Di 31. Okt 17:33:45 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data /local/program/FreeSurfer/freesurfer-7.4.1/bin/recon-all -sd /projects/GRK/spr_freesurfer/data -all -threads 64 -openmp 64 -parallel -long CON01200509a CON01_tmpl -all subjid CON01200509a.long.CON01_tmpl setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data FREESURFER_HOME /local/program/FreeSurfer/freesurfer-7.4.1 Actual FREESURFER_HOME /local/program/FreeSurfer/freesurfer-7.4.1 build-stamp.txt: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 Linux jsfc172 4.18.0-477.27.1.el8_8.x86_64 #1 SMP Wed Sep 20 15:55:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 524288 memorylocked unlimited maxproc 1028684 maxlocks unlimited maxsignal 1028684 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 14Gi 236Gi 10Mi 671Mi 233Gi Swap: 0B 0B 0B SLURM_JOB_ID 530710 ######################################## program versions used 7.4.1 (freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:45-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/10/31-16:33:46-GMT BuildTime: Jun 13 2023 23:42:21 BuildStamp: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 User: xxxxxxxx Machine: jsfc172 Platform: Linux PlatformVersion: 4.18.0-477.27.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 8.5.0 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 /local/program/FreeSurfer/freesurfer-7.4.1/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 /local/program/FreeSurfer/freesurfer-7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### longmc -long CON01200509a CON01_tmpl -s CON01200509a.long.CON01_tmpl Di 31. Okt 17:33:49 CET 2023 setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl /local/program/FreeSurfer/freesurfer-7.4.1/bin/longmc -long CON01200509a CON01_tmpl -s CON01200509a.long.CON01_tmpl freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 longmc 7.4.1 Linux jsfc172 4.18.0-477.27.1.el8_8.x86_64 #1 SMP Wed Sep 20 15:55:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux pid 22019 mri_convert -at /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta -odt uchar -rt cubic /projects/GRK/spr_freesurfer/data/CON01200509a/mri/orig/001.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/orig.mgz mri_convert -at /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta -odt uchar -rt cubic /projects/GRK/spr_freesurfer/data/CON01200509a/mri/orig/001.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/orig.mgz reading from /projects/GRK/spr_freesurfer/data/CON01200509a/mri/orig/001.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 /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.01018 -0.00563 0.00977; -0.01028 0.99979 -0.01778 -0.04305; 0.00544 0.01784 0.99983 -1.05141; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 301.512 1000, flo=0, fhi=0.999, dest_type=0 writing to /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/orig.mgz... mri_convert -at /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta -rt cubic /projects/GRK/spr_freesurfer/data/CON01200509a/mri/orig/001.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/rawavg.mgz mri_convert -at /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta -rt cubic /projects/GRK/spr_freesurfer/data/CON01200509a/mri/orig/001.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/rawavg.mgz reading from /projects/GRK/spr_freesurfer/data/CON01200509a/mri/orig/001.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 /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.01018 -0.00563 0.00977; -0.01028 0.99979 -0.01778 -0.04305; 0.00544 0.01784 0.99983 -1.05141; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/rawavg.mgz... Started at Di 31. Okt 17:33:49 CET 2023 Ended at Di 31. Okt 17:34:21 CET 2023 Longmc-Run-Time-Sec 32 Longmc-Run-Time-Min 0,64 Longmc-Run-Time-Hours 0,01 longmc Done /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/brainmask.mgz ./brainmask_CON01_tmpl.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/talairach.lta transforms/talairach.lta cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/aseg.mgz aseg_CON01_tmpl.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/surf/lh.white /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf/lh.orig cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/surf/lh.white /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf/lh.orig_white cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/surf/lh.pial /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf/lh.orig_pial /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/surf/rh.white /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf/rh.orig cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/surf/rh.white /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf/rh.orig_white cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/surf/rh.pial /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf/rh.orig_pial /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts Started at Di 31. Okt 17:33:48 CET 2023 Ended at Di 31. Okt 17:34:35 CET 2023 rca-long-tp-init Done #-------------------------------------------- #@# MotionCor Di 31. Okt 17:34:35 CET 2023 #-------------------------------------------- #@# Talairach Di 31. Okt 17:34:35 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri cp /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/talairach.xfm /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /local/program/FreeSurfer/freesurfer-7.4.1/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.4.1 --src: orig.mgz src image (geometry). --trg: /local/program/FreeSurfer/freesurfer-7.4.1/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 1.01100 0.00767 -0.00039 -0.66119; 0.01238 1.01173 0.31820 1.03509; -0.01911 -0.44038 1.08771 -6.45149; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Di 31. Okt 17:34:38 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6316, pval=0.3663 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Di 31. Okt 17:34:38 CET 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri /local/program/FreeSurfer/freesurfer-7.4.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.4.1 Linux jsfc172 4.18.0-477.27.1.el8_8.x86_64 #1 SMP Wed Sep 20 15:55:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Di 31. Okt 17:34:39 CET 2023 tmpdir is ./tmp.mri_nu_correct.mni.23042 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.23042/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.23042/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.23042/ones.mgz 7.4.1 cwd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.23042/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.23042/ones.mgz sysname Linux hostname jsfc172 machine x86_64 user xxxxxxxx input ./tmp.mri_nu_correct.mni.23042/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.23042/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.23042/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23042/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23042/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23042/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23042/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23042/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23042/input.mean.dat sysname Linux hostname jsfc172 machine x86_64 user xxxxxxxx whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.23042/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.23042/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23042/ones.mgz --i ./tmp.mri_nu_correct.mni.23042/nu0.mgz --sum ./tmp.mri_nu_correct.mni.23042/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23042/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23042/ones.mgz --i ./tmp.mri_nu_correct.mni.23042/nu0.mgz --sum ./tmp.mri_nu_correct.mni.23042/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23042/output.mean.dat sysname Linux hostname jsfc172 machine x86_64 user xxxxxxxx whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.23042/ones.mgz Loading ./tmp.mri_nu_correct.mni.23042/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.23042/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.23042/nu0.mgz ./tmp.mri_nu_correct.mni.23042/nu0.mgz mul 1.28079372769481477780 Saving result to './tmp.mri_nu_correct.mni.23042/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.23042/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.23042/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.23042/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. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 8, i2 = 48 #mri_make_uchar# mapping 21 124 to 3 110 : b -18.94 m 1.0429 : thresh 18.1609 maxsat 262.672 : nzero 13640544 nsat 241 Di 31. Okt 17:37:49 CET 2023 mri_nu_correct.mni done mri_add_xform_to_header -c /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Di 31. Okt 17:37:50 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --ants-n4 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 1.01100 0.00767 -0.00039 -0.66119; 0.01238 1.01173 0.31820 1.03509; -0.01911 -0.44038 1.08771 -6.45149; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 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 102 gm peak at 71 (71), valley at 0 (-1) csf peak at 35, setting threshold to 59 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 83 (83), valley at 38 (38) csf peak at 20, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 16 seconds. #-------------------------------------------- #@# Skull Stripping Di 31. Okt 17:41:57 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_mask -keep_mask_deletion_edits T1.mgz brainmask_CON01_tmpl.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 maskval=0, outval=0 Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_CON01_tmpl.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 maskval=255, outval=255 Writing masked volume to brainmask.auto.mgz...done. cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Di 31. Okt 17:42:01 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri #-------------------------------------- #@# CA Normalize Di 31. Okt 17:42:01 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_ca_normalize -long aseg_CON01_tmpl.mgz -mask brainmask.mgz nu.mgz /local/program/FreeSurfer/freesurfer-7.4.1/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz using longitudinal segmentation volume aseg_CON01_tmpl.mgz to generate control points... using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/local/program/FreeSurfer/freesurfer-7.4.1/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 102 resetting gm mean[0]: 59 --> 59 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (55, 61, 55) --> (198, 211, 211) finding center of left hemi white matter using (103, 111, 133) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 102, using box (85,93,114) --> (120, 129,152) to find MRI wm before smoothing, mri peak at 99 robust fit to distribution - 100 +- 7.1 after smoothing, mri peak at 100, scaling input intensities by 1.020 scaling channel 0 by 1.02 using 246437 sample points... INFO: compute sample coordinates transform 0.97835 0.00515 -0.04159 7.13962; 0.01004 1.05666 0.43640 -72.11282; 0.03921 -0.40452 0.87438 41.99433; 0.00000 0.00000 0.00000 1.00000; INFO: transform used using 97049 total control points for intensity normalization... bias field = 0.943 +- 0.137 496 of 97049 control points discarded using 97049 total control points for intensity normalization... bias field = 1.076 +- 0.138 499 of 97049 control points discarded using 97049 total control points for intensity normalization... bias field = 1.067 +- 0.130 499 of 97049 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 30 seconds. #-------------------------------------- #@# CA Reg Di 31. Okt 17:43:32 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_ca_register -nobigventricles -levels 2 -A 1 -l /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /local/program/FreeSurfer/freesurfer-7.4.1/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/talairach.m3z and applying inverse registration identity.nofile 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 = 64 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/local/program/FreeSurfer/freesurfer-7.4.1/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 setting orig areas to linear transform determinant scaled 7.42 writing talairach.invalid.mgz writing talairach.status.mgz Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 2 #pass# 1 of 1 ************************ enabling zero nodes 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=2, 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 0.592901 #GCAMreg# pass 0 level1 1 level2 1 tsec 54.874 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=2, 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 0.552271 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=2, 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 0.542266 #GCAMreg# pass 0 level1 0 level2 1 tsec 17.927 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=2, 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 0.540236 GCAMregister done in 1.58203 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.12140 (15) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (4419 voxels, overlap=0.608) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (4419 voxels, peak = 11), gca=11.0 gca peak = 0.17690 (16) mri peak = 0.12525 (15) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2931 voxels, overlap=0.728) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2931 voxels, peak = 14), gca=14.2 gca peak = 0.28275 (96) mri peak = 0.10219 (99) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (407 voxels, overlap=0.725) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (407 voxels, peak = 97), gca=97.4 gca peak = 0.18948 (93) mri peak = 0.09333 (96) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (462 voxels, overlap=0.780) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (462 voxels, peak = 98), gca=98.1 gca peak = 0.20755 (55) mri peak = 0.09663 (72) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (547 voxels, overlap=0.018) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (547 voxels, peak = 71), gca=71.2 gca peak = 0.31831 (58) mri peak = 0.08017 (73) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (504 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (504 voxels, peak = 73), gca=73.4 gca peak = 0.11957 (102) mri peak = 0.09801 (95) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (27161 voxels, overlap=0.868) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (27161 voxels, peak = 98), gca=98.4 gca peak = 0.11429 (102) mri peak = 0.08971 (96) Left_Cerebral_White_Matter (2): linear fit = 0.96 x + 0.0 (28141 voxels, overlap=0.823) Left_Cerebral_White_Matter (2): linear fit = 0.96 x + 0.0 (28141 voxels, peak = 98), gca=98.4 gca peak = 0.14521 (59) mri peak = 0.04434 (84) Left_Cerebral_Cortex (3): linear fit = 1.38 x + 0.0 (13063 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.38 x + 0.0 (13063 voxels, peak = 81), gca=81.1 gca peak = 0.14336 (58) mri peak = 0.04068 (80) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (14374 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (14374 voxels, peak = 78), gca=78.0 gca peak = 0.13305 (70) mri peak = 0.11132 (81) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1086 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1086 voxels, peak = 84), gca=83.7 gca peak = 0.15761 (71) mri peak = 0.10787 (79) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1002 voxels, overlap=0.380) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1002 voxels, peak = 78), gca=78.5 gca peak = 0.13537 (57) mri peak = 0.05286 (73) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (14790 voxels, overlap=0.012) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (14790 voxels, peak = 72), gca=72.1 gca peak = 0.13487 (56) mri peak = 0.06441 (70) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (18003 voxels, overlap=0.110) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (18003 voxels, peak = 69), gca=68.6 gca peak = 0.19040 (84) mri peak = 0.08276 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4830 voxels, overlap=0.938) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4830 voxels, peak = 86), gca=86.1 gca peak = 0.18871 (83) mri peak = 0.08627 (81) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4880 voxels, overlap=0.936) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4880 voxels, peak = 84), gca=84.2 gca peak = 0.24248 (57) mri peak = 0.09465 (80) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (243 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (243 voxels, peak = 76), gca=75.5 gca peak = 0.35833 (56) mri peak = 0.10671 (77) Right_Amygdala (54): linear fit = 1.37 x + 0.0 (286 voxels, overlap=0.047) Right_Amygdala (54): linear fit = 1.37 x + 0.0 (286 voxels, peak = 76), gca=76.4 gca peak = 0.12897 (85) mri peak = 0.08488 (89) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3630 voxels, overlap=0.835) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3630 voxels, peak = 86), gca=86.3 gca peak = 0.13127 (83) mri peak = 0.07893 (89) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3667 voxels, overlap=0.655) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3667 voxels, peak = 88), gca=88.4 gca peak = 0.12974 (78) mri peak = 0.08996 (85) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1477 voxels, overlap=0.208) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1477 voxels, peak = 87), gca=87.0 gca peak = 0.17796 (79) mri peak = 0.09364 (88) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1456 voxels, overlap=0.381) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1456 voxels, peak = 87), gca=86.5 gca peak = 0.10999 (80) mri peak = 0.10545 (81) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11797 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11797 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.08768 (92) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (918 voxels, overlap=0.435) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (918 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.08776 (99) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (883 voxels, overlap=0.409) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (883 voxels, peak = 97), gca=96.6 gca peak = 0.20775 (25) mri peak = 0.15218 (19) Third_Ventricle (14): linear fit = 0.71 x + 0.0 (117 voxels, overlap=0.546) Third_Ventricle (14): linear fit = 0.71 x + 0.0 (117 voxels, peak = 18), gca=17.9 gca peak = 0.13297 (21) mri peak = 0.14650 (17) Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (314 voxels, overlap=0.788) Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (314 voxels, peak = 16), gca=15.6 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.33 x + 0.0 estimating mean wm scale to be 0.96 x + 0.0 estimating mean csf scale to be 0.76 x + 0.0 Left_Pallidum too bright - rescaling by 0.973 (from 1.055) to 95.5 (was 98.1) Right_Pallidum too bright - rescaling by 0.980 (from 1.015) to 95.5 (was 97.4) saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 3.08928 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 2 #pass# 1 of 1 ************************ enabling zero nodes 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=2, 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 0.412523 #GCAMreg# pass 0 level1 1 level2 1 tsec 52.487 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=2, 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 0.39961 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=2, 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 0.382686 #GCAMreg# pass 0 level1 0 level2 1 tsec 25.2 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=2, 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 0.37658 GCAMregister done in 3.10607 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 2 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #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=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=2, 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 0.370942 #GCAMreg# pass 0 level1 1 level2 1 tsec 19.262 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=2, 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 0.370942 setting smoothness cost coefficient to 0.031 #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=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=2, 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 0.37095 #GCAMreg# pass 0 level1 0 level2 1 tsec 18.839 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=2, 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 0.37095 label assignment complete, 0 changed (0.00%) GCAMregister done in 1.03102 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 2 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 1 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=2, 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 0.370916 #GCAMreg# pass 0 level1 1 level2 1 tsec 13.267 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=2, 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 0.370916 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 0 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=2, 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 0.370924 #GCAMreg# pass 0 level1 0 level2 1 tsec 13.34 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=2, 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 0.370924 GCAMregister done in 0.91405 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 1132 tmin = 0.3059 Calls to gcamLabelEnergy 961 tmin = 0.268483 Calls to gcamJacobianEnergy 1132 tmin = 0.142967 Calls to gcamSmoothnessEnergy 1132 tmin = 0.47505 Calls to gcamLogLikelihoodTerm 117 tmin = 0.0454667 Calls to gcamLabelTerm 108 tmin = 0.866083 Calls to gcamJacobianTerm 117 tmin = 0.09535 Calls to gcamSmoothnessTerm 117 tmin = 0.0595167 Calls to gcamComputeGradient 117 tmin = 1.94273 Calls to gcamComputeMetricProperties 1478 tmin = 0.513717 mri_ca_register took 0 hours, 10 minutes and 23 seconds. #VMPC# mri_ca_register VmPeak 6307792 FSRUNTIME@ mri_ca_register 0.1731 hours 64 threads #-------------------------------------- #@# SubCort Seg Di 31. Okt 17:53:56 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_fuse_segmentations -a /projects/GRK/spr_freesurfer/data/CON01200509a/mri/aseg.presurf.mgz /projects/GRK/spr_freesurfer/data/CON01200512a/mri/aseg.presurf.mgz /projects/GRK/spr_freesurfer/data/CON01200603a/mri/aseg.presurf.mgz /projects/GRK/spr_freesurfer/data/CON01200609a/mri/aseg.presurf.mgz -c /projects/GRK/spr_freesurfer/data/CON01200509a/mri/aseg.auto_noCCseg.mgz /projects/GRK/spr_freesurfer/data/CON01200512a/mri/aseg.auto_noCCseg.mgz /projects/GRK/spr_freesurfer/data/CON01200603a/mri/aseg.auto_noCCseg.mgz /projects/GRK/spr_freesurfer/data/CON01200609a/mri/aseg.auto_noCCseg.mgz -n /projects/GRK/spr_freesurfer/data/CON01200509a/mri/norm.mgz /projects/GRK/spr_freesurfer/data/CON01200512a/mri/norm.mgz /projects/GRK/spr_freesurfer/data/CON01200603a/mri/norm.mgz /projects/GRK/spr_freesurfer/data/CON01200609a/mri/norm.mgz -t /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200512a_to_CON01_tmpl.lta /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200603a_to_CON01_tmpl.lta /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200609a_to_CON01_tmpl.lta norm.mgz aseg.fused.mgz Input volume: norm.mgz Output aseg: aseg.fused.mgz Loading data for TP 1 Resampling data for TP 1 Loading data for TP 2 Resampling data for TP 2 Loading data for TP 3 Resampling data for TP 3 Loading data for TP 4 Resampling data for TP 4 Fusing... Smoothing temporal bias field with sigma = 3.0 Relabeled 16060 CC labels Writing fused segmentation to aseg.fused.mgz Fusing took 0 minutes and 22 seconds #VMPC# mri_fuse_segmentations VmPeak 1061588 mri_fuse_segmentations done mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align -r /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/aseg.fused.mgz -ri /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/aseg.auto_noCCseg.label_intensities.txt norm.mgz transforms/talairach.m3z /local/program/FreeSurfer/freesurfer-7.4.1/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname jsfc172 machine x86_64 setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align -r /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/aseg.fused.mgz -ri /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/aseg.auto_noCCseg.label_intensities.txt norm.mgz transforms/talairach.m3z /local/program/FreeSurfer/freesurfer-7.4.1/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 reading previously labeled volume from /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/aseg.fused.mgz reading intensity scaling from /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/aseg.auto_noCCseg.label_intensities.txt == Number of threads available to for OpenMP = 64 == reading 1 input volumes reading classifier array from /local/program/FreeSurfer/freesurfer-7.4.1/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 7.42 Atlas used for the 3D morph was /local/program/FreeSurfer/freesurfer-7.4.1/average/RB_all_2020-01-02.gca reading label scales and offsets from /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/aseg.auto_noCCseg.label_intensities.txt reading intensity scales from /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/aseg.auto_noCCseg.label_intensities.txt label Left_Cerebral_Exterior (1): 1.05 + 0.0 label Left_Cerebral_White_Matter (2): 0.98 + 0.0 label Left_Cerebral_Cortex (3): 1.44 + 0.0 label Left_Lateral_Ventricle (4): 0.88 + 0.0 label Left_Inf_Lat_Vent (5): 1.28 + 0.0 label Left_Cerebellum_White_Matter (7): 1.01 + 0.0 label Left_Cerebellum_Cortex (8): 1.33 + 0.0 label (9): 0.00 + 0.0 label Left_Thalamus (10): 1.04 + 0.0 label Left_Caudate (11): 1.12 + 0.0 label Left_Putamen (12): 1.11 + 0.0 label Left_Pallidum (13): 1.04 + 0.0 label Third_Ventricle (14): 0.79 + 0.0 label Fourth_Ventricle (15): 1.16 + 0.0 label Brain_Stem (16): 1.05 + 0.0 label Left_Hippocampus (17): 1.28 + 0.0 label Left_Amygdala (18): 1.32 + 0.0 label CSF (24): 1.05 + 0.0 label Left_Accumbens_area (26): 1.12 + 0.0 label Left_VentralDC (28): 1.09 + 0.0 label Right_Cerebral_Exterior (40): 1.05 + 0.0 label Right_Cerebral_White_Matter (41): 0.98 + 0.0 label Right_Cerebral_Cortex (42): 1.44 + 0.0 label Right_Lateral_Ventricle (43): 1.40 + 0.0 label Right_Inf_Lat_Vent (44): 1.32 + 0.0 label Right_Cerebellum_White_Matter (46): 1.03 + 0.0 label Right_Cerebellum_Cortex (47): 1.33 + 0.0 label (48): 0.00 + 0.0 label Right_Thalamus (49): 1.07 + 0.0 label Right_Caudate (50): 1.25 + 0.0 label Right_Putamen (51): 1.14 + 0.0 label Right_Pallidum (52): 1.04 + 0.0 label Right_Hippocampus (53): 1.32 + 0.0 label Right_Amygdala (54): 1.38 + 0.0 label Right_Accumbens_area (58): 1.25 + 0.0 label Right_VentralDC (60): 1.08 + 0.0 label Fifth_Ventricle (72): 1.05 + 0.0 label (75): 0.00 + 0.0 label (76): 0.00 + 0.0 label WM_hypointensities (77): 0.98 + 0.0 label Left_WM_hypointensities (78): 0.98 + 0.0 label Right_WM_hypointensities (79): 0.98 + 0.0 label non_WM_hypointensities (80): 0.98 + 0.0 label Left_non_WM_hypointensities (81): 0.98 + 0.0 label Right_non_WM_hypointensities (82): 0.98 + 0.0 label (186): 0.00 + 0.0 label (187): 0.00 + 0.0 average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized pass 1: 127535 changed. image ll: -2.203, PF=0.500 pass 2: 37071 changed. image ll: -2.201, PF=0.500 pass 3: 9815 changed. pass 4: 3428 changed. writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 188.584102 mri_ca_label stimesec 0.887148 mri_ca_label ru_maxrss 1419620 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1210561 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 1474 mri_ca_label ru_nivcsw 198 mri_ca_label took 2 minutes and 13 seconds. mri_ca_label done #-------------------------------------- #@# CC Seg Di 31. Okt 17:56:31 CET 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/transforms/cc_up.lta CON01200509a.long.CON01_tmpl will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/transforms/cc_up.lta reading aseg from /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/aseg.auto_noCCseg.mgz reading norm from /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/norm.mgz 22957 voxels in left wm, 75632 in right wm, xrange [117, 131] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 global minimum found at slice 127.0, rotations (-0.86, 0.28) final transformation (x=127.0, yr=-0.864, zr=0.283): 0.99987 -0.00493 -0.01509 3.41801; 0.00493 0.99999 -0.00007 7.38420; 0.01509 0.00000 0.99989 6.09777; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 132 min_x_fornix = 133 min_x_fornix = 140 min_x_fornix = 133 min_x_fornix = 133 cc center is found at 128 120 120 eigenvectors: -0.00052 0.00428 0.99999; -0.20484 -0.97879 0.00408; 0.97879 -0.20484 0.00139; error in mid anterior detected - correcting... writing aseg with callosum to /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #VMPC# mri_cc VmPeak 310740 mri_cc done #-------------------------------------- #@# Merge ASeg Di 31. Okt 17:56:57 CET 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Di 31. Okt 17:56:57 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 256 (src width 256) ************** resampling aseg to account for mismatch with source image *************** normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 440 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 108 white matter peak found at 87 gm peak at 60 (60), valley at 0 (-1) csf peak at 30, setting threshold to 50 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 109 gm peak at 83 (83), valley at 44 (44) csf peak at 20, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 50 seconds. #-------------------------------------------- #@# Mask BFS Di 31. Okt 17:58:50 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1612694 voxels in mask (pct= 9.61) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits -xform /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta brain.finalsurfs.mgz /projects/GRK/spr_freesurfer/data/CON01200509a/mri/brain.finalsurfs.manedit.mgz brain.finalsurfs.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol transform file name is /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta DoAbs = 0 Applying transform to the mask volume maskval=255, outval=255 Writing masked volume to brain.finalsurfs.mgz...done. cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Di 31. Okt 17:58:53 CET 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 MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 320890, nonwhite = 15990044, ambig = 466282, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (101.0): 100.8 +- 6.3 [79.0 --> 125.0] CCS GM (77.0) : 75.1 +- 11.9 [30.0 --> 95.0] white_mean 100.751 white_sigma 6.3488 gray_mean 75.1443 gray_sigma 11.8792 setting bottom of white matter range wm_low to 87.0 setting top of gray matter range gray_hi to 98.9 wm_low 87.0235 wm_hi 125 gray_low 30 gray_hi 98.9026 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=87.0235, wm_hi=125, gray_hi=98.9026 white = 343802, nonwhite = 16211615, ambig = 221799, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 87.0235 wm_hi 125 gray_low 30 gray_hi 98.9026 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 98.9026, wm_low = 87.0235 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=98.9026, wmlow=87.0235 171814 voxels processed (1.02%) 85282 voxels white (0.51%) 86532 voxels non-white (0.52%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=82.0235, gray_hi=98.9026, wsize=13 340717 voxels tested (2.03%) 67922 voxels changed (0.40%) 48165 multi-scale searches (0.29%) Recovering bright white MRIrecoverBrightWhite() wm_low 87.0235 wm_hi 125 slack 6.3488 pct_thresh 0.33 intensity_thresh 131.349 nvox_thresh 8.58 677 voxels tested (0.00%) 428 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=82.0235, hithr=98.9026 smoothing input volume with sigma = 0.250 167230 voxels tested (1.00%) 22881 voxels changed (0.14%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 6099 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 4802 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4729 filled MRIfindBrightNonWM(): 2212 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.1 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 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 0.31 minutes reading wm segmentation from wm.seg.mgz... 15 voxels added to wm to prevent paths from MTL structures to cortex 4131 additional wm voxels added 0 additional wm voxels added SEG EDIT: 63360 voxels turned on, 15190 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+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 23 found - 23 modified | TOTAL: 49 pass 2 (xy-): 0 found - 23 modified | TOTAL: 49 pass 1 (yz+): 19 found - 19 modified | TOTAL: 68 pass 2 (yz+): 0 found - 19 modified | TOTAL: 68 pass 1 (yz-): 21 found - 21 modified | TOTAL: 89 pass 2 (yz-): 0 found - 21 modified | TOTAL: 89 pass 1 (xz+): 19 found - 19 modified | TOTAL: 108 pass 2 (xz+): 0 found - 19 modified | TOTAL: 108 pass 1 (xz-): 23 found - 23 modified | TOTAL: 131 pass 2 (xz-): 0 found - 23 modified | TOTAL: 131 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 35 found - 35 modified | TOTAL: 53 pass 2 (+++): 0 found - 35 modified | TOTAL: 53 pass 1 (+++): 27 found - 27 modified | TOTAL: 80 pass 2 (+++): 0 found - 27 modified | TOTAL: 80 pass 1 (+++): 38 found - 38 modified | TOTAL: 118 pass 2 (+++): 0 found - 38 modified | TOTAL: 118 Iteration Number : 1 pass 1 (++): 174 found - 174 modified | TOTAL: 174 pass 2 (++): 0 found - 174 modified | TOTAL: 174 pass 1 (+-): 137 found - 137 modified | TOTAL: 311 pass 2 (+-): 0 found - 137 modified | TOTAL: 311 pass 1 (--): 196 found - 196 modified | TOTAL: 507 pass 2 (--): 0 found - 196 modified | TOTAL: 507 pass 1 (-+): 91 found - 91 modified | TOTAL: 598 pass 2 (-+): 0 found - 91 modified | TOTAL: 598 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 9 found - 9 modified | TOTAL: 18 pass 2 (xy-): 0 found - 9 modified | TOTAL: 18 pass 1 (yz+): 15 found - 15 modified | TOTAL: 33 pass 2 (yz+): 0 found - 15 modified | TOTAL: 33 pass 1 (yz-): 16 found - 16 modified | TOTAL: 49 pass 2 (yz-): 0 found - 16 modified | TOTAL: 49 pass 1 (xz+): 12 found - 12 modified | TOTAL: 61 pass 2 (xz+): 0 found - 12 modified | TOTAL: 61 pass 1 (xz-): 9 found - 9 modified | TOTAL: 70 pass 2 (xz-): 0 found - 9 modified | TOTAL: 70 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 5 found - 5 modified | TOTAL: 11 pass 2 (+++): 0 found - 5 modified | TOTAL: 11 pass 1 (+++): 0 found - 0 modified | TOTAL: 11 Iteration Number : 2 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 5 found - 5 modified | TOTAL: 12 pass 2 (+-): 0 found - 5 modified | TOTAL: 12 pass 1 (--): 8 found - 8 modified | TOTAL: 20 pass 2 (--): 0 found - 8 modified | TOTAL: 20 pass 1 (-+): 7 found - 7 modified | TOTAL: 27 pass 2 (-+): 0 found - 7 modified | TOTAL: 27 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 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 : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 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 : 5 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 : 6 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 : 6 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 : 6 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 = 965 (out of 526173: 0.183400) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done mri_mask -transfer 255 -keep_mask_deletion_edits -xform /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta wm.mgz /projects/GRK/spr_freesurfer/data/CON01200509a/mri/wm.mgz wm.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol transform file name is /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/transforms/CON01200509a_to_CON01_tmpl.lta DoAbs = 0 Applying transform to the mask volume maskval=255, outval=255 Writing masked volume to wm.mgz...done. cp -p /projects/GRK/spr_freesurfer/data/CON01_tmpl/mri/filled.mgz /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri/filled.mgz #-------------------------------------------- #@# AutoDetGWStats lh Di 31. Okt 18:01:08 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig 7.4.1 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig border white: 268165 voxels (1.60%) border gray 276966 voxels (1.65%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig Auto detecting stats MRIclipBrightWM(): nthresh=56422, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 99.6 +- 7.6 [70.0 --> 110.0] CCS GM (80.0) : 78.9 +- 12.3 [30.0 --> 110.0] white_mean = 99.5819 +/- 7.55645, gray_mean = 78.9497 +/- 12.3052 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=231 nbins=232 intensity peaks found at WM=103+-8.7, GM=77+-8.7 white_mode = 103, gray_mode = 77 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 64.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.6 (was 105.000000) setting MIN_BORDER_WHITE to 77.0 (was 85.000000) setting MAX_CSF to 52.4 (was 40.000000) setting MAX_GRAY to 95.4 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 64.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 40.1 (was 40.000000) When placing the white surface white_border_hi = 110.556; white_border_low = 77; white_outside_low = 64.6948; white_inside_hi = 120; white_outside_hi = 110.556; When placing the pial surface pial_border_hi = 64.6948; pial_border_low = 40.0844; pial_outside_low = 10; pial_inside_hi = 95.4435; pial_outside_hi = 58.5422; #VMPC# mris_autodet_gwstats VmPeak 4498988 mris_autodet_gwstats done #-------------------------------------------- #@# AutoDetGWStats rh Di 31. Okt 18:01:12 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig 7.4.1 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig border white: 268165 voxels (1.60%) border gray 276966 voxels (1.65%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig Auto detecting stats MRIclipBrightWM(): nthresh=56422, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 99.6 +- 7.6 [70.0 --> 110.0] CCS GM (80.0) : 78.9 +- 12.3 [30.0 --> 110.0] white_mean = 99.5819 +/- 7.55645, gray_mean = 78.9497 +/- 12.3052 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=231 nbins=232 intensity peaks found at WM=103+-6.1, GM=77+-9.6 white_mode = 103, gray_mode = 77 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 64.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.6 (was 105.000000) setting MIN_BORDER_WHITE to 77.0 (was 85.000000) setting MAX_CSF to 52.4 (was 40.000000) setting MAX_GRAY to 95.4 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 64.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 40.1 (was 40.000000) When placing the white surface white_border_hi = 110.556; white_border_low = 77; white_outside_low = 64.6948; white_inside_hi = 120; white_outside_hi = 110.556; When placing the pial surface pial_border_hi = 64.6948; pial_border_low = 40.0844; pial_outside_low = 10; pial_inside_hi = 95.4435; pial_outside_hi = 58.5422; #VMPC# mris_autodet_gwstats VmPeak 5612060 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Di 31. Okt 18:01:15 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 64 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --max-cbv-dist 3.5 7.4.1 7.4.1 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 64 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --max-cbv-dist 3.5 Reading in input surface ../surf/lh.orig Not smoothing input surface Area 271826 0.33483 0.12938 0.001103 1.7082 Corner 815478 60.00000 16.28921 0.339513 179.0106 Edge 407739 0.89418 0.21520 0.007602 3.0291 Hinge 407739 12.82615 13.39432 0.000033 179.9884 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=56422, wmmin=5, clip=110 MRIfindBrightNonWM(): 4157 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 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 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6449, nmarked2=0, nripped=6449 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67958: xyz = (-53.6944,8.45142,-27.2437) oxyz = (-53.6944,8.45142,-27.2437) wxzy = (-53.6944,8.45142,-27.2437) pxyz = (0,0,0) CBVO Creating mask 135915 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=6449 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6449, nmarked2=0, nripped=6449 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 2; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135915 Gdiag_no=-1 vno start=0, stop=135915 Replacing 255s with 0s #SI# sigma=2 had to be increased for 210 vertices, nripped=6449 mean border=85.8, 133 (133) missing vertices, mean dist 0.3 [1.4 (%22.9)->0.8 (%77.1))] %40 local maxima, %55 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0054 min Finding expansion regions mean absolute distance = 0.91 +- 1.08 4828 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 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=jsfc1, 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=1425290.2, rms=6.852 001: dt: 0.5000, sse=720690.6, rms=4.492 (34.447%) 002: dt: 0.5000, sse=497860.1, rms=3.420 (23.858%) 003: dt: 0.5000, sse=434019.1, rms=3.039 (11.155%) 004: dt: 0.5000, sse=410930.4, rms=2.880 (5.219%) rms = 2.8422/2.8800, sse=407486.4/410930.4, time step reduction 1 of 3 to 0.250 0 0 1 005: dt: 0.5000, sse=407486.4, rms=2.842 (1.313%) 006: dt: 0.2500, sse=320931.8, rms=2.133 (24.962%) 007: dt: 0.2500, sse=306098.2, rms=1.985 (6.925%) rms = 1.9772/1.9850, sse=305566.6/306098.2, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=305566.6, rms=1.977 (0.394%) rms = 1.9417/1.9772, sse=302187.2/305566.6, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=302187.2, rms=1.942 (1.794%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface 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=6449 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 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6570, nmarked2=0, nripped=6570 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 1; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135915 Gdiag_no=-1 vno start=0, stop=135915 Replacing 255s with 0s #SI# sigma=1 had to be increased for 297 vertices, nripped=6570 mean border=88.3, 73 (13) missing vertices, mean dist -0.3 [0.6 (%64.2)->0.3 (%35.8))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0037 min Finding expansion regions mean absolute distance = 0.51 +- 0.76 5824 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 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=jsfc1, 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=602861.1, rms=3.840 010: dt: 0.5000, sse=402969.3, rms=2.609 (32.046%) 011: dt: 0.5000, sse=383386.4, rms=2.436 (6.649%) rms = 2.5564/2.4360, sse=396232.6/383386.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=324890.2, rms=1.963 (19.412%) 013: dt: 0.2500, sse=307914.8, rms=1.727 (12.018%) rms = 1.6920/1.7272, sse=302300.7/307914.8, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=302300.8, rms=1.692 (2.039%) rms = 1.6561/1.6920, sse=299760.5/302300.7, time step reduction 3 of 3 to 0.062 0 0 1 015: dt: 0.1250, sse=299760.4, rms=1.656 (2.123%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface 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=6570 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6584, nmarked2=0, nripped=6584 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 0.5; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135915 Gdiag_no=-1 vno start=0, stop=135915 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 840 vertices, nripped=6584 mean border=90.3, 107 (5) missing vertices, mean dist -0.2 [0.4 (%65.8)->0.2 (%34.2))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0020 min Finding expansion regions mean absolute distance = 0.37 +- 0.50 4626 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 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=jsfc1, 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=455986.7, rms=2.996 016: dt: 0.5000, sse=391322.1, rms=2.348 (21.648%) rms = 2.3256/2.3477, sse=374573.3/391322.1, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=374573.2, rms=2.326 (0.941%) 018: dt: 0.2500, sse=318480.2, rms=1.721 (25.987%) 019: dt: 0.2500, sse=310466.5, rms=1.589 (7.674%) rms = 1.5945/1.5892, sse=301469.2/310466.5, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 1.5662/1.5892, sse=299977.5/310466.5, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=299977.5, rms=1.566 (1.446%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface 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=6584 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 #FML# MRISripMidline(): nmarked=6607, nmarked2=0, nripped=6607 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 0.25; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135915 Gdiag_no=-1 vno start=0, stop=135915 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 1289 vertices, nripped=6607 mean border=91.0, 182 (4) missing vertices, mean dist -0.1 [0.4 (%55.0)->0.2 (%45.0))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0012 min Finding expansion regions mean absolute distance = 0.30 +- 0.39 3561 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 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=jsfc1, 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=327331.0, rms=1.886 rms = 1.7170/1.8860, sse=340616.9/327331.0, time step reduction 1 of 3 to 0.250 0 1 0 021: dt: 0.5000, sse=340616.9, rms=1.717 (8.960%) 022: dt: 0.2500, sse=311222.3, rms=1.463 (14.780%) 023: dt: 0.2500, sse=290984.0, rms=1.281 (12.484%) rms = 1.3103/1.2806, sse=302786.8/290984.0, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.2396/1.2806, sse=286334.4/290984.0, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=286334.4, rms=1.240 (3.203%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 1.96 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 6087160 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Di 31. Okt 18:03:18 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 64 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --max-cbv-dist 3.5 7.4.1 7.4.1 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/mri setenv SUBJECTS_DIR /projects/GRK/spr_freesurfer/data mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 64 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --max-cbv-dist 3.5 Reading in input surface ../surf/rh.orig Not smoothing input surface Area 271734 0.33370 0.12744 0.001397 2.6985 Corner 815202 60.00000 15.94075 0.445617 177.9368 Edge 407601 0.89205 0.21193 0.023500 3.9255 Hinge 407601 12.62360 13.16564 0.000076 179.9788 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=56422, wmmin=5, clip=110 MRIfindBrightNonWM(): 4157 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 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 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6762, nmarked2=0, nripped=6762 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67935: xyz = (14.7452,9.32222,-18.7263) oxyz = (14.7452,9.32222,-18.7263) wxzy = (14.7452,9.32222,-18.7263) pxyz = (0,0,0) CBVO Creating mask 135869 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=6762 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6762, nmarked2=0, nripped=6762 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 2; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135869 Gdiag_no=-1 vno start=0, stop=135869 Replacing 255s with 0s #SI# sigma=2 had to be increased for 143 vertices, nripped=6762 mean border=86.3, 89 (89) missing vertices, mean dist 0.3 [1.4 (%21.0)->0.7 (%79.0))] %43 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0054 min Finding expansion regions mean absolute distance = 0.88 +- 1.03 4560 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 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=jsfc1, 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=1414572.8, rms=6.856 001: dt: 0.5000, sse=729584.8, rms=4.561 (33.471%) 002: dt: 0.5000, sse=510114.4, rms=3.522 (22.785%) 003: dt: 0.5000, sse=443606.2, rms=3.135 (10.998%) 004: dt: 0.5000, sse=418290.4, rms=2.961 (5.526%) 005: dt: 0.5000, sse=409509.8, rms=2.900 (2.076%) rms = 2.8548/2.9000, sse=404750.0/409509.8, time step reduction 1 of 3 to 0.250 0 0 1 006: dt: 0.5000, sse=404749.9, rms=2.855 (1.558%) 007: dt: 0.2500, sse=312486.4, rms=2.105 (26.256%) 008: dt: 0.2500, sse=296983.8, rms=1.949 (7.431%) rms = 1.9431/1.9488, sse=297305.2/296983.8, time step reduction 2 of 3 to 0.125 0 1 1 009: dt: 0.2500, sse=297305.2, rms=1.943 (0.292%) rms = 1.9117/1.9431, sse=294273.3/297305.2, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=294273.3, rms=1.912 (1.620%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface 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=6762 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 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6819, nmarked2=0, nripped=6819 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 1; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135869 Gdiag_no=-1 vno start=0, stop=135869 Replacing 255s with 0s #SI# sigma=1 had to be increased for 261 vertices, nripped=6819 mean border=88.8, 65 (12) missing vertices, mean dist -0.3 [0.7 (%64.4)->0.3 (%35.6))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0037 min Finding expansion regions mean absolute distance = 0.52 +- 0.78 5504 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 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=jsfc1, 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=584089.7, rms=3.772 011: dt: 0.5000, sse=399040.8, rms=2.629 (30.302%) 012: dt: 0.5000, sse=377652.1, rms=2.480 (5.683%) rms = 2.6096/2.4797, sse=396332.3/377652.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=323109.8, rms=1.999 (19.398%) 014: dt: 0.2500, sse=302614.7, rms=1.770 (11.456%) rms = 1.7266/1.7697, sse=299644.7/302614.7, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=299644.7, rms=1.727 (2.438%) rms = 1.6860/1.7266, sse=296575.7/299644.7, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=296575.7, rms=1.686 (2.349%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface 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=6819 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6847, nmarked2=0, nripped=6847 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 0.5; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135869 Gdiag_no=-1 vno start=0, stop=135869 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 819 vertices, nripped=6847 mean border=90.8, 64 (4) missing vertices, mean dist -0.2 [0.5 (%65.6)->0.2 (%34.4))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0020 min Finding expansion regions mean absolute distance = 0.39 +- 0.52 5638 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 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=jsfc1, 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=458953.4, rms=3.055 017: dt: 0.5000, sse=376137.5, rms=2.381 (22.062%) rms = 2.3654/2.3809, sse=374284.7/376137.5, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=374284.7, rms=2.365 (0.651%) 019: dt: 0.2500, sse=305728.1, rms=1.745 (26.226%) 020: dt: 0.2500, sse=291351.1, rms=1.599 (8.380%) rms = 1.6017/1.5989, sse=292179.7/291351.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.5769/1.5989, sse=289339.7/291351.1, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=289339.8, rms=1.577 (1.375%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface 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=6847 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6921, nmarked2=0, nripped=6921 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.5564580; border_low = 77.0000000; outside_low = 64.6948010; outside_hi = 110.5564580; sigma = 0.25; max_thickness = 7; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135869 Gdiag_no=-1 vno start=0, stop=135869 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 1221 vertices, nripped=6921 mean border=91.5, 182 (4) missing vertices, mean dist -0.1 [0.4 (%55.3)->0.2 (%44.7))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0013 min Finding expansion regions mean absolute distance = 0.32 +- 0.40 4136 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 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=jsfc1, 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=318455.8, rms=1.915 022: dt: 0.5000, sse=314223.0, rms=1.735 (9.402%) rms = 2.2674/1.7347, sse=355869.6/314223.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=273967.9, rms=1.326 (23.545%) rms = 1.3247/1.3263, sse=271910.6/273967.9, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=271910.7, rms=1.325 (0.122%) 025: dt: 0.1250, sse=267068.0, rms=1.217 (8.092%) rms = 1.1920/1.2175, sse=263822.6/267068.0, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=263822.6, rms=1.192 (2.088%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.09 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 6128104 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Di 31. Okt 18:05:29 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 9 non-cortical segments detected only using segment with 7810 vertices erasing segment 1 (vno[0] = 42320) erasing segment 2 (vno[0] = 58312) erasing segment 3 (vno[0] = 59186) erasing segment 4 (vno[0] = 60487) erasing segment 5 (vno[0] = 81630) erasing segment 6 (vno[0] = 84826) erasing segment 7 (vno[0] = 85435) erasing segment 8 (vno[0] = 87358) #-------------------------------------------- #@# CortexLabel+HipAmyg lh Di 31. Okt 18:05:44 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 13 non-cortical segments detected only using segment with 5997 vertices erasing segment 1 (vno[0] = 42320) erasing segment 2 (vno[0] = 50114) erasing segment 3 (vno[0] = 58312) erasing segment 4 (vno[0] = 59186) erasing segment 5 (vno[0] = 60487) erasing segment 6 (vno[0] = 74776) erasing segment 7 (vno[0] = 77269) erasing segment 8 (vno[0] = 77291) erasing segment 9 (vno[0] = 84826) erasing segment 10 (vno[0] = 85435) erasing segment 11 (vno[0] = 87358) erasing segment 12 (vno[0] = 124912) #-------------------------------------------- #@# CortexLabel rh Di 31. Okt 18:05:58 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 6 non-cortical segments detected only using segment with 8078 vertices erasing segment 1 (vno[0] = 70102) erasing segment 2 (vno[0] = 80348) erasing segment 3 (vno[0] = 83017) erasing segment 4 (vno[0] = 85455) erasing segment 5 (vno[0] = 85472) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Di 31. Okt 18:06:12 CET 2023 cd /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 7 non-cortical segments detected only using segment with 6208 vertices erasing segment 1 (vno[0] = 52013) erasing segment 2 (vno[0] = 70102) erasing segment 3 (vno[0] = 80348) erasing segment 4 (vno[0] = 83017) erasing segment 5 (vno[0] = 85455) erasing segment 6 (vno[0] = 85472) #-------------------------------------------- #@# Smooth2 lh Di 31. Okt 18:06:25 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Di 31. Okt 18:06:25 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 29558 of (29558 29561) to complete... Waiting for PID 29561 of (29558 29561) 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 (29558 29561) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Di 31. Okt 18:06:29 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Di 31. Okt 18:06:29 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 29771 of (29771 29774) to complete... Waiting for PID 29774 of (29771 29774) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.6 mm, total surface area = 83907 mm^2 step 000: RMS=0.172 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 580.960184 mris_inflate stimesec 7.543559 mris_inflate ru_maxrss 210724 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 516951 mris_inflate ru_majflt 33 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 60587 mris_inflate ru_nivcsw 13433 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.2 mm, total surface area = 83671 mm^2 step 000: RMS=0.171 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.039 (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/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 580.329407 mris_inflate stimesec 7.558392 mris_inflate ru_maxrss 210640 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 519120 mris_inflate ru_majflt 11 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 58611 mris_inflate ru_nivcsw 13885 PIDs (29771 29774) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Di 31. Okt 18:06:51 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 Di 31. Okt 18:06:52 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/surf reconbatchjobs /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/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 30066 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30069 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30072 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30075 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30078 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30081 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30084 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30087 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30144 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30156 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30159 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... Waiting for PID 30162 of (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 17.496*4pi (219.859) --> -16 handles ICI = 262.9, FI = 1812.0, variation=31772.926 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature 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 133 vertices thresholded to be in k1 ~ [-1.70 0.21], k2 ~ [-0.08 0.23] total integrated curvature = 0.686*4pi (8.617) --> 0 handles ICI = 1.6, FI = 8.9, variation=156.504 104 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 75 vertices thresholded to be in [-0.17 0.11] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.021 mris_curvature done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 7.703*4pi (96.805) --> -7 handles ICI = 254.0, FI = 1755.3, variation=30932.523 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature 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 222 vertices thresholded to be in k1 ~ [-0.15 0.98], k2 ~ [-0.08 0.06] total integrated curvature = 0.719*4pi (9.039) --> 0 handles ICI = 1.6, FI = 8.5, variation=152.348 87 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 117 vertices thresholded to be in [-0.10 0.17] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.021 mris_curvature done. PIDs (30066 30069 30072 30075 30078 30081 30084 30087 30144 30156 30159 30162) completed and logs appended. #-------------------------------------------- #@# Sphere lh Di 31. Okt 18:07:35 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts #-------------------------------------------- #@# Sphere rh Di 31. Okt 18:07:35 CET 2023 /projects/GRK/spr_freesurfer/data/CON01200509a.long.CON01_tmpl/scripts Usage: reconbatchjobs logfile cmdfile1 [cmdfile2 ...] See recon-all script for examples. Linux jsfc172 4.18.0-477.27.1.el8_8.x86_64 #1 SMP Wed Sep 20 15:55:39 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CON01200509a.long.CON01_tmpl exited with ERRORS at Di 31. Okt 18:07:35 CET 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting