to complete... Waiting for PID 100180 of (100171 100174 100177 100180 100183) to complete... Waiting for PID 100183 of (100171 100174 100177 100180 100183) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V1_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 850 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5577 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V2_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 2309 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10325 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.MT_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 343 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 31231_T2_3T --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 759 mri_label2label: Done PIDs (100171 100174 100177 100180 100183) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 100475 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100478 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100481 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100484 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100487 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100490 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100493 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... Waiting for PID 100496 of (100475 100478 100481 100484 100487 100490 100493 100496) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 236 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 777 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 958 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1607 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1721 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 527 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4194 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 673 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3392 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1847 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject 31231_T2_3T --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 531 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1556 mri_label2label: Done PIDs (100475 100478 100481 100484 100487 100490 100493 100496) completed and logs appended. mris_label2annot --s 31231_T2_3T --ctab /opt/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /opt/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label cmdline mris_label2annot --s 31231_T2_3T --ctab /opt/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 subject 31231_T2_3T hemi rh SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data ColorTable /opt/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 118126 unhit vertices Writing annot to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.mpm.vpnl.annot mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 101026 of (101026 101029 101032 101035 101038) to complete... Waiting for PID 101029 of (101026 101029 101032 101035 101038) to complete... Waiting for PID 101032 of (101026 101029 101032 101035 101038) to complete... Waiting for PID 101035 of (101026 101029 101032 101035 101038) to complete... Waiting for PID 101038 of (101026 101029 101032 101035 101038) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 919 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2718 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1703 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2205 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1441 mri_label2label: Done PIDs (101026 101029 101032 101035 101038) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 101150 of (101150 101153 101156 101159) to complete... Waiting for PID 101153 of (101150 101153 101156 101159) to complete... Waiting for PID 101156 of (101150 101153 101156 101159) to complete... Waiting for PID 101159 of (101150 101153 101156 101159) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1498 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1200 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 246 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1424 mri_label2label: Done PIDs (101150 101153 101156 101159) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 101288 of (101288 101299 101309 101322 101331) to complete... Waiting for PID 101299 of (101288 101299 101309 101322 101331) to complete... Waiting for PID 101309 of (101288 101299 101309 101322 101331) to complete... Waiting for PID 101322 of (101288 101299 101309 101322 101331) to complete... Waiting for PID 101331 of (101288 101299 101309 101322 101331) to complete... mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 457 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3689 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 966 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 317 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 714 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 31231_T2_3T --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 31231_T2_3T trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data FREESURFER_HOME /opt/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /scratch/g/tmeier/ChronEx/FS7.2/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white Reading target registration /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 132449 Number of reverse mapping hits = 2 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 293 mri_label2label: Done PIDs (101288 101299 101309 101322 101331) completed and logs appended. mris_label2annot --s 31231_T2_3T --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label cmdline mris_label2annot --s 31231_T2_3T --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 subject 31231_T2_3T hemi rh SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 90782 unhit vertices Writing annot to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.BA_exvivo.annot mris_label2annot --s 31231_T2_3T --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label cmdline mris_label2annot --s 31231_T2_3T --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname cn06.cluster.local machine x86_64 user br74747 subject 31231_T2_3T hemi rh SUBJECTS_DIR /scratch/g/tmeier/ChronEx/FS7.2/data ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 109751 unhit vertices Writing annot to /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 31231_T2_3T rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 226484 Total vertex volume 226284 (mask=0) Saving annotation colortable ./BA_exvivo.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) = 158937 mm^3 (det: 12.257028 ) 969 458 1417 2.304 0.545 0.102 0.030 10 1.2 BA1_exvivo 2883 1774 4370 2.459 0.418 0.088 0.017 18 1.9 BA2_exvivo 1022 681 1020 2.019 0.402 0.120 0.026 7 1.2 BA3a_exvivo 1849 1157 2380 1.916 0.424 0.101 0.024 14 1.7 BA3b_exvivo 1620 940 3036 2.947 0.595 0.099 0.025 10 1.8 BA4a_exvivo 1228 800 1968 2.670 0.609 0.098 0.028 7 1.6 BA4p_exvivo 8695 5269 17409 2.923 0.504 0.101 0.022 72 7.6 BA6_exvivo 4285 2818 8074 2.618 0.414 0.103 0.021 40 3.7 BA44_exvivo 4736 3138 8793 2.569 0.430 0.117 0.023 48 4.5 BA45_exvivo 3295 2468 4296 1.854 0.555 0.152 0.044 52 6.0 V1_exvivo 8241 5573 11030 1.978 0.596 0.141 0.036 118 11.8 V2_exvivo 2035 1367 3216 2.559 0.437 0.117 0.023 18 1.9 MT_exvivo 294 200 641 2.928 0.467 0.088 0.022 1 0.3 perirhinal_exvivo 515 363 1104 2.358 0.885 0.145 0.055 11 1.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 31231_T2_3T rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/mri/wm.mgz... reading input surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... reading input pial surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.pial... reading input white surface /scratch/g/tmeier/ChronEx/FS7.2/data/31231_T2_3T/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 226484 Total vertex volume 226284 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.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) = 158937 mm^3 (det: 12.257028 ) 621 300 834 2.147 0.518 0.098 0.034 6 0.9 BA1_exvivo 1650 974 2649 2.535 0.360 0.076 0.016 9 0.9 BA2_exvivo 913 604 848 2.003 0.371 0.121 0.025 6 1.0 BA3a_exvivo 1443 923 1688 1.856 0.353 0.093 0.018 8 1.1 BA3b_exvivo 1073 591 2160 3.126 0.542 0.107 0.028 8 1.2 BA4a_exvivo 988 660 1567 2.678 0.595 0.093 0.024 4 1.0 BA4p_exvivo 5600 3308 10964 2.900 0.492 0.099 0.024 48 5.2 BA6_exvivo 1077 735 2209 2.599 0.381 0.101 0.020 11 0.9 BA44_exvivo 1290 832 2925 2.883 0.408 0.121 0.022 15 1.2 BA45_exvivo 3132 2318 4036 1.857 0.548 0.147 0.044 46 5.3 V1_exvivo 4120 2938 5302 1.848 0.548 0.155 0.040 67 7.0 V2_exvivo 289 201 432 2.281 0.371 0.128 0.026 3 0.3 MT_exvivo 25 15 49 3.019 0.402 0.053 0.009 0 0.0 perirhinal_exvivo 477 323 1133 2.722 0.626 0.094 0.028 3 0.6 entorhinal_exvivo Started at Thu Feb 9 15:12:31 CST 2023 Ended at Thu Feb 9 18:02:37 CST 2023 #@#%# recon-all-run-time-hours 2.835 recon-all -s 31231_T2_3T finished without error at Thu Feb 9 18:02:37 CST 2023