2020��� 08��� 27��� ��������� 22:53:04 CST cd /usr/local/freesurfer/subjects/mprage setenv SUBJECTS_DIR /usr/local/freesurfer/subjects /usr/local/freesurfer/bin/recon-all -s mprage -i /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii -all subjid mprage setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Linux zhao-VirtualBox 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 16384 kbytes maxproc 3697 maxlocks unlimited maxsignal 3697 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 985M 407M 240M 440K 336M 441M Swap: 948M 555M 392M ######################################## program versions used 7.1.1 (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551) 7.1.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:04-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 mri_motion_correct.fsl 7.1.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2020/08/27-14:53:05-GMT BuildTime: Jul 23 2020 13:43:33 BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: zhao Machine: zhao-VirtualBox Platform: Linux PlatformVersion: 4.15.0-112-generic CompilerName: GCC CompilerVersion: 4.9.2 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/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 /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/subjects/mprage mri_convert /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii /usr/local/freesurfer/subjects/mprage/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii /usr/local/freesurfer/subjects/mprage/mri/orig/001.mgz reading from /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii... TR=2590.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/mprage/mri/orig/001.mgz... @#@FSTIME 2020:08:27:22:53:05 mri_convert N 2 e 1.60 S 0.00 U 1.48 P 92% M 20208 F 3 R 3649 W 0 c 57 w 95 I 26376 O 15560 L 0.18 0.07 0.08 @#@FSLOADPOST 2020:08:27:22:53:07 mri_convert N 2 0.18 0.07 0.08 #-------------------------------------------- #@# MotionCor 2020��� 08��� 27��� ��������� 22:53:07 CST Found 1 runs /usr/local/freesurfer/subjects/mprage/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 /usr/local/freesurfer/subjects/mprage/mri/orig/001.mgz /usr/local/freesurfer/subjects/mprage/mri/rawavg.mgz /usr/local/freesurfer/subjects/mprage mri_convert /usr/local/freesurfer/subjects/mprage/mri/rawavg.mgz /usr/local/freesurfer/subjects/mprage/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/mprage/mri/rawavg.mgz /usr/local/freesurfer/subjects/mprage/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/mprage/mri/rawavg.mgz... TR=2590.00, 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) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 2369 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/mprage/mri/orig.mgz... @#@FSTIME 2020:08:27:22:53:10 mri_convert N 3 e 2.76 S 0.01 U 2.63 P 95% M 30400 F 0 R 13527 W 0 c 70 w 1 I 0 O 696 L 0.16 0.07 0.08 @#@FSLOADPOST 2020:08:27:22:53:13 mri_convert N 3 0.16 0.07 0.08 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/mprage/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/mprage/mri/orig.mgz /usr/local/freesurfer/subjects/mprage/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:08:27:22:53:13 mri_add_xform_to_header N 4 e 0.61 S 0.00 U 0.55 P 90% M 23416 F 14 R 4581 W 0 c 33 w 17 I 3416 O 696 L 0.16 0.07 0.08 @#@FSLOADPOST 2020:08:27:22:53:14 mri_add_xform_to_header N 4 0.16 0.07 0.08 #-------------------------------------------- #@# Talairach 2020��� 08��� 27��� ��������� 22:53:14 CST /usr/local/freesurfer/subjects/mprage/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /usr/local/freesurfer/subjects/mprage/mri /usr/local/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 zhao-VirtualBox 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 08��� 27��� ��������� 22:53:14 CST tmpdir is ./tmp.mri_nu_correct.mni.2519 cd /usr/local/freesurfer/subjects/mprage/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2519/nu0.mgz Using shrink factor: 4 mri_convert ./tmp.mri_nu_correct.mni.2519/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2519/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2519/nu0.mgz... TR=2590.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... 2020��� 08��� 27��� ��������� 22:56:11 CST mri_nu_correct.mni done @#@FSTIME 2020:08:27:22:53:14 mri_nu_correct.mni N 12 e 177.32 S 0.20 U 175.58 P 99% M 490544 F 94 R 141589 W 0 c 2003 w 309 I 26216 O 1328 L 0.16 0.07 0.08 @#@FSLOADPOST 2020:08:27:22:56:11 mri_nu_correct.mni N 12 0.97 0.51 0.26 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at 2020��� 08��� 27��� ��������� 22:56:12 CST Ended at 2020��� 08��� 27��� ��������� 22:56:47 CST talairach_avi done @#@FSTIME 2020:08:27:22:56:12 talairach_avi N 4 e 35.89 S 0.76 U 28.26 P 80% M 255924 F 74 R 396314 W 0 c 1049 w 384 I 282152 O 295344 L 0.97 0.51 0.26 @#@FSLOADPOST 2020:08:27:22:56:47 talairach_avi N 4 0.78 0.52 0.27 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/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: /usr/local/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 67.05859 0.30791 -66.56141 -3084.16577; 174.61514 -6.04417 -129.68279 -6280.19434; -58.84369 8.20201 51.07359 2000.49658; 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 2020��� 08��� 27��� ��������� 22:56:50 CST /usr/local/freesurfer/subjects/mprage/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2020:08:27:22:56:50 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 20% M 5744 F 13 R 205 W 0 c 2 w 20 I 3056 O 0 L 0.78 0.52 0.27 @#@FSLOADPOST 2020:08:27:22:56:50 talairach_afd N 4 0.78 0.52 0.27 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Retrying Talairach align using 3T-based atlas... #-------------------------------------------- #@# Talairach 2020��� 08��� 27��� ��������� 22:56:50 CST /usr/local/freesurfer/subjects/mprage/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /usr/local/freesurfer/subjects/mprage/mri /usr/local/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 zhao-VirtualBox 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 08��� 27��� ��������� 22:56:50 CST tmpdir is ./tmp.mri_nu_correct.mni.2765 cd /usr/local/freesurfer/subjects/mprage/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2765/nu0.mgz Using shrink factor: 4 mri_convert ./tmp.mri_nu_correct.mni.2765/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2765/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2765/nu0.mgz... TR=2590.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... 2020��� 08��� 27��� ��������� 22:59:50 CST mri_nu_correct.mni done @#@FSTIME 2020:08:27:22:56:50 mri_nu_correct.mni N 12 e 179.89 S 0.18 U 176.00 P 97% M 489064 F 108 R 149483 W 0 c 2839 w 334 I 26312 O 1328 L 0.78 0.52 0.27 @#@FSLOADPOST 2020:08:27:22:59:50 mri_nu_correct.mni N 12 1.00 0.75 0.41 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at 2020��� 08��� 27��� ��������� 22:59:50 CST Ended at 2020��� 08��� 27��� ��������� 23:00:22 CST talairach_avi done @#@FSTIME 2020:08:27:22:59:50 talairach_avi N 6 e 32.02 S 0.87 U 24.38 P 78% M 255780 F 80 R 396556 W 0 c 863 w 389 I 283880 O 295312 L 1.00 0.75 0.41 @#@FSLOADPOST 2020:08:27:23:00:22 talairach_avi N 6 0.93 0.76 0.43 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/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: /usr/local/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 2.76140 1.13811 -6.23009 -90.34515; 4.20981 3.44650 2.47010 -131.70905; 3.76946 -2.63401 0.52157 215.39117; 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 2020��� 08��� 27��� ��������� 23:00:24 CST /usr/local/freesurfer/subjects/mprage/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2020:08:27:23:00:24 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 25% M 5624 F 14 R 200 W 0 c 3 w 21 I 3064 O 0 L 0.93 0.76 0.43 @#@FSLOADPOST 2020:08:27:23:00:24 talairach_afd N 4 0.93 0.76 0.43 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach 2020��� 08��� 27��� ��������� 23:00:24 CST /usr/local/freesurfer/subjects/mprage/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /usr/local/freesurfer/subjects/mprage/mri /usr/local/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 zhao-VirtualBox 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 08��� 27��� ��������� 23:00:24 CST tmpdir is ./tmp.mri_nu_correct.mni.3017 cd /usr/local/freesurfer/subjects/mprage/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.3017/nu0.mgz Using shrink factor: 4 mri_convert ./tmp.mri_nu_correct.mni.3017/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.3017/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.3017/nu0.mgz... TR=2590.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... 2020��� 08��� 27��� ��������� 23:03:24 CST mri_nu_correct.mni done @#@FSTIME 2020:08:27:23:00:24 mri_nu_correct.mni N 12 e 179.81 S 0.17 U 177.72 P 98% M 491008 F 72 R 149355 W 0 c 2845 w 292 I 19104 O 1328 L 0.93 0.76 0.43 @#@FSLOADPOST 2020:08:27:23:03:24 mri_nu_correct.mni N 12 1.04 0.89 0.54 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/mprage/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach 7.1.1 Linux zhao-VirtualBox 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 08��� 27��� ��������� 23:03:24 CST tmpdir is transforms/tmp.talairach.3093 /usr/local/freesurfer/subjects/mprage/mri mri_convert orig_nu.mgz transforms/tmp.talairach.3093/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.3093/src.mnc reading from orig_nu.mgz... TR=2590.00, 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) writing to transforms/tmp.talairach.3093/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3093/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 77 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 101.962 Source min/max voxel= -0.000 101.962 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 6.3949 0.0000 1.0000 0.0000 -69.3814 0.0000 0.0000 1.0000 26.9213 Transform center = -6.067 51.790 -17.467 Transform rotations = 0.000 0.000 0.000 Transform trans = 6.395 -69.381 26.921 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 51.652 10.976 50.226 Lattice count = 28 33 21 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 134.191 Source min/max voxel= -0.000 134.191 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070 AFTER init_params() Transform matrix = 2.3774 0.2915 1.7366 50.5401 -1.7275 -0.1798 2.3951 24.1532 0.3416 -2.9386 0.0257 172.2728 Transform center = -6.067 51.790 -17.467 Transform rotations = -1.562 -0.116 -0.628 Transform trans = 26.947 -68.305 35.025 Transform scale = 2.959 2.959 2.959 Transform shear = -0.000 0.000 0.000 Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 45.652 20.976 44.226 Lattice count = 25 29 17 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.018 14.320 Source min/max voxel= 0.018 14.320 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 2.3402 0.2276 1.8112 56.5284 -1.8056 -0.1453 2.3511 25.0046 0.2690 -2.9557 0.0239 173.0819 Transform center = -6.067 51.790 -17.467 Transform rotations = -1.563 -0.091 -0.657 Transform trans = 28.550 -64.421 35.425 Transform scale = 2.968 2.968 2.968 Transform shear = 0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.018 14.320 Source min/max voxel= 0.018 14.320 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 2.1320 -0.1377 2.1029 64.3555 -2.0538 0.5346 2.1172 -11.8075 -0.4723 -2.9465 0.2858 170.6592 Transform center = -6.067 51.790 -17.467 Transform rotations = -1.474 0.158 -0.767 Transform trans = 13.624 -60.434 33.398 Transform scale = 2.998 2.998 2.998 Transform shear = -0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.018 14.320 Source min/max voxel= 0.018 14.320 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 2.1326 -0.1197 2.1027 64.7010 -2.0523 0.5551 2.1130 -12.9073 -0.4741 -2.9449 0.3133 171.0755 Transform center = -6.067 51.790 -17.467 Transform rotations = -1.465 0.159 -0.766 Transform trans = 14.905 -60.403 33.429 Transform scale = 2.997 2.997 2.999 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.018 14.320 Source min/max voxel= 0.018 14.320 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 2.1348 -0.0832 2.1058 63.1419 -2.0519 0.5930 2.1035 -15.0163 -0.4749 -2.9391 0.3653 172.1920 Transform center = -6.067 51.790 -17.467 Transform rotations = -1.447 0.159 -0.766 Transform trans = 15.169 -60.389 33.943 Transform scale = 3.000 2.998 3.000 Transform shear = -0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 lta_convert --src orig_nu.mgz --trg /usr/local/freesurfer/mni/bin/../share/mni_autoreg/average_305.mnc --inxfm transforms/talairach.auto.xfm --outlta transforms/talairach.auto.xfm.lta --subject fsaverage 2020��� 08��� 27��� ��������� 23:03:34 CST talairach done @#@FSTIME 2020:08:27:23:03:24 talairach N 4 e 9.68 S 0.25 U 9.08 P 96% M 40628 F 74 R 72257 W 0 c 1531 w 515 I 30712 O 100488 L 1.04 0.89 0.54 @#@FSLOADPOST 2020:08:27:23:03:34 talairach N 4 1.03 0.90 0.55 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/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: /usr/local/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 2.13489 -0.04646 2.10666 61.51364; -2.05167 0.63008 2.09306 -16.61280; -0.47524 -2.93248 0.41694 172.94336; 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 2020��� 08��� 27��� ��������� 23:03:36 CST /usr/local/freesurfer/subjects/mprage/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2020:08:27:23:03:36 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 25% M 6508 F 16 R 250 W 0 c 1 w 25 I 4288 O 0 L 0.95 0.88 0.55 @#@FSLOADPOST 2020:08:27:23:03:36 talairach_afd N 4 0.95 0.88 0.55 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach ERROR: Talairach failed! Linux zhao-VirtualBox 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mprage exited with ERRORS at 2020��� 08��� 27��� ��������� 23:03:36 CST To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting