Tue Sep 14 11:04:53 EDT 2021 cd /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207 setenv SUBJECTS_DIR /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects /N/u/xionyany/Carbonate/freesurfer/bin/recon-all -subjid p207 -i /N/project/canvas/CANVAS_Dataset/Data/3months/T1/p207_T1.nii.gz -T2 /N/project/canvas/CANVAS_Dataset/Data/3months/T2/p207_T2.nii.gz -T2pial -all -bigventricles -sd /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects -parallel -openmp 4 subjid p207 setenv SUBJECTS_DIR /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects FREESURFER_HOME /N/u/xionyany/Carbonate/freesurfer Actual FREESURFER_HOME /geode2/home/u110/xionyany/Carbonate/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Linux c10 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 60817408 kbytes vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 1027513 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251G 9.2G 205G 12G 36G 228G Swap: 0B 0B 0B ######################################## program versions used 7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) 7.1.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:55-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:56-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.1.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/09/14-15:04:57-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: xionyany Machine: c10 Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /N/u/xionyany/Carbonate/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /N/u/xionyany/Carbonate/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207 mri_convert /N/project/canvas/CANVAS_Dataset/Data/3months/T1/p207_T1.nii.gz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/001.mgz mri_convert /N/project/canvas/CANVAS_Dataset/Data/3months/T1/p207_T1.nii.gz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/001.mgz reading from /N/project/canvas/CANVAS_Dataset/Data/3months/T1/p207_T1.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0454752, -0.998965, 8.61414e-09) j_ras = (0.071394, 0.00325001, -0.997443) k_ras = (0.996411, 0.0453589, 0.071468) writing to /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/001.mgz... @#@FSTIME 2021:09:14:11:05:10 mri_convert N 2 e 6.54 S 0.46 U 2.59 P 46% M 24416 F 0 R 2013 W 0 c 10 w 40 I 21088 O 21096 L 4.63 4.96 5.08 @#@FSLOADPOST 2021:09:14:11:05:16 mri_convert N 2 4.58 4.95 5.08 #-------------------------------------------- #@# T2/FLAIR Input Tue Sep 14 11:05:17 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207 mri_convert --no_scale 1 /N/project/canvas/CANVAS_Dataset/Data/3months/T2/p207_T2.nii.gz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/T2raw.mgz mri_convert --no_scale 1 /N/project/canvas/CANVAS_Dataset/Data/3months/T2/p207_T2.nii.gz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/T2raw.mgz reading from /N/project/canvas/CANVAS_Dataset/Data/3months/T2/p207_T2.nii.gz... TR=3390.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0454752, -0.998965, 8.61414e-09) j_ras = (0.071394, 0.00325001, -0.997443) k_ras = (-0.996411, -0.0453589, -0.071468) writing to /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/T2raw.mgz... @#@FSTIME 2021:09:14:11:05:17 mri_convert N 4 e 11.44 S 0.26 U 2.60 P 25% M 26012 F 0 R 2580 W 0 c 13 w 33 I 14792 O 14792 L 4.61 4.95 5.08 @#@FSLOADPOST 2021:09:14:11:05:29 mri_convert N 4 4.60 4.93 5.07 #-------------------------------------------- #@# MotionCor Tue Sep 14 11:05:29 EDT 2021 Found 1 runs /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig/001.mgz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/rawavg.mgz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207 mri_convert /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/rawavg.mgz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig.mgz --conform mri_convert /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/rawavg.mgz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig.mgz --conform reading from /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0454752, -0.998965, 8.61414e-09) j_ras = (0.071394, 0.00325001, -0.997443) k_ras = (0.996411, 0.0453589, 0.071468) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 1163 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig.mgz... @#@FSTIME 2021:09:14:11:05:35 mri_convert N 3 e 4.33 S 0.04 U 3.33 P 78% M 34532 F 0 R 4216 W 0 c 9 w 29 I 0 O 12656 L 4.55 4.92 5.06 @#@FSLOADPOST 2021:09:14:11:05:39 mri_convert N 3 4.51 4.90 5.06 mri_add_xform_to_header -c /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/transforms/talairach.xfm /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig.mgz /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2021:09:14:11:05:39 mri_add_xform_to_header N 4 e 1.84 S 0.03 U 1.38 P 77% M 20208 F 0 R 1988 W 0 c 4 w 40 I 0 O 12656 L 4.51 4.90 5.06 @#@FSLOADPOST 2021:09:14:11:05:41 mri_add_xform_to_header N 4 4.51 4.90 5.06 #-------------------------------------------- #@# Talairach Tue Sep 14 11:05:42 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /bin/bc /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri /N/u/xionyany/Carbonate/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 Linux c10 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 14 11:05:43 EDT 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.10904 cd /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.10904/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.10904/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.10904/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.10904/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-7.45058e-09, -4.65661e-10, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Sep 14 11:09:12 EDT 2021 mri_nu_correct.mni done @#@FSTIME 2021:09:14:11:05:43 mri_nu_correct.mni N 12 e 209.75 S 0.48 U 201.57 P 96% M 484720 F 0 R 77485 W 0 c 115 w 423 I 0 O 11896 L 4.63 4.92 5.06 @#@FSLOADPOST 2021:09:14:11:09:12 mri_nu_correct.mni N 12 4.97 5.04 5.09 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Sep 14 11:09:13 EDT 2021 Ended at Tue Sep 14 11:10:53 EDT 2021 talairach_avi done @#@FSTIME 2021:09:14:11:09:13 talairach_avi N 4 e 100.89 S 1.44 U 15.66 P 16% M 254192 F 0 R 49082 W 0 c 107 w 1059 I 0 O 295288 L 4.97 5.04 5.09 @#@FSLOADPOST 2021:09:14:11:10:53 talairach_avi N 4 5.16 5.05 5.08 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /N/u/xionyany/Carbonate/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.1.1 --src: orig.mgz src image (geometry). --trg: /N/u/xionyany/Carbonate/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.07710 0.05122 0.08239 2.56766; -0.06225 1.02675 0.06642 -36.14037; -0.08462 -0.04811 1.07790 -23.35184; 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 Tue Sep 14 11:11:00 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6687, pval=0.3663 >= threshold=0.0050) @#@FSTIME 2021:09:14:11:11:00 talairach_afd N 4 e 0.03 S 0.00 U 0.00 P 33% M 2640 F 0 R 759 W 0 c 3 w 32 I 0 O 0 L 5.15 5.05 5.08 @#@FSLOADPOST 2021:09:14:11:11:00 talairach_afd N 4 5.15 5.05 5.08 awk -f /N/u/xionyany/Carbonate/freesurfer/bin/extract_talairach_avi_QA.awk /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/transforms/talairach_avi.log tal_QC_AZS /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/transforms/talairach_avi.log TalAviQA: 0.97596 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Sep 14 11:11:08 EDT 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /bin/bc /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri /N/u/xionyany/Carbonate/freesurfer/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 7.1.1 Linux c10 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 14 11:11:08 EDT 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.11441 cd /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz 7.1.1 cwd /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz sysname Linux hostname c10 machine x86_64 user xionyany input /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.11441/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.11441/input.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.11441/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.11441/input.mean.dat sysname Linux hostname c10 machine x86_64 user xionyany whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.11441/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.11441/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.11441/output.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.11441/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.11441/output.mean.dat sysname Linux hostname c10 machine x86_64 user xionyany whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.11441/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.11441/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz mul 1.25938402912106620932 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.11441/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-7.45058e-09, -4.65661e-10, -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 8 seconds. mapping (11, 89) to ( 3, 110) Tue Sep 14 11:15:07 EDT 2021 mri_nu_correct.mni done @#@FSTIME 2021:09:14:11:11:08 mri_nu_correct.mni N 9 e 238.84 S 1.30 U 225.99 P 95% M 610792 F 0 R 243047 W 0 c 225 w 2040 I 0 O 38600 L 5.05 5.03 5.08 @#@FSLOADPOST 2021:09:14:11:15:07 mri_nu_correct.mni N 9 5.13 5.09 5.09 mri_add_xform_to_header -c /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2021:09:14:11:15:07 mri_add_xform_to_header N 4 e 1.79 S 0.04 U 0.67 P 39% M 20264 F 0 R 1600 W 0 c 1 w 56 I 0 O 8344 L 5.13 5.09 5.09 @#@FSLOADPOST 2021:09:14:11:15:09 mri_add_xform_to_header N 4 5.04 5.07 5.08 #-------------------------------------------- #@# Intensity Normalization Tue Sep 14 11:15:23 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.07710 0.05122 0.08239 2.56766; -0.06225 1.02675 0.06642 -36.14037; -0.08462 -0.04811 1.07790 -23.35184; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 72 (72), valley at 60 (60) csf peak at 38, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 74 (74), valley at 44 (44) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 33 seconds. @#@FSTIME 2021:09:14:11:15:24 mri_normalize N 7 e 93.36 S 0.27 U 104.51 P 112% M 578864 F 0 R 25374 W 0 c 65 w 82 I 0 O 9008 L 4.88 5.04 5.07 @#@FSLOADPOST 2021:09:14:11:16:57 mri_normalize N 7 4.07 4.75 4.97 #-------------------------------------------- #@# Skull Stripping Tue Sep 14 11:16:58 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri mri_em_register -skull nu.mgz /N/u/xionyany/Carbonate/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/N/u/xionyany/Carbonate/freesurfer/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=31.0 skull bounding box = (60, 41, 28) --> (206, 230, 216) finding center of left hemi white matter using (109, 104, 122) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (91,81,99) --> (126, 127,145) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 6.3 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.472 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.494958 @ (0.000, 0.000, 0.000) max log p = -4.367993 @ (-5.263, 5.263, -5.263) max log p = -4.321655 @ (2.632, 2.632, -2.632) max log p = -4.301320 @ (-1.316, -1.316, 1.316) max log p = -4.278746 @ (-0.658, -0.658, -1.974) max log p = -4.278746 @ (0.000, 0.000, 0.000) max log p = -4.278746 @ (0.000, 0.000, 0.000) max log p = -4.278746 @ (0.000, 0.000, 0.000) Found translation: (-4.6, 5.9, -8.6): log p = -4.279 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.240, old_max_log_p =-4.279 (thresh=-4.3) 1.06375 0.00000 0.00000 -12.87413; 0.00000 1.00000 0.00000 5.92105; 0.00000 0.00000 1.07500 -17.53164; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 30 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.221, old_max_log_p =-4.240 (thresh=-4.2) 1.05465 0.01704 -0.13912 2.64089; 0.00000 0.99144 0.14032 -9.71244; 0.13885 -0.12941 1.05669 -15.72438; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 28 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.221, old_max_log_p =-4.221 (thresh=-4.2) 1.05465 0.01704 -0.13912 2.64089; 0.00000 0.99144 0.14032 -9.71244; 0.13885 -0.12941 1.05669 -15.72438; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 28 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.161, old_max_log_p =-4.221 (thresh=-4.2) 1.04765 0.17290 -0.01925 -28.16205; -0.18850 1.03580 0.12154 16.51096; 0.04320 -0.10781 1.12941 -13.34246; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 28 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.126, old_max_log_p =-4.161 (thresh=-4.2) 1.03390 0.13293 -0.02112 -20.98188; -0.15780 1.10153 0.11678 4.59643; 0.03447 -0.10532 1.08769 -9.51680; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.120, old_max_log_p =-4.126 (thresh=-4.1) 1.03390 0.13293 -0.02112 -20.98188; -0.16076 1.12218 0.11897 2.01806; 0.03447 -0.10532 1.08769 -9.51680; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.120, old_max_log_p =-4.120 (thresh=-4.1) 1.03390 0.13293 -0.02112 -20.98188; -0.16076 1.12218 0.11897 2.01806; 0.03447 -0.10532 1.08769 -9.51680; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.112, old_max_log_p =-4.120 (thresh=-4.1) 1.03545 0.12274 -0.01335 -21.24716; -0.15188 1.12266 0.13680 -1.77268; 0.02861 -0.12460 1.08446 -5.87208; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.111, old_max_log_p =-4.112 (thresh=-4.1) 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.111 (old=-4.472) transform before final EM align: 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.5 tol 0.000000 final transform: 1.03423 0.12260 -0.01334 -21.07566; -0.15206 1.12398 0.13696 -1.94129; 0.02857 -0.12446 1.08319 -5.73493; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 932112 FSRUNTIME@ mri_em_register 0.0877 hours 4 threads registration took 5 minutes and 16 seconds. @#@FSTIME 2021:09:14:11:16:58 mri_em_register N 4 e 315.86 S 4.75 U 1087.20 P 345% M 625624 F 0 R 3978280 W 0 c 1720 w 15046 I 0 O 32 L 3.91 4.71 4.95 @#@FSLOADPOST 2021:09:14:11:22:14 mri_em_register N 4 5.06 5.32 5.17 mri_watershed -T1 -brain_atlas /N/u/xionyany/Carbonate/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=116 z=118 r=87 first estimation of the main basin volume: 2764602 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=116, y=98, z=90, Imax=255 CSF=21, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=7852990515 voxels, voxel volume =1.000 = 7852990515 mmm3 = 7852990.464 cm3 done. PostAnalyze...Basin Prior 5 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=130,y=113, z=114, r=9854 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 44928 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 3078 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = 3042 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=63 , nb = 18828 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=58 , nb = 19602 OTHER CSF_MIN=9, CSF_intensity=27, CSF_MAX=56 , nb = 378 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 56, 40, 29, 71 after analyzing : 30, 40, 40, 47 RIGHT_CER before analyzing : 19, 23, 35, 81 after analyzing : 19, 31, 35, 43 LEFT_CER before analyzing : 22, 24, 32, 79 after analyzing : 22, 29, 32, 41 RIGHT_BRAIN before analyzing : 63, 42, 30, 67 after analyzing : 32, 42, 42, 48 LEFT_BRAIN before analyzing : 58, 41, 28, 71 after analyzing : 31, 41, 41, 48 OTHER before analyzing : 56, 69, 77, 93 after analyzing : 56, 74, 77, 78 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.837, std = 7.754 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.05, sigma = 5.89 after rotation: sse = 4.05, sigma = 5.89 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.45, its var is 5.81 before Erosion-Dilatation 1.28% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...52 iterations mri_strip_skull: done peeling brain Brain Size = 1797433 voxels, voxel volume = 1.000 mm3 = 1797433 mmm3 = 1797.433 cm3 MRImask(): AllowDiffGeom = 1 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 25.660156 mri_watershed stimesec 0.543833 mri_watershed ru_maxrss 822268 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 345514 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 3032 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 3097 mri_watershed ru_nivcsw 107 mri_watershed done @#@FSTIME 2021:09:14:11:22:21 mri_watershed N 6 e 22.29 S 0.65 U 25.66 P 118% M 822268 F 0 R 345531 W 0 c 107 w 3098 I 0 O 3032 L 4.89 5.28 5.16 @#@FSLOADPOST 2021:09:14:11:22:43 mri_watershed N 6 4.25 5.10 5.10 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Sep 14 11:22:55 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /N/u/xionyany/Carbonate/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/N/u/xionyany/Carbonate/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (59, 47, 30) --> (201, 173, 207) finding center of left hemi white matter using (106, 89, 119) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (89,74,97) --> (123, 104,140) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 106 +- 5.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.180 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.047799 @ (-10.526, 10.526, -10.526) max log p = -3.884440 @ (5.263, -5.263, -5.263) max log p = -3.804365 @ (2.632, 2.632, 7.895) max log p = -3.787024 @ (-3.947, -3.947, -3.947) max log p = -3.784901 @ (-0.658, 0.658, 1.974) max log p = -3.765866 @ (0.987, -0.987, -3.618) max log p = -3.765866 @ (0.000, 0.000, 0.000) max log p = -3.765866 @ (0.000, 0.000, 0.000) Found translation: (-6.3, 3.6, -13.5): log p = -3.766 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.766, old_max_log_p =-3.766 (thresh=-3.8) 1.00000 0.00000 0.00000 -6.25000; 0.00000 1.00000 0.00000 3.61842; 0.00000 0.00000 1.00000 -13.48685; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.638, old_max_log_p =-3.766 (thresh=-3.8) 1.01369 0.07079 -0.06194 -6.85668; -0.06898 1.05214 0.07349 1.58921; 0.06540 -0.06526 0.99572 -10.38113; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.638, old_max_log_p =-3.638 (thresh=-3.6) 1.01369 0.07079 -0.06194 -6.85668; -0.06898 1.05214 0.07349 1.58921; 0.06540 -0.06526 0.99572 -10.38113; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.624, old_max_log_p =-3.638 (thresh=-3.6) 1.01217 0.11278 -0.04210 -12.73094; -0.11049 1.04960 0.07594 6.08786; 0.04831 -0.06698 0.99659 -8.07839; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 23 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.617, old_max_log_p =-3.624 (thresh=-3.6) 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04842 -0.06714 0.99893 -8.34441; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 23 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.617, old_max_log_p =-3.617 (thresh=-3.6) 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.617 (old=-4.180) transform before final EM align: 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.0 tol 0.000000 final transform: 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 919556 FSRUNTIME@ mri_em_register 0.1085 hours 4 threads registration took 6 minutes and 31 seconds. @#@FSTIME 2021:09:14:11:22:55 mri_em_register N 7 e 390.94 S 2.00 U 636.13 P 163% M 613248 F 0 R 1428833 W 0 c 723 w 5669 I 0 O 32 L 3.98 5.02 5.08 @#@FSLOADPOST 2021:09:14:11:29:26 mri_em_register N 7 2.29 3.77 4.59 #-------------------------------------- #@# CA Normalize Tue Sep 14 11:31:41 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /N/u/xionyany/Carbonate/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/N/u/xionyany/Carbonate/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (59, 47, 30) --> (201, 173, 207) finding center of left hemi white matter using (106, 89, 119) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (89,74,97) --> (123, 104,140) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 106 +- 5.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 1.01335 0.11292 -0.04215 -12.89445; -0.11036 1.04837 0.07585 6.22052; 0.04831 -0.06698 0.99658 -8.07776; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 51, 36) --> (195, 163, 204) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 2 of 137 (1.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (64, 49, 37) --> (135, 158, 205) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 1 of 183 (0.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (125, 129, 60) --> (171, 177, 114) Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 0 of 13 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (80, 129, 59) --> (126, 170, 117) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (109, 123, 97) --> (144, 189, 127) Brain_Stem: limiting intensities to 92.0 --> 132.0 0 of 55 (0.0%) samples deleted using 400 total control points for intensity normalization... bias field = 0.907 +- 0.093 0 of 397 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 51, 36) --> (195, 163, 204) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 211 (0.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (64, 49, 37) --> (135, 158, 205) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 260 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (125, 129, 60) --> (171, 177, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 79 (16.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (80, 129, 59) --> (126, 170, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 64 (21.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (109, 123, 97) --> (144, 189, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 34 of 114 (29.8%) samples deleted using 728 total control points for intensity normalization... bias field = 0.993 +- 0.074 0 of 656 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 51, 36) --> (195, 163, 204) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 322 (6.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (64, 49, 37) --> (135, 158, 205) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 344 (1.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (125, 129, 60) --> (171, 177, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 55 of 124 (44.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (80, 129, 59) --> (126, 170, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 36 of 91 (39.6%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (109, 123, 97) --> (144, 189, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 118 of 167 (70.7%) samples deleted using 1048 total control points for intensity normalization... bias field = 1.003 +- 0.061 0 of 810 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 8 minutes and 27 seconds. @#@FSTIME 2021:09:14:11:33:44 mri_ca_normalize N 8 e 642.28 S 0.65 U 77.16 P 12% M 896080 F 0 R 269863 W 0 c 103 w 460 I 0 O 3928 L 2.09 2.83 4.00 @#@FSLOADPOST 2021:09:14:11:44:26 mri_ca_normalize N 8 2.08 2.28 3.11 #-------------------------------------- #@# CA Reg Tue Sep 14 11:45:52 EDT 2021 /N/project/canvas/CANVAS_Dataset/Segmeted_Data/3months/subjects/p207/mri mri_ca_register -bigventricles -smoothness 0.5 -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /N/u/xionyany/Carbonate/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.m3z handling expanded ventricles... l_smoothness = 0.50 using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/N/u/xionyany/Carbonate/freesurfer/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 registering ventricular system... using threshold 45.2 from atlas ventricle (20.3 +- 5.0) and caudate (70.1 +- 5.0) distributions for initial ventricular estimate caudate distribution could not be robustly estimated - using atlas caudate (70.1) and ventricle density (0.0 + 2*0.1) to set threshold 0.3 pass 0 complete, 0 added pass 1 complete, 0 added pass 2 complete, 0 added pass 3 complete, 0 added pass 4 complete, 0 added pass 5 complete, 0 added pass 6 complete, 0 added pass 0 complete, 0 added pass 1 complete, 0 added pass 2 complete, 0 added pass 3 complete, 0 added pass 4 complete, 0 added pass 5 complete, 0 added pass 6 complete, 0 added pass 7 complete, 0 added pass 8 complete, 0 added pass 1 of ventricular alignment /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 135 msec #FOTS# QuadFit found better minimum quadopt=(dt=29820.7,rms=0.409436) vs oldopt=(dt=21300.5,rms=0.411115) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 143 msec #FOTS# QuadFit found better minimum quadopt=(dt=17040.4,rms=0.408324) vs oldopt=(dt=21300.5,rms=0.408382) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 145 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 186 msec #FOTS# QuadFit found better minimum quadopt=(dt=4260.1,rms=0.408256) vs oldopt=(dt=5325.12,rms=0.408258) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 141 msec #FOTS# QuadFit found better minimum quadopt=(dt=17305.6,rms=0.404109) vs oldopt=(dt=21632,rms=0.404801) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 144 msec #FOTS# QuadFit found better minimum quadopt=(dt=7571.2,rms=0.40165) vs oldopt=(dt=5408,rms=0.401836) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=7571.2,rms=0.400713) vs oldopt=(dt=5408,rms=0.400873) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 137 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec #FOTS# QuadFit found better minimum quadopt=(dt=6489.6,rms=0.399214) vs oldopt=(dt=5408,rms=0.399217) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 138 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 138 msec #FOTS# QuadFit found better minimum quadopt=(dt=7571.2,rms=0.398355) vs oldopt=(dt=5408,rms=0.398398) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=17305.6,rms=0.397931) vs oldopt=(dt=21632,rms=0.397959) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 139 msec #FOTS# QuadFit found better minimum quadopt=(dt=7571.2,rms=0.397531) vs oldopt=(dt=5408,rms=0.397582) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 135 msec #FOTS# QuadFit found better minimum quadopt=(dt=17305.6,rms=0.397215) vs oldopt=(dt=21632,rms=0.397264) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec #FOTS# QuadFit found better minimum quadopt=(dt=7571.2,rms=0.396829) vs oldopt=(dt=5408,rms=0.396873) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 137 msec #FOTS# QuadFit found better minimum quadopt=(dt=7571.2,rms=0.396656) vs oldopt=(dt=5408,rms=0.396692) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 141 msec #FOTS# QuadFit found better minimum quadopt=(dt=69222.4,rms=0.3958) vs oldopt=(dt=86528,rms=0.395873) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 137 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 180 msec #FOTS# QuadFit found better minimum quadopt=(dt=121139,rms=0.393612) vs oldopt=(dt=86528,rms=0.393847) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=3244.8,rms=0.393339) vs oldopt=(dt=5408,rms=0.393424) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=811.2,rms=0.393336) vs oldopt=(dt=1352,rms=0.393336) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 137 msec #FOTS# QuadFit found better minimum quadopt=(dt=1951.49,rms=0.392729) vs oldopt=(dt=1393.92,rms=0.392882) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 135 msec #FOTS# QuadFit found better minimum quadopt=(dt=1115.14,rms=0.389532) vs oldopt=(dt=1393.92,rms=0.389658) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 138 msec #FOTS# QuadFit found better minimum quadopt=(dt=13381.6,rms=0.386381) vs oldopt=(dt=22302.7,rms=0.387301) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 184 msec #FOTS# QuadFit found better minimum quadopt=(dt=836.352,rms=0.385246) vs oldopt=(dt=1393.92,rms=0.385545) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 138 msec #FOTS# QuadFit found better minimum quadopt=(dt=1672.7,rms=0.385099) vs oldopt=(dt=1393.92,rms=0.385106) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 185 msec #FOTS# QuadFit found better minimum quadopt=(dt=4460.54,rms=0.384571) vs oldopt=(dt=5575.68,rms=0.384606) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 141 msec #FOTS# QuadFit found better minimum quadopt=(dt=836.352,rms=0.38428) vs oldopt=(dt=1393.92,rms=0.384365) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 135 msec #FOTS# QuadFit found better minimum quadopt=(dt=7805.95,rms=0.383843) vs oldopt=(dt=5575.68,rms=0.383873) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 142 msec #FOTS# QuadFit found better minimum quadopt=(dt=1115.14,rms=0.383226) vs oldopt=(dt=1393.92,rms=0.383228) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec #FOTS# QuadFit found better minimum quadopt=(dt=1951.49,rms=0.383137) vs oldopt=(dt=1393.92,rms=0.383149) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec #FOTS# QuadFit found better minimum quadopt=(dt=4460.54,rms=0.382817) vs oldopt=(dt=5575.68,rms=0.382854) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 193 msec #FOTS# QuadFit found better minimum quadopt=(dt=487.872,rms=0.382665) vs oldopt=(dt=348.48,rms=0.382697) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=836.352,rms=0.382598) vs oldopt=(dt=1393.92,rms=0.382616) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=26763.3,rms=0.381741) vs oldopt=(dt=22302.7,rms=0.381747) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 140 msec #FOTS# QuadFit found better minimum quadopt=(dt=1115.14,rms=0.380716) vs oldopt=(dt=1393.92,rms=0.380777) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 184 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 187 msec #FOTS# QuadFit found better minimum quadopt=(dt=4734.98,rms=0.372855) vs oldopt=(dt=5918.72,rms=0.373704) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 140 msec #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.369513) vs oldopt=(dt=369.92,rms=0.370035) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 139 msec #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.368509) vs oldopt=(dt=1479.68,rms=0.368656) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 134 msec #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.367663) vs oldopt=(dt=369.92,rms=0.367757) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 137 msec #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.367145) vs oldopt=(dt=1479.68,rms=0.367193) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 135 msec #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.366522) vs oldopt=(dt=369.92,rms=0.366598) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 135 msec #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.366048) vs oldopt=(dt=1479.68,rms=0.366053) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.365562) vs oldopt=(dt=369.92,rms=0.365625) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 258 msec #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.364576) vs oldopt=(dt=369.92,rms=0.364615) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 141 msec #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.364335) vs oldopt=(dt=369.92,rms=0.364385) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 187 msec #FOTS# QuadFit found better minimum quadopt=(dt=3551.23,rms=0.363352) vs oldopt=(dt=5918.72,rms=0.363516) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 141 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 322 msec #FOTS# QuadFit found better minimum quadopt=(dt=33144.8,rms=0.35786) vs oldopt=(dt=23674.9,rms=0.358196) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 136 msec #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.355964) vs oldopt=(dt=369.92,rms=0.355971) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 191 msec #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.35591) vs oldopt=(dt=369.92,rms=0.355917) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 143 msec #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.355898) vs oldopt=(dt=369.92,rms=0.355899) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 145 msec #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.354421) vs oldopt=(dt=414.72,rms=0.355075) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 145 msec #FOTS# QuadFit found better minimum quadopt=(dt=1327.1,rms=0.348147) vs oldopt=(dt=1658.88,rms=0.349047) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 140 msec #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.345554) vs oldopt=(dt=103.68,rms=0.346003) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 145 msec #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.345159) vs oldopt=(dt=103.68,rms=0.345231) /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 139 msec /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/gcamorph.cpp:16539 interval took 143 msec ERROR: mri_ca_register with non-zero status 1 Linux c10 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s p207 exited with ERRORS at Tue Sep 14 13:35:52 EDT 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting