2020��� 09��� 03��� ��������� 21:04:54 CST cd /usr/local/freesurfer/subjects/test2 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects /usr/local/freesurfer/bin/recon-all -s test2 -i 2018MPRAGE.nii -all subjid test2 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 649M 63M 9.5M 272M 183M Swap: 948M 455M 493M ######################################## 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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:54-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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: 2020/09/03-13:04:55-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/test2 mri_convert /usr/local/freesurfer/subjects/2018MPRAGE.nii /usr/local/freesurfer/subjects/test2/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/2018MPRAGE.nii /usr/local/freesurfer/subjects/test2/mri/orig/001.mgz reading from /usr/local/freesurfer/subjects/2018MPRAGE.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/test2/mri/orig/001.mgz... @#@FSTIME 2020:09:03:21:04:55 mri_convert N 2 e 1.58 S 0.01 U 1.46 P 92% M 19936 F 3 R 3632 W 0 c 87 w 76 I 26600 O 15280 L 0.35 0.25 0.10 @#@FSLOADPOST 2020:09:03:21:04:57 mri_convert N 2 0.35 0.25 0.10 #-------------------------------------------- #@# MotionCor 2020��� 09��� 03��� ��������� 21:04:57 CST Found 1 runs /usr/local/freesurfer/subjects/test2/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/test2/mri/orig/001.mgz /usr/local/freesurfer/subjects/test2/mri/rawavg.mgz /usr/local/freesurfer/subjects/test2 mri_convert /usr/local/freesurfer/subjects/test2/mri/rawavg.mgz /usr/local/freesurfer/subjects/test2/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/test2/mri/rawavg.mgz /usr/local/freesurfer/subjects/test2/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/test2/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 2333 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/test2/mri/orig.mgz... @#@FSTIME 2020:09:03:21:05:00 mri_convert N 3 e 3.42 S 0.01 U 2.65 P 78% M 30192 F 2 R 13505 W 0 c 444 w 3 I 320 O 704 L 0.33 0.25 0.10 @#@FSLOADPOST 2020:09:03:21:05:04 mri_convert N 3 0.38 0.26 0.10 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/test2/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/test2/mri/orig.mgz /usr/local/freesurfer/subjects/test2/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:09:03:21:05:04 mri_add_xform_to_header N 4 e 0.58 S 0.00 U 0.54 P 95% M 23356 F 14 R 4581 W 0 c 66 w 19 I 3424 O 704 L 0.38 0.26 0.10 @#@FSLOADPOST 2020:09:03:21:05:04 mri_add_xform_to_header N 4 0.38 0.26 0.10 #-------------------------------------------- #@# Talairach 2020��� 09��� 03��� ��������� 21:05:05 CST /usr/local/freesurfer/subjects/test2/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/test2/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��� 09��� 03��� ��������� 21:05:05 CST tmpdir is ./tmp.mri_nu_correct.mni.2887 cd /usr/local/freesurfer/subjects/test2/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2887/nu0.mgz Using shrink factor: 4 mri_convert ./tmp.mri_nu_correct.mni.2887/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2887/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2887/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��� 09��� 03��� ��������� 21:08:07 CST mri_nu_correct.mni done @#@FSTIME 2020:09:03:21:05:05 mri_nu_correct.mni N 12 e 182.74 S 0.27 U 173.56 P 95% M 481684 F 258 R 154823 W 0 c 10391 w 492 I 38824 O 1344 L 0.38 0.26 0.10 @#@FSLOADPOST 2020:09:03:21:08:07 mri_nu_correct.mni N 12 1.05 0.70 0.31 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at 2020��� 09��� 03��� ��������� 21:08:08 CST Ended at 2020��� 09��� 03��� ��������� 21:08:37 CST talairach_avi done @#@FSTIME 2020:09:03:21:08:07 talairach_avi N 4 e 29.72 S 0.76 U 22.07 P 76% M 255868 F 63 R 396392 W 0 c 1888 w 383 I 281392 O 295312 L 1.05 0.70 0.31 @#@FSLOADPOST 2020:09:03:21:08:37 talairach_avi N 4 0.90 0.69 0.32 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 9.27467 -10.90154 11.60181 700.38770; -72.15580 41.84029 5.33033 -1957.04590; 28.11513 -10.98805 -3.46955 444.07690; 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��� 09��� 03��� ��������� 21:08:39 CST /usr/local/freesurfer/subjects/test2/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 2020:09:03:21:08:39 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 25% M 5804 F 13 R 204 W 0 c 3 w 20 I 3032 O 0 L 0.83 0.68 0.32 @#@FSLOADPOST 2020:09:03:21:08:40 talairach_afd N 4 0.83 0.68 0.32 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��� 09��� 03��� ��������� 21:08:40 CST /usr/local/freesurfer/subjects/test2/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/test2/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��� 09��� 03��� ��������� 21:08:40 CST tmpdir is ./tmp.mri_nu_correct.mni.3144 cd /usr/local/freesurfer/subjects/test2/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.3144/nu0.mgz Using shrink factor: 4 mri_convert ./tmp.mri_nu_correct.mni.3144/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.3144/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.3144/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��� 09��� 03��� ��������� 21:11:36 CST mri_nu_correct.mni done @#@FSTIME 2020:09:03:21:08:40 mri_nu_correct.mni N 12 e 176.55 S 0.18 U 174.16 P 98% M 500604 F 97 R 148236 W 0 c 8176 w 321 I 24176 O 1344 L 0.83 0.68 0.32 @#@FSLOADPOST 2020:09:03:21:11:36 mri_nu_correct.mni N 12 0.99 0.83 0.45 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��� 09��� 03��� ��������� 21:11:36 CST Ended at 2020��� 09��� 03��� ��������� 21:12:09 CST talairach_avi done @#@FSTIME 2020:09:03:21:11:36 talairach_avi N 6 e 33.02 S 0.77 U 23.12 P 72% M 255756 F 92 R 396532 W 0 c 3138 w 450 I 289432 O 295312 L 0.99 0.83 0.45 @#@FSLOADPOST 2020:09:03:21:12:09 talairach_avi N 6 1.01 0.85 0.47 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 3.19257 -0.75188 -0.07829 43.08014; -10.32960 20.25408 -4.03988 -1171.48047; -5.89988 12.59599 2.23394 -670.65063; 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��� 09��� 03��� ��������� 21:12:12 CST /usr/local/freesurfer/subjects/test2/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 2020:09:03:21:12:12 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 26% M 5808 F 13 R 208 W 0 c 2 w 23 I 3592 O 0 L 1.01 0.85 0.47 @#@FSLOADPOST 2020:09:03:21:12:12 talairach_afd N 4 1.01 0.85 0.47 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��� 09��� 03��� ��������� 21:12:12 CST /usr/local/freesurfer/subjects/test2/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/test2/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��� 09��� 03��� ��������� 21:12:12 CST tmpdir is ./tmp.mri_nu_correct.mni.3409 cd /usr/local/freesurfer/subjects/test2/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.3409/nu0.mgz Using shrink factor: 4 mri_convert ./tmp.mri_nu_correct.mni.3409/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.3409/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.3409/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��� 09��� 03��� ��������� 21:15:12 CST mri_nu_correct.mni done @#@FSTIME 2020:09:03:21:12:12 mri_nu_correct.mni N 12 e 180.05 S 0.17 U 177.42 P 98% M 501012 F 93 R 148336 W 0 c 6106 w 307 I 23032 O 1344 L 1.01 0.85 0.47 @#@FSLOADPOST 2020:09:03:21:15:12 mri_nu_correct.mni N 12 1.00 0.92 0.57 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/test2/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��� 09��� 03��� ��������� 21:15:12 CST tmpdir is transforms/tmp.talairach.3486 /usr/local/freesurfer/subjects/test2/mri mri_convert orig_nu.mgz transforms/tmp.talairach.3486/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.3486/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.3486/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3486/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 = -0.000 102.981 Source min/max voxel= -0.000 102.981 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 -2.9754 0.0000 1.0000 0.0000 -63.4105 0.0000 0.0000 1.0000 21.0742 Transform center = 3.303 45.819 -11.620 Transform rotations = 0.000 0.000 0.000 Transform trans = -2.975 -63.410 21.074 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 = 52.050 11.176 29.828 Lattice count = 27 21 27 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 135.618 Source min/max voxel= -0.000 135.618 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 = 2.7656 -0.8944 -0.4696 11.0560 0.9480 2.7707 0.3058 -138.8882 0.3490 -0.4384 2.8905 55.9952 Transform center = 3.303 45.819 -11.620 Transform rotations = -0.151 -0.119 0.330 Transform trans = -18.637 -58.175 15.092 Transform scale = 2.944 2.944 2.944 Transform shear = -0.000 0.000 0.000 Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 46.050 1.176 19.828 Lattice count = 24 17 27 Source volume size: 87 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.046 14.330 Source min/max voxel= 0.046 14.330 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 = 2.8184 -0.9416 0.0041 19.3746 0.9300 2.7856 0.4531 -137.5410 -0.1474 -0.4285 2.9368 59.8073 Transform center = 3.303 45.819 -11.620 Transform rotations = -0.145 0.050 0.319 Transform trans = -17.810 -57.918 17.184 Transform scale = 2.972 2.972 2.972 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 = 0.046 14.330 Source min/max voxel= 0.046 14.330 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 = 2.7170 1.2348 -0.2580 -40.6347 -1.2292 2.7292 0.1178 -116.5605 0.2836 -0.0010 2.9821 52.8306 Transform center = 3.303 45.819 -11.620 Transform rotations = -0.000 -0.095 -0.425 Transform trans = 24.614 -42.757 30.689 Transform scale = 2.996 2.996 2.996 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 = 0.046 14.330 Source min/max voxel= 0.046 14.330 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 = 2.7483 1.1630 -0.2610 -37.4798 -1.1577 2.7606 0.1110 -118.3140 0.2836 -0.0010 2.9821 52.8306 Transform center = 3.303 45.819 -11.620 Transform rotations = -0.000 -0.095 -0.399 Transform trans = 24.614 -42.757 30.689 Transform scale = 2.996 2.996 2.996 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 = 0.046 14.330 Source min/max voxel= 0.046 14.330 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 = 2.7483 1.1606 -0.2711 -37.4911 -1.1577 2.7615 0.0869 -118.6336 0.2836 0.0250 2.9820 51.6370 Transform center = 3.303 45.819 -11.620 Transform rotations = 0.008 -0.095 -0.399 Transform trans = 24.614 -42.757 30.689 Transform scale = 2.996 2.996 2.996 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��� 09��� 03��� ��������� 21:15:23 CST talairach done @#@FSTIME 2020:09:03:21:15:12 talairach N 4 e 11.53 S 0.20 U 9.27 P 82% M 40592 F 71 R 72351 W 0 c 2106 w 514 I 30528 O 100488 L 1.00 0.92 0.57 @#@FSLOADPOST 2020:09:03:21:15:23 talairach N 4 1.16 0.96 0.59 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 2.74826 1.15823 -0.28124 -37.49821; -1.15765 2.76215 0.06283 -118.94360; 0.28362 0.05104 2.98171 50.94087; 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��� 09��� 03��� ��������� 21:15:26 CST /usr/local/freesurfer/subjects/test2/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 2020:09:03:21:15:26 talairach_afd N 4 e 0.01 S 0.00 U 0.00 P 30% M 6640 F 16 R 252 W 0 c 3 w 25 I 4288 O 0 L 1.07 0.94 0.58 @#@FSLOADPOST 2020:09:03:21:15:26 talairach_afd N 4 1.07 0.94 0.58 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 test2 exited with ERRORS at 2020��� 09��� 03��� ��������� 21:15:26 CST To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting