2020��� 09��� 22��� ��������� 10:08:30 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-i origfinal.mgz -s monkey2 -autorecon1 -no-wsgcaatlas -wsthresh 35
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        718M        469M        9.0M        804M        1.1G
Swap:          2.0G        1.0G        1.0G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-02:08:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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/monkey2

 mri_convert /usr/local/freesurfer/subjects/monkey_t1/origfinal.mgz /usr/local/freesurfer/subjects/monkey2/mri/orig/001.mgz 

mri_convert /usr/local/freesurfer/subjects/monkey_t1/origfinal.mgz /usr/local/freesurfer/subjects/monkey2/mri/orig/001.mgz 
reading from /usr/local/freesurfer/subjects/monkey_t1/origfinal.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 /usr/local/freesurfer/subjects/monkey2/mri/orig/001.mgz...
@#@FSTIME  2020:09:22:10:08:31 mri_convert N 2 e 3.69 S 0.03 U 3.52 P 96% M 73100 F 0 R 16961 W 0 c 450 w 3 I 25976 O 33632 L 0.16 0.61 0.81
@#@FSLOADPOST 2020:09:22:10:08:34 mri_convert N 2 0.16 0.61 0.81
#--------------------------------------------
#@# MotionCor 2020��� 09��� 22��� ��������� 10:08:35 CST
Found 1 runs
/usr/local/freesurfer/subjects/monkey2/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/monkey2/mri/orig/001.mgz /usr/local/freesurfer/subjects/monkey2/mri/rawavg.mgz 

/usr/local/freesurfer/subjects/monkey2

 mri_convert /usr/local/freesurfer/subjects/monkey2/mri/rawavg.mgz /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz --conform 

mri_convert /usr/local/freesurfer/subjects/monkey2/mri/rawavg.mgz /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz --conform 
reading from /usr/local/freesurfer/subjects/monkey2/mri/rawavg.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)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 2368.99 1000, flo=0, fhi=0.999, dest_type=0
writing to /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz...
@#@FSTIME  2020:09:22:10:08:38 mri_convert N 3 e 4.98 S 0.05 U 4.80 P 97% M 89944 F 0 R 21134 W 0 c 440 w 1 I 0 O 8672 L 0.23 0.62 0.81
@#@FSLOADPOST 2020:09:22:10:08:43 mri_convert N 3 0.29 0.63 0.82

 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/monkey2/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz 

INFO: extension is mgz
@#@FSTIME  2020:09:22:10:08:44 mri_add_xform_to_header N 4 e 0.84 S 0.01 U 0.79 P 96% M 23220 F 0 R 4584 W 0 c 91 w 1 I 0 O 8672 L 0.29 0.63 0.82
@#@FSLOADPOST 2020:09:22:10:08:44 mri_add_xform_to_header N 4 0.29 0.63 0.82
#--------------------------------------------
#@# Talairach 2020��� 09��� 22��� ��������� 10:08:44 CST
/usr/local/freesurfer/subjects/monkey2/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/monkey2/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 7.1.0
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
2020��� 09��� 22��� ��������� 10:08:45 CST
tmpdir is ./tmp.mri_nu_correct.mni.6685
cd /usr/local/freesurfer/subjects/monkey2/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.6685/nu0.mgz
Using shrink factor: 4
mri_convert ./tmp.mri_nu_correct.mni.6685/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.6685/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
reading from ./tmp.mri_nu_correct.mni.6685/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��� 22��� ��������� 10:13:55 CST
mri_nu_correct.mni done
@#@FSTIME  2020:09:22:10:08:45 mri_nu_correct.mni N 12 e 310.71 S 0.19 U 303.60 P 97% M 487896 F 0 R 149649 W 0 c 25878 w 121 I 0 O 15936 L 0.29 0.63 0.82
@#@FSLOADPOST 2020:09:22:10:13:55 mri_nu_correct.mni N 12 1.10 0.95 0.91

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...
Started at 2020��� 09��� 22��� ��������� 10:13:55 CST
Ended   at 2020��� 09��� 22��� ��������� 10:14:26 CST
talairach_avi done
@#@FSTIME  2020:09:22:10:13:55 talairach_avi N 4 e 31.21 S 0.75 U 23.84 P 78% M 255832 F 11 R 396410 W 0 c 2309 w 229 I 131400 O 295288 L 1.10 0.95 0.91
@#@FSLOADPOST 2020:09:22:10:14:26 talairach_avi N 4 1.05 0.95 0.91

 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
7.1.0

--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
 1.04906  -0.49303   0.02434  -22.10571;
 0.13898  -0.42994   1.28140  -7.19537;
-0.29593  -1.63871   0.04157   229.89775;
 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��� 22��� ��������� 10:14:29 CST
/usr/local/freesurfer/subjects/monkey2/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  2020:09:22:10:14:29 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 40% M 5796 F 2 R 206 W 0 c 1 w 3 I 296 O 0 L 1.05 0.95 0.91
@#@FSLOADPOST 2020:09:22:10:14:29 talairach_afd N 4 1.05 0.95 0.91

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��� 22��� ��������� 10:14:29 CST
/usr/local/freesurfer/subjects/monkey2/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/monkey2/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 7.1.0
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
2020��� 09��� 22��� ��������� 10:14:29 CST
tmpdir is ./tmp.mri_nu_correct.mni.6932
cd /usr/local/freesurfer/subjects/monkey2/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.6932/nu0.mgz
Using shrink factor: 4
mri_convert ./tmp.mri_nu_correct.mni.6932/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.6932/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
reading from ./tmp.mri_nu_correct.mni.6932/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��� 22��� ��������� 10:19:39 CST
mri_nu_correct.mni done
@#@FSTIME  2020:09:22:10:14:29 mri_nu_correct.mni N 12 e 310.63 S 0.18 U 304.56 P 98% M 503408 F 3 R 149776 W 0 c 26227 w 125 I 544 O 15936 L 1.05 0.95 0.91
@#@FSLOADPOST 2020:09:22:10:19:39 mri_nu_correct.mni N 12 1.03 1.01 0.95

 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��� 22��� ��������� 10:19:39 CST
Ended   at 2020��� 09��� 22��� ��������� 10:20:12 CST
talairach_avi done
@#@FSTIME  2020:09:22:10:19:39 talairach_avi N 6 e 32.32 S 0.72 U 24.75 P 78% M 255924 F 7 R 396516 W 0 c 2370 w 186 I 42312 O 295296 L 1.03 1.01 0.95
@#@FSLOADPOST 2020:09:22:10:20:12 talairach_avi N 6 0.95 0.99 0.95

 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
7.1.0

--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
 1.05501  -0.25920   0.00062  -52.42123;
 0.01327   0.71176   0.87619  -139.55736;
-0.13279  -1.27675   0.48227   158.48111;
 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��� 22��� ��������� 10:20:14 CST
/usr/local/freesurfer/subjects/monkey2/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0021, pval=0.0000 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME  2020:09:22:10:20:14 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 75% M 5596 F 0 R 207 W 0 c 3 w 1 I 0 O 0 L 0.95 0.99 0.95
@#@FSLOADPOST 2020:09:22:10:20:14 talairach_afd N 4 0.95 0.99 0.95

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��� 22��� ��������� 10:20:14 CST
/usr/local/freesurfer/subjects/monkey2/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/monkey2/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 7.1.0
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
2020��� 09��� 22��� ��������� 10:20:14 CST
tmpdir is ./tmp.mri_nu_correct.mni.7190
cd /usr/local/freesurfer/subjects/monkey2/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.7190/nu0.mgz
Using shrink factor: 4
mri_convert ./tmp.mri_nu_correct.mni.7190/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.7190/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
reading from ./tmp.mri_nu_correct.mni.7190/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��� 22��� ��������� 10:25:25 CST
mri_nu_correct.mni done
@#@FSTIME  2020:09:22:10:20:14 mri_nu_correct.mni N 12 e 311.25 S 0.18 U 305.24 P 98% M 503144 F 0 R 149749 W 0 c 26107 w 121 I 0 O 15936 L 0.95 0.99 0.95
@#@FSLOADPOST 2020:09:22:10:25:25 mri_nu_correct.mni N 12 1.00 1.00 0.99

 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

/usr/local/freesurfer/subjects/monkey2/mri
/usr/local/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach 7.1.0
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
2020��� 09��� 22��� ��������� 10:25:25 CST
tmpdir is transforms/tmp.talairach.7269
/usr/local/freesurfer/subjects/monkey2/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.7269/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.7269/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.7269/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7269/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 107 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =   -0.000   97.772
Source min/max voxel=   -0.000   97.772

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  -80.1217 
                         0.0000    1.0000    0.0000 -141.6418 
                         0.0000    0.0000    1.0000  -26.0519 

Transform center   =   80.449  124.051   35.506
Transform rotations  =    0.000    0.000    0.000
Transform trans    =  -80.122 -141.642  -26.052
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      =  164.652  106.976  126.226
Lattice count      =       48       53       23

Source volume size:  87  by 116  by 117 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =   -0.000  116.728
Source min/max voxel=   -0.000  116.728

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    =    1.2738   -0.2300   -0.1070  -72.2618 
                         0.2269    1.2780   -0.0458 -163.1710 
                         0.1134    0.0262    1.2936  -72.2551 

Transform center   =   80.449  124.051   35.506
Transform rotations  =    0.020   -0.087    0.176
Transform trans    =  -82.571 -112.054  -49.455
Transform scale    =    1.299    1.299    1.299
Transform shear    =    0.000   -0.000   -0.000

Source volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  174.652   96.976  136.226
Lattice count      =       49       55       23

Source volume size:  87  by 116  by 117 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.009   13.577
Source min/max voxel=    0.009   13.577

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    =    1.2925   -0.1174   -0.1878  -85.1127 
                         0.1144    1.3060   -0.0287 -159.2243 
                         0.1896    0.0119    1.2975  -73.3887 

Transform center   =   80.449  124.051   35.506
Transform rotations  =    0.009   -0.145    0.088
Transform trans    =  -82.808 -113.079  -46.100
Transform scale    =    1.311    1.311    1.311
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 117 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.009   13.577
Source min/max voxel=    0.009   13.577

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    =    1.2292   -0.0926   -0.0159  -89.8320 
                         0.0928    1.2292    0.0154 -135.8131 
                         0.0147   -0.0165    1.2325  -68.0737 

Transform center   =   80.449  124.051   35.506
Transform rotations  =   -0.013   -0.012    0.075
Transform trans    =  -83.442  -99.377  -60.687
Transform scale    =    1.233    1.233    1.233
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 117 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.009   13.577
Source min/max voxel=    0.009   13.577

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    =    1.2265   -0.0708   -0.0227  -92.9896 
                         0.0711    1.2176    0.0431 -133.1713 
                         0.0208   -0.0460    1.2656  -64.0678 

Transform center   =   80.449  124.051   35.506
Transform rotations  =   -0.036   -0.016    0.058
Transform trans    =  -84.358  -98.933  -58.671
Transform scale    =    1.229    1.220    1.267
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 117 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.009   13.577
Source min/max voxel=    0.009   13.577

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    =    1.2239   -0.1018   -0.0034  -90.8018 
                         0.0945    1.1359    0.0358 -124.4798 
                         0.0002   -0.0396    1.2545  -60.6735 

Transform center   =   80.449  124.051   35.506
Transform rotations  =   -0.032   -0.000    0.083
Transform trans    =  -85.533  -98.749  -56.531
Transform scale    =    1.228    1.140    1.255
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��� 22��� ��������� 10:25:36 CST
talairach done
@#@FSTIME  2020:09:22:10:25:25 talairach N 4 e 11.07 S 0.16 U 10.49 P 96% M 40564 F 21 R 72408 W 0 c 2386 w 327 I 5416 O 100960 L 1.00 1.00 0.99
@#@FSLOADPOST 2020:09:22:10:25:36 talairach N 4 1.00 1.00 0.99

 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
7.1.0

--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
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 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��� 22��� ��������� 10:25:39 CST
/usr/local/freesurfer/subjects/monkey2/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7074, pval=0.4932 >= threshold=0.0050)
@#@FSTIME  2020:09:22:10:25:39 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 33% M 6448 F 7 R 247 W 0 c 2 w 9 I 1840 O 0 L 1.00 1.00 0.99
@#@FSLOADPOST 2020:09:22:10:25:39 talairach_afd N 4 1.00 1.00 0.99
#--------------------------------------------
#@# Nu Intensity Correction 2020��� 09��� 22��� ��������� 10:25:39 CST

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 

/usr/bin/bc
/usr/local/freesurfer/subjects/monkey2/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
nIters 2
mri_nu_correct.mni 7.1.0
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
2020��� 09��� 22��� ��������� 10:25:39 CST
tmpdir is ./tmp.mri_nu_correct.mni.7453
cd /usr/local/freesurfer/subjects/monkey2/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.7453/nu0.mgz
Using shrink factor: 4
mri_binarize --i ./tmp.mri_nu_correct.mni.7453/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.7453/ones.mgz

7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.7453/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.7453/ones.mgz 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      ./tmp.mri_nu_correct.mni.7453/nu0.mgz
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.7453/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777215 voxels in final mask
Count: 16777215 16777215.000000 16777216 99.999994
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7453/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7453/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7453/input.mean.dat

7.1.0
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7453/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7453/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7453/input.mean.dat 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao
whitesurfname  white
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.7453/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.7453/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7453/ones.mgz --i ./tmp.mri_nu_correct.mni.7453/nu0.mgz --sum ./tmp.mri_nu_correct.mni.7453/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7453/output.mean.dat

7.1.0
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7453/ones.mgz --i ./tmp.mri_nu_correct.mni.7453/nu0.mgz --sum ./tmp.mri_nu_correct.mni.7453/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7453/output.mean.dat 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao
whitesurfname  white
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.7453/ones.mgz
Loading ./tmp.mri_nu_correct.mni.7453/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.7453/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.7453/nu0.mgz ./tmp.mri_nu_correct.mni.7453/nu0.mgz mul 1.37210724178406494806
Saving result to './tmp.mri_nu_correct.mni.7453/nu0.mgz' (type = MGH )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.7453/nu0.mgz nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.7453/nu0.mgz nu.mgz --like orig.mgz 
reading from ./tmp.mri_nu_correct.mni.7453/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 nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping ( 5, 103) to ( 3, 110)
 
 
2020��� 09��� 22��� ��������� 10:31:19 CST
mri_nu_correct.mni done
@#@FSTIME  2020:09:22:10:25:39 mri_nu_correct.mni N 9 e 340.38 S 0.63 U 333.76 P 98% M 614824 F 33 R 515462 W 0 c 28586 w 232 I 6680 O 40184 L 1.00 1.00 0.99
@#@FSLOADPOST 2020:09:22:10:31:19 mri_nu_correct.mni N 9 1.09 1.06 1.01

 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/monkey2/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
@#@FSTIME  2020:09:22:10:31:19 mri_add_xform_to_header N 4 e 0.93 S 0.01 U 0.89 P 96% M 23452 F 17 R 4578 W 0 c 80 w 18 I 3288 O 7712 L 1.09 1.06 1.01
@#@FSLOADPOST 2020:09:22:10:31:20 mri_add_xform_to_header N 4 1.09 1.06 1.01
#--------------------------------------------
#@# Intensity Normalization 2020��� 09��� 22��� ��������� 10:31:20 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz 

using max gradient = 1.000
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from nu.mgz...
normalizing image...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 12
Starting OpenSpline(): npoints = 12
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 89
gm peak at 62 (62), valley at 28 (28)
csf peak at 20, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 51 (51), valley at 39 (39)
csf peak at 26, setting threshold to 42
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 5 minutes and 0 seconds.
@#@FSTIME  2020:09:22:10:31:20 mri_normalize N 7 e 301.85 S 0.31 U 296.06 P 98% M 584088 F 7 R 263303 W 0 c 25131 w 8 I 1512 O 7856 L 1.09 1.06 1.01
@#@FSLOADPOST 2020:09:22:10:36:22 mri_normalize N 7 1.05 1.06 1.01
#--------------------------------------------
#@# Skull Stripping 2020��� 09��� 22��� ��������� 10:36:22 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_watershed -T1 -h 35 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz

*************************WATERSHED**************************
Sorting...
      T1-weighted MRI image
      Count how many 110 voxels are present :  108113

      Find the largest 110-component...
             heap usage = 168604 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 83408 voxels
      first estimation of the COG coord: x=124 y=109 z=106 r=79
      first estimation of the main basin volume: 2123621 voxels
      global maximum in x=118, y=87, z=84, Imax=255
      CSF=20, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 35 percent
done.
Analyze...

      main basin size= 1806422 voxels, voxel volume =1.000 
                     = 1806422 mmm3 = 1806.422 cm3
done.
PostAnalyze...
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
      ambiguous basin, non merged: 5 ambiguous voxels; size: 13149 voxels
done.

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=99,y=108, z=95, r=10663 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 45414
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    21,      21,        21,   62
  after  analyzing :    21,      23,        25,   32
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...65 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 72.824, std = 10.184

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 38.57, sigma = 103.89
      after  rotation: sse = 38.57, sigma = 103.89
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is 48.77, its var is 75.28   
      before Erosion-Dilatation 44.93% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...44 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1816049 voxels, voxel volume = 1.000 mm3
           = 1816049 mmm3 = 1816.049 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    14.357890
mri_watershed stimesec    0.134001
mri_watershed ru_maxrss   345668
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   116512
mri_watershed ru_majflt   8
mri_watershed ru_nswap    0
mri_watershed ru_inblock  8496
mri_watershed ru_oublock  3040
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    37
mri_watershed ru_nivcsw   1347
mri_watershed done
@#@FSTIME  2020:09:22:10:36:22 mri_watershed N 5 e 14.82 S 0.14 U 14.35 P 97% M 345668 F 9 R 116811 W 0 c 1354 w 44 I 8576 O 3040 L 1.05 1.06 1.01
@#@FSLOADPOST 2020:09:22:10:36:37 mri_watershed N 5 1.04 1.05 1.00

 cp brainmask.auto.mgz brainmask.mgz 


Started at 2020��� 09��� 22��� ��������� 10:08:30 CST 
Ended   at 2020��� 09��� 22��� ��������� 10:36:38 CST
#@#%# recon-all-run-time-hours 0.469
recon-all -s monkey2 finished without error at 2020��� 09��� 22��� ��������� 10:36:38 CST



#New# invocation of recon-all 



2020��� 09��� 22��� ��������� 14:30:13 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        1.2G         81M         24M        725M        631M
Swap:          2.0G        189M        1.8G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-06:30:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 22��� ��������� 14:30:14 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 43 (43)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 43 (43)
csf peak at 31, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 7 seconds.
@#@FSTIME  2020:09:22:14:30:14 mri_normalize N 5 e 308.40 S 0.31 U 302.34 P 98% M 583716 F 6 R 263310 W 0 c 11735 w 18 I 4648 O 3032 L 0.08 0.04 0.01
@#@FSLOADPOST 2020:09:22:14:35:22 mri_normalize N 5 1.03 0.69 0.31
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 22��� ��������� 14:35:22 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:22:14:35:22 mri_mask N 5 e 2.62 S 0.03 U 2.54 P 98% M 74288 F 21 R 17263 W 0 c 126 w 31 I 7152 O 2960 L 1.03 0.69 0.31
@#@FSLOADPOST 2020:09:22:14:35:25 mri_mask N 5 1.02 0.69 0.31
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 22��� ��������� 14:35:25 CST

 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:22:14:35:25 AntsDenoiseImageFs N 4 e 64.38 S 0.09 U 63.80 P 99% M 350532 F 19 R 86503 W 0 c 2695 w 23 I 4624 O 2992 L 1.02 0.69 0.31
@#@FSLOADPOST 2020:09:22:14:36:29 AntsDenoiseImageFs N 4 1.01 0.76 0.36

 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz 

wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.4 +- 6.0 [79.0 --> 125.0]
CCS GM (72.0) : 69.7 +- 11.0 [30.0 --> 95.0]
 white_mean 104.448
 white_sigma 5.99953
 gray_mean 69.7268
 gray_sigma 11.0082
setting bottom of white matter range wm_low to 80.7
setting top of gray matter range gray_hi to 91.7
 wm_low 80.735
 wm_hi  125
 gray_low 30
 gray_hi  91.7432
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.735
 wm_hi  125
 gray_low 30
 gray_hi  91.7432
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 91.7432, wm_low = 80.735
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.7432, wmlow=80.735
    107392 voxels processed (0.64%)
     48975 voxels white (0.29%)
     58417 voxels non-white (0.35%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.735, gray_hi=91.7432, wsize=13
    178297 voxels tested (1.06%)
     45010 voxels changed (0.27%)
     35214 multi-scale searches  (0.21%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.735
 wm_hi 125
 slack 5.99953
 pct_thresh 0.33
 intensity_thresh 131
 nvox_thresh 8.58
      753 voxels tested (0.00%)
      637 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.735, hithr=91.7432
  smoothing input volume with sigma = 0.250
    77061 voxels tested (0.46%)
    12560 voxels changed (0.07%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 4917 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3261 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3025 filled
MRIfindBrightNonWM(): 1069 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.3 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:22:14:36:29 mri_segment N 5 e 198.20 S 0.33 U 193.71 P 97% M 147004 F 16 R 291155 W 0 c 7797 w 19 I 3896 O 608 L 1.01 0.76 0.36
@#@FSLOADPOST 2020:09:22:14:39:48 mri_segment N 5 1.00 0.88 0.49

 mri_pretess wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   6
pass   1 (yz+):   7 found -   7 modified     |    TOTAL:  13
pass   2 (yz+):   0 found -   7 modified     |    TOTAL:  13
pass   1 (yz-):   8 found -   8 modified     |    TOTAL:  21
pass   2 (yz-):   0 found -   8 modified     |    TOTAL:  21
pass   1 (xz+):   7 found -   7 modified     |    TOTAL:  28
pass   2 (xz+):   0 found -   7 modified     |    TOTAL:  28
pass   1 (xz-):   8 found -   8 modified     |    TOTAL:  36
pass   2 (xz-):   0 found -   8 modified     |    TOTAL:  36
Iteration Number : 1
pass   1 (+++):  71 found -  71 modified     |    TOTAL:  71
pass   2 (+++):   0 found -  71 modified     |    TOTAL:  71
pass   1 (+++):  46 found -  46 modified     |    TOTAL: 117
pass   2 (+++):   0 found -  46 modified     |    TOTAL: 117
pass   1 (+++):  79 found -  79 modified     |    TOTAL: 196
pass   2 (+++):   0 found -  79 modified     |    TOTAL: 196
pass   1 (+++):  54 found -  54 modified     |    TOTAL: 250
pass   2 (+++):   0 found -  54 modified     |    TOTAL: 250
Iteration Number : 1
pass   1 (++): 195 found - 195 modified     |    TOTAL: 195
pass   2 (++):   0 found - 195 modified     |    TOTAL: 195
pass   1 (+-): 210 found - 210 modified     |    TOTAL: 405
pass   2 (+-):   0 found - 210 modified     |    TOTAL: 405
pass   1 (--): 207 found - 207 modified     |    TOTAL: 612
pass   2 (--):   0 found - 207 modified     |    TOTAL: 612
pass   1 (-+): 195 found - 195 modified     |    TOTAL: 807
pass   2 (-+):   0 found - 195 modified     |    TOTAL: 807
Iteration Number : 2
pass   1 (xy+):  23 found -  23 modified     |    TOTAL:  23
pass   2 (xy+):   0 found -  23 modified     |    TOTAL:  23
pass   1 (xy-):  13 found -  13 modified     |    TOTAL:  36
pass   2 (xy-):   0 found -  13 modified     |    TOTAL:  36
pass   1 (yz+):  22 found -  22 modified     |    TOTAL:  58
pass   2 (yz+):   0 found -  22 modified     |    TOTAL:  58
pass   1 (yz-):  15 found -  15 modified     |    TOTAL:  73
pass   2 (yz-):   0 found -  15 modified     |    TOTAL:  73
pass   1 (xz+):  21 found -  21 modified     |    TOTAL:  94
pass   2 (xz+):   0 found -  21 modified     |    TOTAL:  94
pass   1 (xz-):  14 found -  14 modified     |    TOTAL: 108
pass   2 (xz-):   0 found -  14 modified     |    TOTAL: 108
Iteration Number : 2
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  10
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  10
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  12
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  12
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  14
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  14
Iteration Number : 2
pass   1 (++):   7 found -   7 modified     |    TOTAL:   7
pass   2 (++):   0 found -   7 modified     |    TOTAL:   7
pass   1 (+-):  12 found -  12 modified     |    TOTAL:  19
pass   2 (+-):   0 found -  12 modified     |    TOTAL:  19
pass   1 (--):   8 found -   8 modified     |    TOTAL:  27
pass   2 (--):   0 found -   8 modified     |    TOTAL:  27
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  31
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  31
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   7
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   8
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  10
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  10
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   5
pass   1 (--):   2 found -   2 modified     |    TOTAL:   7
pass   2 (--):   0 found -   2 modified     |    TOTAL:   7
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   8
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   8
Iteration Number : 4
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1268 (out of 319372: 0.397029)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:14:39:48 mri_pretess N 4 e 6.42 S 0.02 U 4.62 P 72% M 56784 F 16 R 12972 W 0 c 992 w 18 I 3472 O 608 L 1.00 0.88 0.49
@#@FSLOADPOST 2020:09:22:14:39:54 mri_pretess N 4 1.00 0.89 0.50
#--------------------------------------------
#@# Fill 2020��� 09��� 22��� ��������� 14:39:54 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 771 (min = 350, max = 1400), aspect = 4.64 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 4363 (min = 350, max = 790), aspect = 0.63 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 304609 voxels filled...
filling volume: pass 2 of 3...total of 16405437 voxels filled...
filling volume: pass 3 of 3...total of 305222 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 304609 voxels filled...
filling volume: pass 2 of 3...total of 16405437 voxels filled...
filling volume: pass 3 of 3...total of 305222 voxels filled...done.
filling degenerate left hemisphere surface locations...
491 voxels filled
19 voxels filled
2 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
491 voxels filled
19 voxels filled
2 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16404881 voxels filled...
filling volume: pass 3 of 3...total of 305778 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16404881 voxels filled...
filling volume: pass 3 of 3...total of 305778 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  305385 ambiguous voxels remaining
9:  188156 ambiguous voxels remaining
8:  181451 ambiguous voxels remaining
7:  74216 ambiguous voxels remaining
6:  5442 ambiguous voxels remaining
5:  2666 ambiguous voxels remaining
4:  1469 ambiguous voxels remaining
3:  589 ambiguous voxels remaining
2:  141 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:22:14:39:54 mri_fill N 12 e 37.83 S 0.12 U 36.87 P 97% M 111472 F 17 R 77489 W 0 c 1808 w 20 I 4072 O 216 L 1.00 0.89 0.50
@#@FSLOADPOST 2020:09:22:14:40:32 mri_fill N 12 1.00 0.90 0.52
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 22��� ��������� 14:40:32 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 11 (out of 180173: 0.006105)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:14:40:32 mri_pretess N 4 e 2.93 S 0.00 U 2.24 P 76% M 40388 F 0 R 8843 W 0 c 455 w 1 I 0 O 208 L 1.00 0.90 0.52
@#@FSLOADPOST 2020:09:22:14:40:35 mri_pretess N 4 1.00 0.90 0.52

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 50 vertices, 58 faces
slice 60: 1389 vertices, 1554 faces
slice 70: 13283 vertices, 13828 faces
slice 80: 30873 vertices, 31588 faces
slice 90: 49749 vertices, 50601 faces
slice 100: 70672 vertices, 71643 faces
slice 110: 92862 vertices, 93706 faces
slice 120: 111644 vertices, 112497 faces
slice 130: 124899 vertices, 125521 faces
slice 140: 132602 vertices, 132995 faces
slice 150: 134710 vertices, 134962 faces
slice 160: 134710 vertices, 134962 faces
slice 170: 134710 vertices, 134962 faces
slice 180: 134710 vertices, 134962 faces
slice 190: 134710 vertices, 134962 faces
slice 200: 134710 vertices, 134962 faces
slice 210: 134710 vertices, 134962 faces
slice 220: 134710 vertices, 134962 faces
slice 230: 134710 vertices, 134962 faces
slice 240: 134710 vertices, 134962 faces
slice 250: 134710 vertices, 134962 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:14:40:35 mri_tessellate N 3 e 2.40 S 0.02 U 2.31 P 97% M 37908 F 16 R 8485 W 0 c 103 w 19 I 3736 O 6328 L 1.00 0.90 0.52
@#@FSLOADPOST 2020:09:22:14:40:37 mri_tessellate N 3 1.00 0.90 0.52

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   134710 voxel in cpt #1: X=-252 [v=134710,e=404886,f=269924] located at (1.499777, -30.625233, 8.862890)
For the whole surface: X=-252 [v=134710,e=404886,f=269924]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:14:40:37 mris_extract_main_component N 2 e 1.05 S 0.08 U 0.90 P 94% M 270220 F 17 R 74297 W 0 c 86 w 26 I 4592 O 9488 L 1.00 0.90 0.52
@#@FSLOADPOST 2020:09:22:14:40:39 mris_extract_main_component N 2 1.00 0.90 0.52
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 22��� ��������� 14:40:39 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 3 (out of 125620: 0.002388)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:14:40:39 mri_pretess N 4 e 2.64 S 0.02 U 2.01 P 76% M 40520 F 0 R 8848 W 0 c 403 w 1 I 0 O 208 L 1.00 0.90 0.52
@#@FSLOADPOST 2020:09:22:14:40:41 mri_pretess N 4 1.00 0.90 0.52

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 768 vertices, 853 faces
slice 80: 6356 vertices, 6751 faces
slice 90: 19730 vertices, 20321 faces
slice 100: 34550 vertices, 35294 faces
slice 110: 55427 vertices, 56236 faces
slice 120: 72781 vertices, 73522 faces
slice 130: 84986 vertices, 85496 faces
slice 140: 92520 vertices, 92860 faces
slice 150: 94336 vertices, 94520 faces
slice 160: 94336 vertices, 94520 faces
slice 170: 94336 vertices, 94520 faces
slice 180: 94336 vertices, 94520 faces
slice 190: 94336 vertices, 94520 faces
slice 200: 94336 vertices, 94520 faces
slice 210: 94336 vertices, 94520 faces
slice 220: 94336 vertices, 94520 faces
slice 230: 94336 vertices, 94520 faces
slice 240: 94336 vertices, 94520 faces
slice 250: 94336 vertices, 94520 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:14:40:41 mri_tessellate N 3 e 2.33 S 0.01 U 2.24 P 97% M 34264 F 0 R 7602 W 0 c 118 w 1 I 0 O 4432 L 1.00 0.90 0.52
@#@FSLOADPOST 2020:09:22:14:40:44 mri_tessellate N 3 1.00 0.90 0.53

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   94320 voxel in cpt #1: X=-186 [v=94320,e=283518,f=189012] located at (55.354568, -22.945345, 11.461610)
   16 voxel in cpt #2: X=2 [v=16,e=42,f=28] located at (48.625000, -38.375000, 29.000000)
For the whole surface: X=-184 [v=94336,e=283560,f=189040]
2 components have been found
keeping component #1 with 94320 vertices
done

@#@FSTIME  2020:09:22:14:40:44 mris_extract_main_component N 2 e 0.70 S 0.06 U 0.60 P 94% M 191024 F 0 R 52131 W 0 c 77 w 1 I 0 O 6648 L 1.00 0.90 0.53
@#@FSLOADPOST 2020:09:22:14:40:44 mris_extract_main_component N 2 1.00 0.90 0.53
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 22��� ��������� 14:40:44 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:14:40:44 mris_smooth N 5 e 3.94 S 0.07 U 3.80 P 98% M 218164 F 17 R 61063 W 0 c 166 w 21 I 4040 O 9488 L 1.00 0.90 0.53
@#@FSLOADPOST 2020:09:22:14:40:48 mris_smooth N 5 1.00 0.91 0.53
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 22��� ��������� 14:40:48 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:14:40:48 mris_smooth N 5 e 2.77 S 0.04 U 2.66 P 97% M 155692 F 0 R 43003 W 0 c 130 w 1 I 0 O 6648 L 1.00 0.91 0.53
@#@FSLOADPOST 2020:09:22:14:40:51 mris_smooth N 5 1.00 0.91 0.53
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 22��� ��������� 14:40:51 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 46.6 mm, total surface area = 74859 mm^2

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.130 (target=0.015)   
step 010: RMS=0.114 (target=0.015)   
step 015: RMS=0.107 (target=0.015)   
step 020: RMS=0.104 (target=0.015)   
step 025: RMS=0.100 (target=0.015)   
step 030: RMS=0.099 (target=0.015)   
step 035: RMS=0.098 (target=0.015)   
step 040: RMS=0.097 (target=0.015)   
step 045: RMS=0.097 (target=0.015)   
step 050: RMS=0.097 (target=0.015)   
step 055: RMS=0.097 (target=0.015)   
step 060: RMS=0.097 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    19.977425
mris_inflate stimesec    0.092006
mris_inflate ru_maxrss   281640
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   76934
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  9488
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   738
@#@FSTIME  2020:09:22:14:40:51 mris_inflate N 3 e 20.28 S 0.10 U 19.97 P 98% M 281816 F 19 R 76936 W 0 c 744 w 22 I 4552 O 9488 L 1.00 0.91 0.53
@#@FSLOADPOST 2020:09:22:14:41:12 mris_inflate N 3 1.00 0.91 0.54
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 22��� ��������� 14:41:12 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 41.2 mm, total surface area = 52340 mm^2

step 000: RMS=0.158 (target=0.015)   
step 005: RMS=0.132 (target=0.015)   
step 010: RMS=0.115 (target=0.015)   
step 015: RMS=0.107 (target=0.015)   
step 020: RMS=0.102 (target=0.015)   
step 025: RMS=0.101 (target=0.015)   
step 030: RMS=0.100 (target=0.015)   
step 035: RMS=0.098 (target=0.015)   
step 040: RMS=0.097 (target=0.015)   
step 045: RMS=0.096 (target=0.015)   
step 050: RMS=0.096 (target=0.015)   
step 055: RMS=0.096 (target=0.015)   
step 060: RMS=0.096 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    14.230387
mris_inflate stimesec    0.083637
mris_inflate ru_maxrss   199420
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   53969
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  6648
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   560
@#@FSTIME  2020:09:22:14:41:12 mris_inflate N 3 e 14.46 S 0.09 U 14.23 P 99% M 199572 F 0 R 53971 W 0 c 564 w 1 I 0 O 6648 L 1.00 0.91 0.54
@#@FSLOADPOST 2020:09:22:14:41:26 mris_inflate N 3 1.00 0.92 0.55

Started at 2020��� 09��� 22��� ��������� 14:30:13 CST 
Ended   at 2020��� 09��� 22��� ��������� 14:41:26 CST
#@#%# recon-all-run-time-hours 0.187
recon-all -s monkey2 finished without error at 2020��� 09��� 22��� ��������� 14:41:26 CST



#New# invocation of recon-all 



2020��� 09��� 22��� ��������� 15:40:36 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        1.2G        301M         24M        510M        645M
Swap:          2.0G        187M        1.8G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-07:40:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 22��� ��������� 15:40:37 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 282 control points...
control point 111 @ (153, 19, 95), MRI=0, skipping!!!!!
error: No such file or directory
error: !!!!! 4739893 control points rejected for being out of bounds !!!!!!

only using 281 control points from file, mean 77.1, scaling by 1.43...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
control point 111 @ (153, 19, 95), MRI=0, skipping!!!!!
error: No such file or directory
error: !!!!! 4739893 control points rejected for being out of bounds !!!!!!

building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
control point 111 @ (153, 19, 95), MRI=0, skipping!!!!!
error: No such file or directory
error: !!!!! 4739893 control points rejected for being out of bounds !!!!!!

white matter peak found at 110
white matter peak found at 111
gm peak at 65 (65), valley at 24 (24)
csf peak at 10, setting threshold to 46
control point 111 @ (153, 19, 95), MRI=0, skipping!!!!!
error: No such file or directory
error: !!!!! 4739893 control points rejected for being out of bounds !!!!!!

building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
control point 111 @ (153, 19, 95), MRI=0, skipping!!!!!
error: No such file or directory
error: !!!!! 4739893 control points rejected for being out of bounds !!!!!!

white matter peak found at 110
white matter peak found at 110
gm peak at 64 (64), valley at 22 (22)
csf peak at 10, setting threshold to 46
control point 111 @ (153, 19, 95), MRI=0, skipping!!!!!
error: No such file or directory
error: !!!!! 4739893 control points rejected for being out of bounds !!!!!!

building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 57 seconds.
@#@FSTIME  2020:09:22:15:40:37 mri_normalize N 7 e 358.84 S 0.36 U 355.44 P 99% M 583036 F 2 R 312314 W 0 c 11274 w 7 I 368 O 3040 L 0.15 0.12 0.09
@#@FSLOADPOST 2020:09:22:15:46:36 mri_normalize N 7 1.00 0.74 0.40
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 22��� ��������� 15:46:36 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:22:15:46:36 mri_mask N 5 e 2.63 S 0.01 U 2.59 P 99% M 74188 F 17 R 17261 W 0 c 95 w 29 I 2800 O 2968 L 1.00 0.74 0.40
@#@FSLOADPOST 2020:09:22:15:46:38 mri_mask N 5 1.00 0.75 0.40
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 22��� ��������� 15:46:38 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -1.000000 16777216 -0.000006
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -1.000000 16777216 -0.000006
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: -1 deletes, -1 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:22:15:46:46 AntsDenoiseImageFs N 4 e 61.91 S 0.10 U 61.47 P 99% M 350676 F 19 R 86505 W 0 c 1796 w 22 I 4392 O 3016 L 1.00 0.75 0.40
@#@FSLOADPOST 2020:09:22:15:47:48 AntsDenoiseImageFs N 4 1.00 0.80 0.45

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 106.0 +- 7.0 [79.0 --> 125.0]
CCS GM (71.0) : 69.2 +- 10.4 [30.0 --> 95.0]
 white_mean 105.959
 white_sigma 6.96133
 gray_mean 69.2075
 gray_sigma 10.4063
setting bottom of white matter range wm_low to 79.6
setting top of gray matter range gray_hi to 90.0
 wm_low 79.6138
 wm_hi  125
 gray_low 30
 gray_hi  90.0201
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.6138
 wm_hi  125
 gray_low 30
 gray_hi  90.0201
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.0201, wm_low = 79.6138
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.0201, wmlow=79.6138
    128387 voxels processed (0.77%)
     57051 voxels white (0.34%)
     71336 voxels non-white (0.43%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.6138, gray_hi=90.0201, wsize=13
    213774 voxels tested (1.27%)
     49645 voxels changed (0.30%)
     58138 multi-scale searches  (0.35%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.6138
 wm_hi 125
 slack 6.96133
 pct_thresh 0.33
 intensity_thresh 131.961
 nvox_thresh 8.58
     2598 voxels tested (0.02%)
     2112 voxels changed (0.01%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.6138, hithr=90.0201
  smoothing input volume with sigma = 0.250
    73147 voxels tested (0.44%)
    14177 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 6859 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
4144 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 2943 filled
MRIfindBrightNonWM(): 3078 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.7 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:22:15:47:48 mri_segment N 6 e 222.41 S 0.15 U 221.18 P 99% M 147340 F 10 R 142367 W 0 c 6862 w 12 I 1736 O 728 L 1.00 0.80 0.45
@#@FSLOADPOST 2020:09:22:15:51:30 mri_segment N 6 1.00 0.91 0.57

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):  18 found -  18 modified     |    TOTAL:  23
pass   2 (xy-):   0 found -  18 modified     |    TOTAL:  23
pass   1 (yz+):  12 found -  12 modified     |    TOTAL:  35
pass   2 (yz+):   0 found -  12 modified     |    TOTAL:  35
pass   1 (yz-):  10 found -  10 modified     |    TOTAL:  45
pass   2 (yz-):   0 found -  10 modified     |    TOTAL:  45
pass   1 (xz+):  15 found -  15 modified     |    TOTAL:  60
pass   2 (xz+):   0 found -  15 modified     |    TOTAL:  60
pass   1 (xz-):  20 found -  20 modified     |    TOTAL:  80
pass   2 (xz-):   0 found -  20 modified     |    TOTAL:  80
Iteration Number : 1
pass   1 (+++):  95 found -  95 modified     |    TOTAL:  95
pass   2 (+++):   0 found -  95 modified     |    TOTAL:  95
pass   1 (+++):  70 found -  70 modified     |    TOTAL: 165
pass   2 (+++):   0 found -  70 modified     |    TOTAL: 165
pass   1 (+++):  82 found -  82 modified     |    TOTAL: 247
pass   2 (+++):   0 found -  82 modified     |    TOTAL: 247
pass   1 (+++):  43 found -  43 modified     |    TOTAL: 290
pass   2 (+++):   0 found -  43 modified     |    TOTAL: 290
Iteration Number : 1
pass   1 (++): 208 found - 208 modified     |    TOTAL: 208
pass   2 (++):   0 found - 208 modified     |    TOTAL: 208
pass   1 (+-): 272 found - 272 modified     |    TOTAL: 480
pass   2 (+-):   1 found - 273 modified     |    TOTAL: 481
pass   3 (+-):   0 found - 273 modified     |    TOTAL: 481
pass   1 (--): 184 found - 184 modified     |    TOTAL: 665
pass   2 (--):   2 found - 186 modified     |    TOTAL: 667
pass   3 (--):   0 found - 186 modified     |    TOTAL: 667
pass   1 (-+): 260 found - 260 modified     |    TOTAL: 927
pass   2 (-+):   0 found - 260 modified     |    TOTAL: 927
Iteration Number : 2
pass   1 (xy+):  28 found -  28 modified     |    TOTAL:  28
pass   2 (xy+):   0 found -  28 modified     |    TOTAL:  28
pass   1 (xy-):  21 found -  21 modified     |    TOTAL:  49
pass   2 (xy-):   0 found -  21 modified     |    TOTAL:  49
pass   1 (yz+):  43 found -  43 modified     |    TOTAL:  92
pass   2 (yz+):   0 found -  43 modified     |    TOTAL:  92
pass   1 (yz-):  28 found -  28 modified     |    TOTAL: 120
pass   2 (yz-):   0 found -  28 modified     |    TOTAL: 120
pass   1 (xz+):  20 found -  20 modified     |    TOTAL: 140
pass   2 (xz+):   0 found -  20 modified     |    TOTAL: 140
pass   1 (xz-):  16 found -  16 modified     |    TOTAL: 156
pass   2 (xz-):   0 found -  16 modified     |    TOTAL: 156
Iteration Number : 2
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   7 found -   7 modified     |    TOTAL:  13
pass   2 (+++):   0 found -   7 modified     |    TOTAL:  13
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  17
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  17
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  27
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  27
Iteration Number : 2
pass   1 (++):  17 found -  17 modified     |    TOTAL:  17
pass   2 (++):   0 found -  17 modified     |    TOTAL:  17
pass   1 (+-):  13 found -  13 modified     |    TOTAL:  30
pass   2 (+-):   0 found -  13 modified     |    TOTAL:  30
pass   1 (--):  14 found -  14 modified     |    TOTAL:  44
pass   2 (--):   0 found -  14 modified     |    TOTAL:  44
pass   1 (-+):  12 found -  12 modified     |    TOTAL:  56
pass   2 (-+):   0 found -  12 modified     |    TOTAL:  56
Iteration Number : 3
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   5 found -   5 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   5 modified     |    TOTAL:   9
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  11
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  11
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  13
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  13
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:  13
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   3 found -   3 modified     |    TOTAL:   5
pass   2 (--):   0 found -   3 modified     |    TOTAL:   5
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   6
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1558 (out of 378137: 0.412020)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 0 WM ON voxels
  kept 0 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:22:15:51:30 mri_pretess N 5 e 5.53 S 0.01 U 5.41 P 98% M 57128 F 16 R 17104 W 0 c 474 w 18 I 3472 O 728 L 1.00 0.91 0.57
@#@FSLOADPOST 2020:09:22:15:51:36 mri_pretess N 5 1.00 0.91 0.57
#--------------------------------------------
#@# Fill 2020��� 09��� 22��� ��������� 15:51:36 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 799 (min = 350, max = 1400), aspect = 4.08 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 5081 (min = 350, max = 790), aspect = 0.62 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 361683 voxels filled...
filling volume: pass 2 of 3...total of 16348147 voxels filled...
filling volume: pass 3 of 3...total of 362512 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 361683 voxels filled...
filling volume: pass 2 of 3...total of 16348147 voxels filled...
filling volume: pass 3 of 3...total of 362512 voxels filled...done.
filling degenerate left hemisphere surface locations...
571 voxels filled
19 voxels filled
1 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
571 voxels filled
19 voxels filled
1 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16347517 voxels filled...
filling volume: pass 3 of 3...total of 363142 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16347517 voxels filled...
filling volume: pass 3 of 3...total of 363142 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  362749 ambiguous voxels remaining
9:  219864 ambiguous voxels remaining
8:  201479 ambiguous voxels remaining
7:  11199 ambiguous voxels remaining
6:  5105 ambiguous voxels remaining
5:  2950 ambiguous voxels remaining
4:  1527 ambiguous voxels remaining
3:  692 ambiguous voxels remaining
2:  296 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
badRH = 0/82806, badLH=97552/280337
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
error: Please check filled volume.  Cerebellum may be included.

@#@FSTIME  2020:09:22:15:51:36 mri_fill N 12 e 38.25 S 0.11 U 37.88 P 99% M 111632 F 10 R 77486 W 0 c 1484 w 13 I 2240 O 240 L 1.00 0.91 0.57
@#@FSLOADPOST 2020:09:22:15:52:14 mri_fill N 12 1.00 0.93 0.59
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 22��� ��������� 15:52:14 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 6 (out of 280343: 0.002140)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:15:52:14 mri_pretess N 4 e 1.80 S 0.01 U 1.75 P 98% M 40312 F 0 R 8842 W 0 c 154 w 1 I 0 O 232 L 1.00 0.93 0.59
@#@FSLOADPOST 2020:09:22:15:52:16 mri_pretess N 4 1.00 0.93 0.59

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 74 vertices, 84 faces
slice 60: 3517 vertices, 3854 faces
slice 70: 22980 vertices, 23751 faces
slice 80: 49527 vertices, 50789 faces
slice 90: 83640 vertices, 85252 faces
slice 100: 117987 vertices, 119512 faces
slice 110: 152130 vertices, 153567 faces
slice 120: 181380 vertices, 182822 faces
slice 130: 203260 vertices, 204347 faces
slice 140: 215941 vertices, 216669 faces
slice 150: 220128 vertices, 220608 faces
slice 160: 220128 vertices, 220608 faces
slice 170: 220128 vertices, 220608 faces
slice 180: 220128 vertices, 220608 faces
slice 190: 220128 vertices, 220608 faces
slice 200: 220128 vertices, 220608 faces
slice 210: 220128 vertices, 220608 faces
slice 220: 220128 vertices, 220608 faces
slice 230: 220128 vertices, 220608 faces
slice 240: 220128 vertices, 220608 faces
slice 250: 220128 vertices, 220608 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:15:52:16 mri_tessellate N 3 e 2.41 S 0.01 U 2.37 P 98% M 45220 F 16 R 10326 W 0 c 88 w 18 I 3728 O 10336 L 1.00 0.93 0.59
@#@FSLOADPOST 2020:09:22:15:52:18 mri_tessellate N 3 1.00 0.93 0.60

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   220128 voxel in cpt #1: X=-480 [v=220128,e=661824,f=441216] located at (20.217833, -30.815670, 5.476437)
For the whole surface: X=-480 [v=220128,e=661824,f=441216]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:15:52:18 mris_extract_main_component N 2 e 1.67 S 0.15 U 1.49 P 98% M 437216 F 16 R 121265 W 0 c 94 w 22 I 4184 O 15504 L 1.00 0.93 0.60
@#@FSLOADPOST 2020:09:22:15:52:20 mris_extract_main_component N 2 1.00 0.93 0.60
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 22��� ��������� 15:52:20 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1 (out of 82807: 0.001208)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:15:52:20 mri_pretess N 4 e 1.66 S 0.00 U 1.63 P 98% M 40428 F 0 R 8846 W 0 c 141 w 1 I 0 O 232 L 1.00 0.93 0.60
@#@FSLOADPOST 2020:09:22:15:52:22 mri_pretess N 4 1.00 0.93 0.60

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 132 vertices, 166 faces
slice 70: 3115 vertices, 3222 faces
slice 80: 7994 vertices, 8200 faces
slice 90: 15332 vertices, 15689 faces
slice 100: 26380 vertices, 26831 faces
slice 110: 37047 vertices, 37448 faces
slice 120: 45544 vertices, 45867 faces
slice 130: 50605 vertices, 50820 faces
slice 140: 53596 vertices, 53746 faces
slice 150: 54186 vertices, 54288 faces
slice 160: 54186 vertices, 54288 faces
slice 170: 54186 vertices, 54288 faces
slice 180: 54186 vertices, 54288 faces
slice 190: 54186 vertices, 54288 faces
slice 200: 54186 vertices, 54288 faces
slice 210: 54186 vertices, 54288 faces
slice 220: 54186 vertices, 54288 faces
slice 230: 54186 vertices, 54288 faces
slice 240: 54186 vertices, 54288 faces
slice 250: 54186 vertices, 54288 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:15:52:22 mri_tessellate N 3 e 2.20 S 0.01 U 2.18 P 99% M 30428 F 0 R 6630 W 0 c 82 w 1 I 0 O 2552 L 1.00 0.93 0.60
@#@FSLOADPOST 2020:09:22:15:52:24 mri_tessellate N 3 1.08 0.95 0.60

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   54186 voxel in cpt #1: X=-102 [v=54186,e=162864,f=108576] located at (55.730667, -28.228195, 54.995258)
For the whole surface: X=-102 [v=54186,e=162864,f=108576]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:15:52:24 mris_extract_main_component N 2 e 0.37 S 0.05 U 0.31 P 98% M 112456 F 0 R 30079 W 0 c 49 w 2 I 0 O 3816 L 1.08 0.95 0.60
@#@FSLOADPOST 2020:09:22:15:52:24 mris_extract_main_component N 2 1.08 0.95 0.60
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 22��� ��������� 15:52:24 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:15:52:24 mris_smooth N 5 e 6.53 S 0.13 U 6.35 P 99% M 351744 F 17 R 99610 W 0 c 230 w 21 I 4048 O 15504 L 1.08 0.95 0.60
@#@FSLOADPOST 2020:09:22:15:52:31 mris_smooth N 5 1.07 0.95 0.61
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 22��� ��������� 15:52:31 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:15:52:31 mris_smooth N 5 e 1.57 S 0.03 U 1.53 P 99% M 92484 F 0 R 24818 W 0 c 74 w 1 I 0 O 3824 L 1.07 0.95 0.61
@#@FSLOADPOST 2020:09:22:15:52:33 mris_smooth N 5 1.07 0.95 0.61
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 22��� ��������� 15:52:33 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 54.8 mm, total surface area = 122675 mm^2

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.130 (target=0.015)   
step 010: RMS=0.114 (target=0.015)   
step 015: RMS=0.107 (target=0.015)   
step 020: RMS=0.102 (target=0.015)   
step 025: RMS=0.098 (target=0.015)   
step 030: RMS=0.097 (target=0.015)   
step 035: RMS=0.096 (target=0.015)   
step 040: RMS=0.095 (target=0.015)   
step 045: RMS=0.095 (target=0.015)   
step 050: RMS=0.094 (target=0.015)   
step 055: RMS=0.095 (target=0.015)   
step 060: RMS=0.096 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.5 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    32.336497
mris_inflate stimesec    0.144162
mris_inflate ru_maxrss   455356
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   125552
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4568
mris_inflate ru_oublock  15504
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    23
mris_inflate ru_nivcsw   1022
@#@FSTIME  2020:09:22:15:52:33 mris_inflate N 3 e 32.67 S 0.16 U 32.33 P 99% M 455640 F 19 R 125554 W 0 c 1026 w 24 I 4568 O 15504 L 1.07 0.95 0.61
@#@FSLOADPOST 2020:09:22:15:53:05 mris_inflate N 3 1.04 0.95 0.62
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 22��� ��������� 15:53:05 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 33.6 mm, total surface area = 30576 mm^2

step 000: RMS=0.155 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.112 (target=0.015)   
step 015: RMS=0.107 (target=0.015)   
step 020: RMS=0.102 (target=0.015)   
step 025: RMS=0.099 (target=0.015)   
step 030: RMS=0.099 (target=0.015)   
step 035: RMS=0.099 (target=0.015)   
step 040: RMS=0.099 (target=0.015)   
step 045: RMS=0.098 (target=0.015)   
step 050: RMS=0.098 (target=0.015)   
step 055: RMS=0.098 (target=0.015)   
step 060: RMS=0.099 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.1 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    7.602161
mris_inflate stimesec    0.047812
mris_inflate ru_maxrss   118120
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32371
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  3824
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   312
@#@FSTIME  2020:09:22:15:53:05 mris_inflate N 3 e 7.71 S 0.05 U 7.60 P 99% M 118356 F 0 R 32373 W 0 c 315 w 1 I 0 O 3824 L 1.04 0.95 0.62
@#@FSLOADPOST 2020:09:22:15:53:13 mris_inflate N 3 1.03 0.96 0.63

Started at 2020��� 09��� 22��� ��������� 15:40:36 CST 
Ended   at 2020��� 09��� 22��� ��������� 15:53:13 CST
#@#%# recon-all-run-time-hours 0.210
recon-all -s monkey2 finished without error at 2020��� 09��� 22��� ��������� 15:53:13 CST



#New# invocation of recon-all 



2020��� 09��� 22��� ��������� 16:17:36 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        1.1G        419M         24M        418M        671M
Swap:          2.0G        208M        1.8G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-08:17:37-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 22��� ��������� 16:17:37 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 131 control points...
only using 131 control points from file, mean 93.0, scaling by 1.18...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 18
Starting OpenSpline(): npoints = 18
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 111
gm peak at 63 (63), valley at 19 (19)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 62 (62), valley at 19 (19)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 56 seconds.
@#@FSTIME  2020:09:22:16:17:37 mri_normalize N 7 e 357.42 S 0.38 U 354.71 P 99% M 582976 F 2 R 312317 W 0 c 10976 w 6 I 352 O 3072 L 0.04 0.11 0.19
@#@FSLOADPOST 2020:09:22:16:23:34 mri_normalize N 7 1.00 0.74 0.47
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 22��� ��������� 16:23:34 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:22:16:23:34 mri_mask N 5 e 2.64 S 0.02 U 2.59 P 99% M 74188 F 17 R 17257 W 0 c 101 w 31 I 5840 O 2992 L 1.00 0.74 0.47
@#@FSLOADPOST 2020:09:22:16:23:37 mri_mask N 5 1.00 0.74 0.47
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 22��� ��������� 16:23:37 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -1.000000 16777216 -0.000006
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -1.000000 16777216 -0.000006
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: -1 deletes, -1 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:22:16:23:44 AntsDenoiseImageFs N 4 e 63.60 S 0.12 U 63.19 P 99% M 350624 F 20 R 86505 W 0 c 1819 w 23 I 4504 O 3040 L 1.00 0.75 0.47
@#@FSLOADPOST 2020:09:22:16:24:48 AntsDenoiseImageFs N 4 1.00 0.80 0.51

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 105.3 +- 6.7 [79.0 --> 125.0]
CCS GM (71.0) : 69.0 +- 11.1 [30.0 --> 95.0]
 white_mean 105.257
 white_sigma 6.74529
 gray_mean 68.9923
 gray_sigma 11.1451
setting bottom of white matter range wm_low to 80.1
setting top of gray matter range gray_hi to 91.3
 wm_low 80.1374
 wm_hi  125
 gray_low 30
 gray_hi  91.2825
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.1374
 wm_hi  125
 gray_low 30
 gray_hi  91.2825
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 91.2825, wm_low = 80.1374
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.2825, wmlow=80.1374
    118415 voxels processed (0.71%)
     55145 voxels white (0.33%)
     63270 voxels non-white (0.38%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.1374, gray_hi=91.2825, wsize=13
    200312 voxels tested (1.19%)
     47235 voxels changed (0.28%)
     47108 multi-scale searches  (0.28%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.1374
 wm_hi 125
 slack 6.74529
 pct_thresh 0.33
 intensity_thresh 131.745
 nvox_thresh 8.58
     2724 voxels tested (0.02%)
     2251 voxels changed (0.01%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.1374, hithr=91.2825
  smoothing input volume with sigma = 0.250
    77638 voxels tested (0.46%)
    14382 voxels changed (0.09%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 6389 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
4337 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 2743 filled
MRIfindBrightNonWM(): 4491 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.5 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:22:16:24:48 mri_segment N 6 e 211.85 S 0.40 U 210.19 P 99% M 147304 F 11 R 299404 W 0 c 6921 w 13 I 1936 O 728 L 1.00 0.80 0.51
@#@FSLOADPOST 2020:09:22:16:28:19 mri_segment N 6 1.00 0.91 0.62

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  12 found -  12 modified     |    TOTAL:  12
pass   2 (xy+):   0 found -  12 modified     |    TOTAL:  12
pass   1 (xy-):   9 found -   9 modified     |    TOTAL:  21
pass   2 (xy-):   0 found -   9 modified     |    TOTAL:  21
pass   1 (yz+):  11 found -  11 modified     |    TOTAL:  32
pass   2 (yz+):   0 found -  11 modified     |    TOTAL:  32
pass   1 (yz-):   6 found -   6 modified     |    TOTAL:  38
pass   2 (yz-):   0 found -   6 modified     |    TOTAL:  38
pass   1 (xz+):  12 found -  12 modified     |    TOTAL:  50
pass   2 (xz+):   0 found -  12 modified     |    TOTAL:  50
pass   1 (xz-):  21 found -  21 modified     |    TOTAL:  71
pass   2 (xz-):   0 found -  21 modified     |    TOTAL:  71
Iteration Number : 1
pass   1 (+++): 101 found - 101 modified     |    TOTAL: 101
pass   2 (+++):   0 found - 101 modified     |    TOTAL: 101
pass   1 (+++):  93 found -  93 modified     |    TOTAL: 194
pass   2 (+++):   0 found -  93 modified     |    TOTAL: 194
pass   1 (+++):  91 found -  91 modified     |    TOTAL: 285
pass   2 (+++):   0 found -  91 modified     |    TOTAL: 285
pass   1 (+++):  63 found -  63 modified     |    TOTAL: 348
pass   2 (+++):   0 found -  63 modified     |    TOTAL: 348
Iteration Number : 1
pass   1 (++): 234 found - 234 modified     |    TOTAL: 234
pass   2 (++):   0 found - 234 modified     |    TOTAL: 234
pass   1 (+-): 278 found - 278 modified     |    TOTAL: 512
pass   2 (+-):   0 found - 278 modified     |    TOTAL: 512
pass   1 (--): 231 found - 231 modified     |    TOTAL: 743
pass   2 (--):   1 found - 232 modified     |    TOTAL: 744
pass   3 (--):   0 found - 232 modified     |    TOTAL: 744
pass   1 (-+): 252 found - 252 modified     |    TOTAL: 996
pass   2 (-+):   0 found - 252 modified     |    TOTAL: 996
Iteration Number : 2
pass   1 (xy+):  18 found -  18 modified     |    TOTAL:  18
pass   2 (xy+):   0 found -  18 modified     |    TOTAL:  18
pass   1 (xy-):  19 found -  19 modified     |    TOTAL:  37
pass   2 (xy-):   0 found -  19 modified     |    TOTAL:  37
pass   1 (yz+):  28 found -  28 modified     |    TOTAL:  65
pass   2 (yz+):   0 found -  28 modified     |    TOTAL:  65
pass   1 (yz-):  27 found -  27 modified     |    TOTAL:  92
pass   2 (yz-):   0 found -  27 modified     |    TOTAL:  92
pass   1 (xz+):  26 found -  26 modified     |    TOTAL: 118
pass   2 (xz+):   0 found -  26 modified     |    TOTAL: 118
pass   1 (xz-):  30 found -  30 modified     |    TOTAL: 148
pass   2 (xz-):   0 found -  30 modified     |    TOTAL: 148
Iteration Number : 2
pass   1 (+++):   9 found -   9 modified     |    TOTAL:   9
pass   2 (+++):   0 found -   9 modified     |    TOTAL:   9
pass   1 (+++):  19 found -  19 modified     |    TOTAL:  28
pass   2 (+++):   0 found -  19 modified     |    TOTAL:  28
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  30
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  30
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  32
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  32
Iteration Number : 2
pass   1 (++):  15 found -  15 modified     |    TOTAL:  15
pass   2 (++):   0 found -  15 modified     |    TOTAL:  15
pass   1 (+-):  18 found -  18 modified     |    TOTAL:  33
pass   2 (+-):   0 found -  18 modified     |    TOTAL:  33
pass   1 (--):  19 found -  19 modified     |    TOTAL:  52
pass   2 (--):   0 found -  19 modified     |    TOTAL:  52
pass   1 (-+):  16 found -  16 modified     |    TOTAL:  68
pass   2 (-+):   0 found -  16 modified     |    TOTAL:  68
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   5 found -   5 modified     |    TOTAL:   8
pass   2 (yz+):   0 found -   5 modified     |    TOTAL:   8
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  12
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  12
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:  12
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  14
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  14
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   6
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   6
pass   1 (--):   1 found -   1 modified     |    TOTAL:   7
pass   2 (--):   0 found -   1 modified     |    TOTAL:   7
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   7
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1689 (out of 378266: 0.446511)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 0 WM ON voxels
  kept 0 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:22:16:28:19 mri_pretess N 5 e 5.20 S 0.02 U 5.08 P 98% M 57136 F 16 R 17105 W 0 c 462 w 18 I 3472 O 720 L 1.00 0.91 0.62
@#@FSLOADPOST 2020:09:22:16:28:25 mri_pretess N 5 1.00 0.91 0.62
#--------------------------------------------
#@# Fill 2020��� 09��� 22��� ��������� 16:28:25 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 771 (min = 350, max = 1400), aspect = 4.64 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 5290 (min = 350, max = 790), aspect = 0.66 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 360657 voxels filled...
filling volume: pass 2 of 3...total of 16348836 voxels filled...
filling volume: pass 3 of 3...total of 361823 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 360657 voxels filled...
filling volume: pass 2 of 3...total of 16348836 voxels filled...
filling volume: pass 3 of 3...total of 361823 voxels filled...done.
filling degenerate left hemisphere surface locations...
574 voxels filled
15 voxels filled
3 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
574 voxels filled
15 voxels filled
3 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16348238 voxels filled...
filling volume: pass 3 of 3...total of 362421 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16348238 voxels filled...
filling volume: pass 3 of 3...total of 362421 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  362028 ambiguous voxels remaining
9:  240176 ambiguous voxels remaining
8:  229650 ambiguous voxels remaining
7:  14182 ambiguous voxels remaining
6:  5682 ambiguous voxels remaining
5:  2876 ambiguous voxels remaining
4:  1436 ambiguous voxels remaining
3:  920 ambiguous voxels remaining
2:  134 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.7 minutes
badRH = 112389/284572, badLH=1051/77850
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
error: Please check filled volume.  Cerebellum may be included.

@#@FSTIME  2020:09:22:16:28:25 mri_fill N 12 e 40.91 S 0.08 U 40.61 P 99% M 111916 F 10 R 77483 W 0 c 1554 w 13 I 2240 O 240 L 1.00 0.91 0.62
@#@FSLOADPOST 2020:09:22:16:29:06 mri_fill N 12 1.00 0.92 0.64
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 22��� ��������� 16:29:06 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 77850: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:16:29:06 mri_pretess N 4 e 1.35 S 0.01 U 1.32 P 98% M 40452 F 0 R 8849 W 0 c 97 w 1 I 0 O 232 L 1.00 0.92 0.64
@#@FSLOADPOST 2020:09:22:16:29:07 mri_pretess N 4 1.00 0.92 0.64

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 1751 vertices, 1844 faces
slice 70: 5793 vertices, 5938 faces
slice 80: 10901 vertices, 11093 faces
slice 90: 15681 vertices, 15919 faces
slice 100: 24139 vertices, 24566 faces
slice 110: 34072 vertices, 34381 faces
slice 120: 41897 vertices, 42163 faces
slice 130: 46295 vertices, 46478 faces
slice 140: 49155 vertices, 49265 faces
slice 150: 49630 vertices, 49698 faces
slice 160: 49630 vertices, 49698 faces
slice 170: 49630 vertices, 49698 faces
slice 180: 49630 vertices, 49698 faces
slice 190: 49630 vertices, 49698 faces
slice 200: 49630 vertices, 49698 faces
slice 210: 49630 vertices, 49698 faces
slice 220: 49630 vertices, 49698 faces
slice 230: 49630 vertices, 49698 faces
slice 240: 49630 vertices, 49698 faces
slice 250: 49630 vertices, 49698 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:16:29:07 mri_tessellate N 3 e 2.27 S 0.00 U 2.25 P 99% M 29984 F 16 R 6521 W 0 c 86 w 18 I 3728 O 2336 L 1.00 0.92 0.64
@#@FSLOADPOST 2020:09:22:16:29:09 mri_tessellate N 3 1.00 0.93 0.64

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   49630 voxel in cpt #1: X=-68 [v=49630,e=149094,f=99396] located at (0.951239, -30.307980, 51.982449)
For the whole surface: X=-68 [v=49630,e=149094,f=99396]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:16:29:09 mris_extract_main_component N 2 e 0.46 S 0.04 U 0.35 P 86% M 103532 F 18 R 27558 W 0 c 56 w 24 I 4504 O 3496 L 1.00 0.93 0.64
@#@FSLOADPOST 2020:09:22:16:29:10 mris_extract_main_component N 2 1.00 0.93 0.64
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 22��� ��������� 16:29:10 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 8 (out of 284580: 0.002811)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:16:29:10 mri_pretess N 4 e 1.98 S 0.01 U 1.93 P 98% M 40464 F 0 R 8849 W 0 c 156 w 1 I 0 O 232 L 1.00 0.93 0.64
@#@FSLOADPOST 2020:09:22:16:29:12 mri_pretess N 4 1.00 0.93 0.64

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 50: 465 vertices, 532 faces
slice 60: 9792 vertices, 10348 faces
slice 70: 30876 vertices, 31658 faces
slice 80: 58309 vertices, 59584 faces
slice 90: 91634 vertices, 93073 faces
slice 100: 121285 vertices, 122742 faces
slice 110: 154860 vertices, 156329 faces
slice 120: 183601 vertices, 185063 faces
slice 130: 205167 vertices, 206237 faces
slice 140: 217729 vertices, 218469 faces
slice 150: 221070 vertices, 221558 faces
slice 160: 221070 vertices, 221558 faces
slice 170: 221070 vertices, 221558 faces
slice 180: 221070 vertices, 221558 faces
slice 190: 221070 vertices, 221558 faces
slice 200: 221070 vertices, 221558 faces
slice 210: 221070 vertices, 221558 faces
slice 220: 221070 vertices, 221558 faces
slice 230: 221070 vertices, 221558 faces
slice 240: 221070 vertices, 221558 faces
slice 250: 221070 vertices, 221558 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:16:29:12 mri_tessellate N 3 e 2.54 S 0.02 U 2.51 P 99% M 45228 F 0 R 10340 W 0 c 94 w 2 I 0 O 10376 L 1.00 0.93 0.64
@#@FSLOADPOST 2020:09:22:16:29:14 mri_tessellate N 3 1.00 0.93 0.64

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   221070 voxel in cpt #1: X=-488 [v=221070,e=664674,f=443116] located at (32.926212, -32.547947, -1.342837)
For the whole surface: X=-488 [v=221070,e=664674,f=443116]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:16:29:14 mris_extract_main_component N 2 e 1.83 S 0.15 U 1.66 P 99% M 439360 F 0 R 121844 W 0 c 98 w 10 I 72 O 15568 L 1.00 0.93 0.64
@#@FSLOADPOST 2020:09:22:16:29:16 mris_extract_main_component N 2 1.00 0.93 0.64
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 22��� ��������� 16:29:16 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:16:29:16 mris_smooth N 5 e 1.59 S 0.03 U 1.53 P 98% M 85624 F 17 R 22801 W 0 c 72 w 20 I 4040 O 3496 L 1.00 0.93 0.64
@#@FSLOADPOST 2020:09:22:16:29:18 mris_smooth N 5 1.00 0.93 0.64
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 22��� ��������� 16:29:18 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:16:29:18 mris_smooth N 5 e 7.03 S 0.14 U 6.84 P 99% M 353536 F 0 R 100098 W 0 c 238 w 2 I 8 O 15576 L 1.00 0.93 0.64
@#@FSLOADPOST 2020:09:22:16:29:25 mris_smooth N 5 1.00 0.93 0.65
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 22��� ��������� 16:29:25 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 35.3 mm, total surface area = 28442 mm^2

step 000: RMS=0.150 (target=0.015)   
step 005: RMS=0.127 (target=0.015)   
step 010: RMS=0.110 (target=0.015)   
step 015: RMS=0.100 (target=0.015)   
step 020: RMS=0.097 (target=0.015)   
step 025: RMS=0.094 (target=0.015)   
step 030: RMS=0.093 (target=0.015)   
step 035: RMS=0.090 (target=0.015)   
step 040: RMS=0.090 (target=0.015)   
step 045: RMS=0.090 (target=0.015)   
step 050: RMS=0.091 (target=0.015)   
step 055: RMS=0.091 (target=0.015)   
step 060: RMS=0.091 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.1 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    7.668584
mris_inflate stimesec    0.043775
mris_inflate ru_maxrss   109052
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29487
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  3496
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   316
@#@FSTIME  2020:09:22:16:29:25 mris_inflate N 3 e 7.77 S 0.04 U 7.66 P 99% M 109152 F 19 R 29489 W 0 c 320 w 22 I 4552 O 3496 L 1.00 0.93 0.65
@#@FSLOADPOST 2020:09:22:16:29:33 mris_inflate N 3 1.00 0.93 0.65
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 22��� ��������� 16:29:33 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 53.3 mm, total surface area = 121896 mm^2

step 000: RMS=0.159 (target=0.015)   
step 005: RMS=0.131 (target=0.015)   
step 010: RMS=0.114 (target=0.015)   
step 015: RMS=0.106 (target=0.015)   
step 020: RMS=0.103 (target=0.015)   
step 025: RMS=0.100 (target=0.015)   
step 030: RMS=0.098 (target=0.015)   
step 035: RMS=0.097 (target=0.015)   
step 040: RMS=0.096 (target=0.015)   
step 045: RMS=0.095 (target=0.015)   
step 050: RMS=0.094 (target=0.015)   
step 055: RMS=0.095 (target=0.015)   
step 060: RMS=0.095 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.6 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    33.512638
mris_inflate stimesec    0.165591
mris_inflate ru_maxrss   457904
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   126195
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  15576
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   2222
@#@FSTIME  2020:09:22:16:29:33 mris_inflate N 3 e 36.06 S 0.18 U 33.51 P 93% M 458076 F 0 R 126197 W 0 c 2227 w 1 I 0 O 15576 L 1.00 0.93 0.65
@#@FSLOADPOST 2020:09:22:16:30:09 mris_inflate N 3 1.21 0.99 0.68

Started at 2020��� 09��� 22��� ��������� 16:17:36 CST 
Ended   at 2020��� 09��� 22��� ��������� 16:30:09 CST
#@#%# recon-all-run-time-hours 0.209
recon-all -s monkey2 finished without error at 2020��� 09��� 22��� ��������� 16:30:09 CST



#New# invocation of recon-all 



2020��� 09��� 22��� ��������� 18:28:21 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        1.1G        486M         24M        356M        677M
Swap:          2.0G        220M        1.8G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:21-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-10:28:22-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 22��� ��������� 18:28:22 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 415 control points...
only using 415 control points from file, mean 82.6, scaling by 1.33...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 111
gm peak at 66 (66), valley at 26 (26)
csf peak at 33, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 22 (22)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 45 seconds.
@#@FSTIME  2020:09:22:18:28:22 mri_normalize N 7 e 346.80 S 0.35 U 344.13 P 99% M 582952 F 3 R 316388 W 0 c 10627 w 7 I 552 O 3024 L 0.21 0.15 0.06
@#@FSLOADPOST 2020:09:22:18:34:09 mri_normalize N 7 1.00 0.74 0.37
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 22��� ��������� 18:34:09 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:22:18:34:09 mri_mask N 5 e 2.61 S 0.02 U 2.54 P 97% M 74072 F 17 R 17258 W 0 c 111 w 31 I 5888 O 2952 L 1.00 0.74 0.37
@#@FSLOADPOST 2020:09:22:18:34:11 mri_mask N 5 1.00 0.75 0.37
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 22��� ��������� 18:34:12 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -1.000000 16777216 -0.000006
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -1.000000 16777216 -0.000006
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: -1 deletes, -1 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:22:18:34:18 AntsDenoiseImageFs N 4 e 61.62 S 0.08 U 61.20 P 99% M 350552 F 19 R 86510 W 0 c 1796 w 22 I 4408 O 3000 L 1.00 0.75 0.38
@#@FSLOADPOST 2020:09:22:18:35:20 AntsDenoiseImageFs N 4 1.11 0.83 0.43

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 104.9 +- 6.1 [79.0 --> 125.0]
CCS GM (71.0) : 69.4 +- 10.4 [30.0 --> 95.0]
 white_mean 104.875
 white_sigma 6.12543
 gray_mean 69.3848
 gray_sigma 10.4182
setting bottom of white matter range wm_low to 79.8
setting top of gray matter range gray_hi to 90.2
 wm_low 79.803
 wm_hi  125
 gray_low 30
 gray_hi  90.2211
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.803
 wm_hi  125
 gray_low 30
 gray_hi  90.2211
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.2211, wm_low = 79.803
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.2211, wmlow=79.803
    125413 voxels processed (0.75%)
     54080 voxels white (0.32%)
     71333 voxels non-white (0.43%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.803, gray_hi=90.2211, wsize=13
    212188 voxels tested (1.26%)
     47610 voxels changed (0.28%)
     53604 multi-scale searches  (0.32%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.803
 wm_hi 125
 slack 6.12543
 pct_thresh 0.33
 intensity_thresh 131.125
 nvox_thresh 8.58
      908 voxels tested (0.01%)
      698 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.803, hithr=90.2211
  smoothing input volume with sigma = 0.250
    72680 voxels tested (0.43%)
    13567 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 6598 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3427 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3532 filled
MRIfindBrightNonWM(): 1928 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.5 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:22:18:35:20 mri_segment N 6 e 212.88 S 0.16 U 211.71 P 99% M 147632 F 9 R 137424 W 0 c 6285 w 11 I 1640 O 696 L 1.11 0.83 0.43
@#@FSLOADPOST 2020:09:22:18:38:53 mri_segment N 6 1.04 0.94 0.56

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):   8 found -   8 modified     |    TOTAL:   8
pass   2 (xy+):   0 found -   8 modified     |    TOTAL:   8
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  13
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  13
pass   1 (yz+):   7 found -   7 modified     |    TOTAL:  20
pass   2 (yz+):   0 found -   7 modified     |    TOTAL:  20
pass   1 (yz-):   7 found -   7 modified     |    TOTAL:  27
pass   2 (yz-):   0 found -   7 modified     |    TOTAL:  27
pass   1 (xz+):  15 found -  15 modified     |    TOTAL:  42
pass   2 (xz+):   0 found -  15 modified     |    TOTAL:  42
pass   1 (xz-):  10 found -  10 modified     |    TOTAL:  52
pass   2 (xz-):   0 found -  10 modified     |    TOTAL:  52
Iteration Number : 1
pass   1 (+++):  68 found -  68 modified     |    TOTAL:  68
pass   2 (+++):   0 found -  68 modified     |    TOTAL:  68
pass   1 (+++):  66 found -  66 modified     |    TOTAL: 134
pass   2 (+++):   0 found -  66 modified     |    TOTAL: 134
pass   1 (+++):  79 found -  79 modified     |    TOTAL: 213
pass   2 (+++):   0 found -  79 modified     |    TOTAL: 213
pass   1 (+++):  48 found -  48 modified     |    TOTAL: 261
pass   2 (+++):   0 found -  48 modified     |    TOTAL: 261
Iteration Number : 1
pass   1 (++): 170 found - 170 modified     |    TOTAL: 170
pass   2 (++):   0 found - 170 modified     |    TOTAL: 170
pass   1 (+-): 225 found - 225 modified     |    TOTAL: 395
pass   2 (+-):   0 found - 225 modified     |    TOTAL: 395
pass   1 (--): 208 found - 208 modified     |    TOTAL: 603
pass   2 (--):   0 found - 208 modified     |    TOTAL: 603
pass   1 (-+): 263 found - 263 modified     |    TOTAL: 866
pass   2 (-+):   0 found - 263 modified     |    TOTAL: 866
Iteration Number : 2
pass   1 (xy+):  21 found -  21 modified     |    TOTAL:  21
pass   2 (xy+):   0 found -  21 modified     |    TOTAL:  21
pass   1 (xy-):  16 found -  16 modified     |    TOTAL:  37
pass   2 (xy-):   0 found -  16 modified     |    TOTAL:  37
pass   1 (yz+):  30 found -  30 modified     |    TOTAL:  67
pass   2 (yz+):   0 found -  30 modified     |    TOTAL:  67
pass   1 (yz-):  17 found -  17 modified     |    TOTAL:  84
pass   2 (yz-):   0 found -  17 modified     |    TOTAL:  84
pass   1 (xz+):  17 found -  17 modified     |    TOTAL: 101
pass   2 (xz+):   0 found -  17 modified     |    TOTAL: 101
pass   1 (xz-):  20 found -  20 modified     |    TOTAL: 121
pass   2 (xz-):   0 found -  20 modified     |    TOTAL: 121
Iteration Number : 2
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):  15 found -  15 modified     |    TOTAL:  19
pass   2 (+++):   0 found -  15 modified     |    TOTAL:  19
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  25
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  25
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  27
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  27
Iteration Number : 2
pass   1 (++):  15 found -  15 modified     |    TOTAL:  15
pass   2 (++):   0 found -  15 modified     |    TOTAL:  15
pass   1 (+-):  13 found -  13 modified     |    TOTAL:  28
pass   2 (+-):   0 found -  13 modified     |    TOTAL:  28
pass   1 (--):   4 found -   4 modified     |    TOTAL:  32
pass   2 (--):   0 found -   4 modified     |    TOTAL:  32
pass   1 (-+):  13 found -  13 modified     |    TOTAL:  45
pass   2 (-+):   0 found -  13 modified     |    TOTAL:  45
Iteration Number : 3
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   5
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   7
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   9
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   9
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  12
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  12
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  15
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  15
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   5 modified     |    TOTAL:   5
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 5
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 6
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 6
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 6
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1400 (out of 367673: 0.380773)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 0 WM ON voxels
  kept 0 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:22:18:38:53 mri_pretess N 5 e 5.45 S 0.01 U 5.32 P 98% M 57088 F 16 R 17105 W 0 c 506 w 18 I 3472 O 696 L 1.04 0.94 0.56
@#@FSLOADPOST 2020:09:22:18:38:58 mri_pretess N 5 1.04 0.94 0.56
#--------------------------------------------
#@# Fill 2020��� 09��� 22��� ��������� 18:38:58 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 799 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 5014 (min = 350, max = 790), aspect = 0.63 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 350656 voxels filled...
filling volume: pass 2 of 3...total of 16359295 voxels filled...
filling volume: pass 3 of 3...total of 351364 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 350656 voxels filled...
filling volume: pass 2 of 3...total of 16359295 voxels filled...
filling volume: pass 3 of 3...total of 351364 voxels filled...done.
filling degenerate left hemisphere surface locations...
523 voxels filled
23 voxels filled
1 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
523 voxels filled
23 voxels filled
1 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16358727 voxels filled...
filling volume: pass 3 of 3...total of 351932 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16358727 voxels filled...
filling volume: pass 3 of 3...total of 351932 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  351539 ambiguous voxels remaining
9:  210599 ambiguous voxels remaining
8:  178187 ambiguous voxels remaining
7:  11887 ambiguous voxels remaining
6:  4740 ambiguous voxels remaining
5:  2607 ambiguous voxels remaining
4:  1249 ambiguous voxels remaining
3:  597 ambiguous voxels remaining
2:  179 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.7 minutes
badRH = 0/82290, badLH=91775/269643
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
error: Please check filled volume.  Cerebellum may be included.

@#@FSTIME  2020:09:22:18:38:58 mri_fill N 12 e 40.42 S 0.11 U 40.04 P 99% M 111584 F 10 R 77486 W 0 c 1552 w 13 I 2240 O 240 L 1.04 0.94 0.56
@#@FSLOADPOST 2020:09:22:18:39:39 mri_fill N 12 1.02 0.95 0.58
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 22��� ��������� 18:39:39 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 2 (out of 269645: 0.000742)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:18:39:39 mri_pretess N 4 e 1.71 S 0.00 U 1.68 P 98% M 40412 F 0 R 8846 W 0 c 145 w 1 I 0 O 232 L 1.02 0.95 0.58
@#@FSLOADPOST 2020:09:22:18:39:41 mri_pretess N 4 1.02 0.95 0.58

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 139 vertices, 152 faces
slice 60: 3505 vertices, 3851 faces
slice 70: 21133 vertices, 21774 faces
slice 80: 45920 vertices, 47032 faces
slice 90: 79655 vertices, 81158 faces
slice 100: 114473 vertices, 115901 faces
slice 110: 147856 vertices, 149129 faces
slice 120: 175459 vertices, 176724 faces
slice 130: 195555 vertices, 196476 faces
slice 140: 207864 vertices, 208456 faces
slice 150: 211978 vertices, 212326 faces
slice 160: 211978 vertices, 212326 faces
slice 170: 211978 vertices, 212326 faces
slice 180: 211978 vertices, 212326 faces
slice 190: 211978 vertices, 212326 faces
slice 200: 211978 vertices, 212326 faces
slice 210: 211978 vertices, 212326 faces
slice 220: 211978 vertices, 212326 faces
slice 230: 211978 vertices, 212326 faces
slice 240: 211978 vertices, 212326 faces
slice 250: 211978 vertices, 212326 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:18:39:41 mri_tessellate N 3 e 2.41 S 0.02 U 2.30 P 96% M 44652 F 16 R 10154 W 0 c 86 w 18 I 3728 O 9952 L 1.02 0.95 0.58
@#@FSLOADPOST 2020:09:22:18:39:43 mri_tessellate N 3 1.02 0.95 0.58

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   211978 voxel in cpt #1: X=-348 [v=211978,e=636978,f=424652] located at (20.760027, -30.793423, 4.531390)
For the whole surface: X=-348 [v=211978,e=636978,f=424652]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:18:39:43 mris_extract_main_component N 2 e 1.63 S 0.13 U 1.45 P 97% M 421152 F 18 R 116748 W 0 c 91 w 26 I 4512 O 14928 L 1.02 0.95 0.58
@#@FSLOADPOST 2020:09:22:18:39:45 mris_extract_main_component N 2 1.02 0.95 0.58
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 22��� ��������� 18:39:45 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 2 (out of 82292: 0.002430)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:18:39:45 mri_pretess N 4 e 1.64 S 0.01 U 1.60 P 98% M 40368 F 0 R 8845 W 0 c 147 w 1 I 0 O 232 L 1.02 0.95 0.58
@#@FSLOADPOST 2020:09:22:18:39:46 mri_pretess N 4 1.02 0.95 0.59

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 564 vertices, 624 faces
slice 70: 4024 vertices, 4137 faces
slice 80: 9146 vertices, 9375 faces
slice 90: 16155 vertices, 16518 faces
slice 100: 27188 vertices, 27668 faces
slice 110: 37900 vertices, 38335 faces
slice 120: 46354 vertices, 46709 faces
slice 130: 51415 vertices, 51661 faces
slice 140: 54483 vertices, 54669 faces
slice 150: 55106 vertices, 55240 faces
slice 160: 55106 vertices, 55240 faces
slice 170: 55106 vertices, 55240 faces
slice 180: 55106 vertices, 55240 faces
slice 190: 55106 vertices, 55240 faces
slice 200: 55106 vertices, 55240 faces
slice 210: 55106 vertices, 55240 faces
slice 220: 55106 vertices, 55240 faces
slice 230: 55106 vertices, 55240 faces
slice 240: 55106 vertices, 55240 faces
slice 250: 55106 vertices, 55240 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:18:39:46 mri_tessellate N 3 e 2.24 S 0.01 U 2.22 P 99% M 30460 F 0 R 6650 W 0 c 84 w 2 I 8 O 2592 L 1.02 0.95 0.59
@#@FSLOADPOST 2020:09:22:18:39:49 mri_tessellate N 3 1.02 0.95 0.59

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   55106 voxel in cpt #1: X=-134 [v=55106,e=165720,f=110480] located at (56.160580, -28.860796, 54.764870)
For the whole surface: X=-134 [v=55106,e=165720,f=110480]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:18:39:49 mris_extract_main_component N 2 e 0.37 S 0.03 U 0.33 P 98% M 114408 F 0 R 30608 W 0 c 49 w 1 I 0 O 3888 L 1.02 0.95 0.59
@#@FSLOADPOST 2020:09:22:18:39:49 mris_extract_main_component N 2 1.02 0.95 0.59
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 22��� ��������� 18:39:49 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:18:39:49 mris_smooth N 5 e 6.32 S 0.11 U 6.15 P 99% M 338612 F 17 R 95793 W 0 c 217 w 20 I 4040 O 14928 L 1.02 0.95 0.59
@#@FSLOADPOST 2020:09:22:18:39:55 mris_smooth N 5 1.01 0.95 0.59
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 22��� ��������� 18:39:55 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:18:39:55 mris_smooth N 5 e 1.57 S 0.04 U 1.51 P 99% M 93952 F 0 R 25225 W 0 c 78 w 2 I 8 O 3888 L 1.01 0.95 0.59
@#@FSLOADPOST 2020:09:22:18:39:57 mris_smooth N 5 1.01 0.95 0.59
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 22��� ��������� 18:39:57 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 54.1 mm, total surface area = 118685 mm^2

step 000: RMS=0.151 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.107 (target=0.015)   
step 015: RMS=0.099 (target=0.015)   
step 020: RMS=0.096 (target=0.015)   
step 025: RMS=0.091 (target=0.015)   
step 030: RMS=0.090 (target=0.015)   
step 035: RMS=0.087 (target=0.015)   
step 040: RMS=0.086 (target=0.015)   
step 045: RMS=0.086 (target=0.015)   
step 050: RMS=0.085 (target=0.015)   
step 055: RMS=0.085 (target=0.015)   
step 060: RMS=0.086 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.5 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    30.560700
mris_inflate stimesec    0.135594
mris_inflate ru_maxrss   438848
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   120882
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4560
mris_inflate ru_oublock  14928
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    22
mris_inflate ru_nivcsw   993
@#@FSTIME  2020:09:22:18:39:57 mris_inflate N 3 e 30.90 S 0.15 U 30.56 P 99% M 439116 F 19 R 120884 W 0 c 996 w 23 I 4560 O 14928 L 1.01 0.95 0.59
@#@FSLOADPOST 2020:09:22:18:40:28 mris_inflate N 3 1.01 0.96 0.61
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 22��� ��������� 18:40:28 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 34.0 mm, total surface area = 31223 mm^2

step 000: RMS=0.159 (target=0.015)   
step 005: RMS=0.133 (target=0.015)   
step 010: RMS=0.117 (target=0.015)   
step 015: RMS=0.109 (target=0.015)   
step 020: RMS=0.106 (target=0.015)   
step 025: RMS=0.104 (target=0.015)   
step 030: RMS=0.103 (target=0.015)   
step 035: RMS=0.101 (target=0.015)   
step 040: RMS=0.100 (target=0.015)   
step 045: RMS=0.101 (target=0.015)   
step 050: RMS=0.101 (target=0.015)   
step 055: RMS=0.101 (target=0.015)   
step 060: RMS=0.101 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.1 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    7.759600
mris_inflate stimesec    0.047972
mris_inflate ru_maxrss   120304
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32983
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  3888
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   307
@#@FSTIME  2020:09:22:18:40:28 mris_inflate N 3 e 7.85 S 0.05 U 7.76 P 99% M 120436 F 0 R 32985 W 0 c 310 w 1 I 0 O 3888 L 1.01 0.96 0.61
@#@FSLOADPOST 2020:09:22:18:40:36 mris_inflate N 3 1.00 0.96 0.61

Started at 2020��� 09��� 22��� ��������� 18:28:21 CST 
Ended   at 2020��� 09��� 22��� ��������� 18:40:36 CST
#@#%# recon-all-run-time-hours 0.204
recon-all -s monkey2 finished without error at 2020��� 09��� 22��� ��������� 18:40:36 CST



#New# invocation of recon-all 



2020��� 09��� 22��� ��������� 20:24:16 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        1.0G        703M         24M        219M        756M
Swap:          2.0G        304M        1.7G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/22-12:24:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 22��� ��������� 20:24:17 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:22:20:24:17 mri_mask N 5 e 2.70 S 0.04 U 2.61 P 98% M 74320 F 5 R 17278 W 0 c 147 w 10 I 7144 O 2952 L 0.07 0.10 0.04
@#@FSLOADPOST 2020:09:22:20:24:20 mri_mask N 5 0.15 0.12 0.04
#--------------------------------------------
#@# Fill 2020��� 09��� 22��� ��������� 20:24:20 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 799 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 5016 (min = 350, max = 790), aspect = 0.63 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 350827 voxels filled...
filling volume: pass 2 of 3...total of 16359174 voxels filled...
filling volume: pass 3 of 3...total of 351485 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 350827 voxels filled...
filling volume: pass 2 of 3...total of 16359174 voxels filled...
filling volume: pass 3 of 3...total of 351485 voxels filled...done.
filling degenerate left hemisphere surface locations...
538 voxels filled
23 voxels filled
1 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
538 voxels filled
23 voxels filled
1 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16358591 voxels filled...
filling volume: pass 3 of 3...total of 352068 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16358591 voxels filled...
filling volume: pass 3 of 3...total of 352068 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  351675 ambiguous voxels remaining
9:  210733 ambiguous voxels remaining
8:  178309 ambiguous voxels remaining
7:  11932 ambiguous voxels remaining
6:  4769 ambiguous voxels remaining
5:  2628 ambiguous voxels remaining
4:  1263 ambiguous voxels remaining
3:  604 ambiguous voxels remaining
2:  181 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.7 minutes
badRH = 0/82290, badLH=91862/269779
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
error: Please check filled volume.  Cerebellum may be included.

@#@FSTIME  2020:09:22:20:24:20 mri_fill N 12 e 40.74 S 0.10 U 39.61 P 97% M 111496 F 6 R 77495 W 0 c 2183 w 7 I 1568 O 240 L 0.15 0.12 0.04
@#@FSLOADPOST 2020:09:22:20:25:01 mri_fill N 12 0.56 0.23 0.09
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 22��� ��������� 20:25:01 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:   4
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:   4
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 5 (out of 269784: 0.001853)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:20:25:01 mri_pretess N 4 e 2.34 S 0.00 U 1.84 P 78% M 40224 F 16 R 8835 W 0 c 326 w 18 I 3472 O 232 L 0.56 0.23 0.09
@#@FSLOADPOST 2020:09:22:20:25:03 mri_pretess N 4 0.56 0.23 0.09

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 139 vertices, 152 faces
slice 60: 3570 vertices, 3922 faces
slice 70: 21211 vertices, 21854 faces
slice 80: 46068 vertices, 47183 faces
slice 90: 79821 vertices, 81326 faces
slice 100: 114639 vertices, 116069 faces
slice 110: 148028 vertices, 149303 faces
slice 120: 175631 vertices, 176898 faces
slice 130: 195719 vertices, 196640 faces
slice 140: 208012 vertices, 208604 faces
slice 150: 212126 vertices, 212474 faces
slice 160: 212126 vertices, 212474 faces
slice 170: 212126 vertices, 212474 faces
slice 180: 212126 vertices, 212474 faces
slice 190: 212126 vertices, 212474 faces
slice 200: 212126 vertices, 212474 faces
slice 210: 212126 vertices, 212474 faces
slice 220: 212126 vertices, 212474 faces
slice 230: 212126 vertices, 212474 faces
slice 240: 212126 vertices, 212474 faces
slice 250: 212126 vertices, 212474 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:20:25:03 mri_tessellate N 3 e 2.49 S 0.01 U 2.41 P 97% M 44452 F 5 R 10162 W 0 c 119 w 8 I 1224 O 9960 L 0.56 0.23 0.09
@#@FSLOADPOST 2020:09:22:20:25:06 mri_tessellate N 3 0.60 0.24 0.09

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   212126 voxel in cpt #1: X=-348 [v=212126,e=637422,f=424948] located at (20.765221, -30.819216, 4.537186)
For the whole surface: X=-348 [v=212126,e=637422,f=424948]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:20:25:06 mris_extract_main_component N 2 e 1.63 S 0.13 U 1.42 P 95% M 421036 F 17 R 116785 W 0 c 124 w 23 I 4224 O 14936 L 0.60 0.24 0.09
@#@FSLOADPOST 2020:09:22:20:25:07 mris_extract_main_component N 2 0.60 0.24 0.09
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 22��� ��������� 20:25:07 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 2 (out of 82292: 0.002430)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:22:20:25:07 mri_pretess N 4 e 2.31 S 0.00 U 1.77 P 76% M 40292 F 0 R 8844 W 0 c 304 w 1 I 0 O 232 L 0.60 0.24 0.09
@#@FSLOADPOST 2020:09:22:20:25:10 mri_pretess N 4 0.60 0.24 0.09

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 564 vertices, 624 faces
slice 70: 4024 vertices, 4137 faces
slice 80: 9146 vertices, 9375 faces
slice 90: 16155 vertices, 16518 faces
slice 100: 27188 vertices, 27668 faces
slice 110: 37900 vertices, 38335 faces
slice 120: 46354 vertices, 46709 faces
slice 130: 51415 vertices, 51661 faces
slice 140: 54483 vertices, 54669 faces
slice 150: 55106 vertices, 55240 faces
slice 160: 55106 vertices, 55240 faces
slice 170: 55106 vertices, 55240 faces
slice 180: 55106 vertices, 55240 faces
slice 190: 55106 vertices, 55240 faces
slice 200: 55106 vertices, 55240 faces
slice 210: 55106 vertices, 55240 faces
slice 220: 55106 vertices, 55240 faces
slice 230: 55106 vertices, 55240 faces
slice 240: 55106 vertices, 55240 faces
slice 250: 55106 vertices, 55240 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:22:20:25:10 mri_tessellate N 3 e 2.33 S 0.00 U 2.26 P 97% M 30456 F 0 R 6655 W 0 c 119 w 1 I 0 O 2592 L 0.60 0.24 0.09
@#@FSLOADPOST 2020:09:22:20:25:12 mri_tessellate N 3 1.19 0.37 0.13

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   55106 voxel in cpt #1: X=-134 [v=55106,e=165720,f=110480] located at (56.160580, -28.860796, 54.764870)
For the whole surface: X=-134 [v=55106,e=165720,f=110480]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:22:20:25:12 mris_extract_main_component N 2 e 0.42 S 0.05 U 0.33 P 90% M 114220 F 0 R 30609 W 0 c 61 w 1 I 0 O 3888 L 1.19 0.37 0.13
@#@FSLOADPOST 2020:09:22:20:25:13 mris_extract_main_component N 2 1.19 0.37 0.13
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 22��� ��������� 20:25:13 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:20:25:13 mris_smooth N 5 e 6.31 S 0.13 U 6.08 P 98% M 338336 F 5 R 95852 W 0 c 282 w 7 I 1296 O 14936 L 1.19 0.37 0.13
@#@FSLOADPOST 2020:09:22:20:25:19 mris_smooth N 5 1.18 0.38 0.14
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 22��� ��������� 20:25:19 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:22:20:25:19 mris_smooth N 5 e 1.65 S 0.03 U 1.56 P 96% M 93560 F 0 R 25219 W 0 c 108 w 1 I 0 O 3888 L 1.18 0.38 0.14
@#@FSLOADPOST 2020:09:22:20:25:21 mris_smooth N 5 1.16 0.39 0.14
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 22��� ��������� 20:25:21 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 54.1 mm, total surface area = 118761 mm^2

step 000: RMS=0.152 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.107 (target=0.015)   
step 015: RMS=0.100 (target=0.015)   
step 020: RMS=0.095 (target=0.015)   
step 025: RMS=0.092 (target=0.015)   
step 030: RMS=0.090 (target=0.015)   
step 035: RMS=0.087 (target=0.015)   
step 040: RMS=0.086 (target=0.015)   
step 045: RMS=0.086 (target=0.015)   
step 050: RMS=0.086 (target=0.015)   
step 055: RMS=0.086 (target=0.015)   
step 060: RMS=0.086 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.6 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    33.017665
mris_inflate stimesec    0.131560
mris_inflate ru_maxrss   438552
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   120908
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  14936
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   1185
@#@FSTIME  2020:09:22:20:25:21 mris_inflate N 3 e 33.52 S 0.14 U 33.01 P 98% M 438864 F 19 R 120911 W 0 c 1190 w 22 I 4552 O 14936 L 1.16 0.39 0.14
@#@FSLOADPOST 2020:09:22:20:25:54 mris_inflate N 3 1.10 0.45 0.17
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 22��� ��������� 20:25:54 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 34.0 mm, total surface area = 31223 mm^2

step 000: RMS=0.159 (target=0.015)   
step 005: RMS=0.133 (target=0.015)   
step 010: RMS=0.117 (target=0.015)   
step 015: RMS=0.109 (target=0.015)   
step 020: RMS=0.106 (target=0.015)   
step 025: RMS=0.104 (target=0.015)   
step 030: RMS=0.103 (target=0.015)   
step 035: RMS=0.101 (target=0.015)   
step 040: RMS=0.100 (target=0.015)   
step 045: RMS=0.101 (target=0.015)   
step 050: RMS=0.101 (target=0.015)   
step 055: RMS=0.101 (target=0.015)   
step 060: RMS=0.101 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.1 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    8.343651
mris_inflate stimesec    0.039750
mris_inflate ru_maxrss   119972
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32983
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  3888
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   440
@#@FSTIME  2020:09:22:20:25:54 mris_inflate N 3 e 8.63 S 0.04 U 8.34 P 97% M 120164 F 0 R 32986 W 0 c 443 w 1 I 0 O 3888 L 1.10 0.45 0.17
@#@FSLOADPOST 2020:09:22:20:26:03 mris_inflate N 3 1.08 0.47 0.18
#--------------------------------------------
#@# QSphere lh 2020��� 09��� 22��� ��������� 20:26:03 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.279...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.578, avgs=0
005/300: dt: 0.9000, rms radial error=176.324, avgs=0
010/300: dt: 0.9000, rms radial error=175.777, avgs=0
015/300: dt: 0.9000, rms radial error=175.058, avgs=0
020/300: dt: 0.9000, rms radial error=174.240, avgs=0
025/300: dt: 0.9000, rms radial error=173.364, avgs=0
030/300: dt: 0.9000, rms radial error=172.457, avgs=0
035/300: dt: 0.9000, rms radial error=171.533, avgs=0
040/300: dt: 0.9000, rms radial error=170.601, avgs=0
045/300: dt: 0.9000, rms radial error=169.666, avgs=0
050/300: dt: 0.9000, rms radial error=168.732, avgs=0
055/300: dt: 0.9000, rms radial error=167.801, avgs=0
060/300: dt: 0.9000, rms radial error=166.872, avgs=0
065/300: dt: 0.9000, rms radial error=165.948, avgs=0
070/300: dt: 0.9000, rms radial error=165.028, avgs=0
075/300: dt: 0.9000, rms radial error=164.114, avgs=0
080/300: dt: 0.9000, rms radial error=163.205, avgs=0
085/300: dt: 0.9000, rms radial error=162.301, avgs=0
090/300: dt: 0.9000, rms radial error=161.402, avgs=0
095/300: dt: 0.9000, rms radial error=160.508, avgs=0
100/300: dt: 0.9000, rms radial error=159.620, avgs=0
105/300: dt: 0.9000, rms radial error=158.737, avgs=0
110/300: dt: 0.9000, rms radial error=157.859, avgs=0
115/300: dt: 0.9000, rms radial error=156.987, avgs=0
120/300: dt: 0.9000, rms radial error=156.120, avgs=0
125/300: dt: 0.9000, rms radial error=155.258, avgs=0
130/300: dt: 0.9000, rms radial error=154.402, avgs=0
135/300: dt: 0.9000, rms radial error=153.550, avgs=0
140/300: dt: 0.9000, rms radial error=152.704, avgs=0
145/300: dt: 0.9000, rms radial error=151.862, avgs=0
150/300: dt: 0.9000, rms radial error=151.026, avgs=0
155/300: dt: 0.9000, rms radial error=150.194, avgs=0
160/300: dt: 0.9000, rms radial error=149.368, avgs=0
165/300: dt: 0.9000, rms radial error=148.546, avgs=0
170/300: dt: 0.9000, rms radial error=147.728, avgs=0
175/300: dt: 0.9000, rms radial error=146.916, avgs=0
180/300: dt: 0.9000, rms radial error=146.108, avgs=0
185/300: dt: 0.9000, rms radial error=145.306, avgs=0
190/300: dt: 0.9000, rms radial error=144.508, avgs=0
195/300: dt: 0.9000, rms radial error=143.714, avgs=0
200/300: dt: 0.9000, rms radial error=142.925, avgs=0
205/300: dt: 0.9000, rms radial error=142.141, avgs=0
210/300: dt: 0.9000, rms radial error=141.362, avgs=0
215/300: dt: 0.9000, rms radial error=140.587, avgs=0
220/300: dt: 0.9000, rms radial error=139.816, avgs=0
225/300: dt: 0.9000, rms radial error=139.050, avgs=0
230/300: dt: 0.9000, rms radial error=138.289, avgs=0
235/300: dt: 0.9000, rms radial error=137.532, avgs=0
240/300: dt: 0.9000, rms radial error=136.779, avgs=0
245/300: dt: 0.9000, rms radial error=136.031, avgs=0
250/300: dt: 0.9000, rms radial error=135.287, avgs=0
255/300: dt: 0.9000, rms radial error=134.547, avgs=0
260/300: dt: 0.9000, rms radial error=133.812, avgs=0
265/300: dt: 0.9000, rms radial error=133.081, avgs=0
270/300: dt: 0.9000, rms radial error=132.354, avgs=0
275/300: dt: 0.9000, rms radial error=131.632, avgs=0
280/300: dt: 0.9000, rms radial error=130.913, avgs=0
285/300: dt: 0.9000, rms radial error=130.199, avgs=0
290/300: dt: 0.9000, rms radial error=129.489, avgs=0
295/300: dt: 0.9000, rms radial error=128.783, avgs=0
300/300: dt: 0.9000, rms radial error=128.082, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 0.72 +- 0.55 (0.00-->10.20) (max @ vno 26418 --> 26419)
face area 0.00 +- 0.03 (-0.78-->0.31)
epoch 1 (K=10.0), pass 1, starting sse = 29820.04
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00049
epoch 2 (K=40.0), pass 1, starting sse = 7981.93
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/13 = 0.00132
epoch 3 (K=160.0), pass 1, starting sse = 3093.00
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/13 = 0.00340
epoch 4 (K=640.0), pass 1, starting sse = 2208.96
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/13 = 0.00547
final distance error %100000.00
writing spherical brain to ../surf/lh.qsphere.nofix
mris_sphere utimesec    194.633977
mris_sphere stimesec    0.613999
mris_sphere ru_maxrss   1482392
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   532801
mris_sphere ru_majflt   85
mris_sphere ru_nswap    0
mris_sphere ru_inblock  15824
mris_sphere ru_oublock  14936
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    95
mris_sphere ru_nivcsw   8592
spherical transformation took 0.0549 hours
FSRUNTIME@ mris_sphere  0.0549 hours 1 threads
@#@FSTIME  2020:09:22:20:26:03 mris_sphere N 9 e 197.79 S 0.67 U 194.63 P 98% M 1484304 F 100 R 532808 W 0 c 8624 w 111 I 18400 O 14936 L 1.08 0.47 0.18
@#@FSLOADPOST 2020:09:22:20:29:21 mris_sphere N 9 1.01 0.75 0.35
#--------------------------------------------
#@# QSphere rh 2020��� 09��� 22��� ��������� 20:29:21 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.641...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=169.523, avgs=0
005/300: dt: 0.9000, rms radial error=169.279, avgs=0
010/300: dt: 0.9000, rms radial error=168.757, avgs=0
015/300: dt: 0.9000, rms radial error=168.075, avgs=0
020/300: dt: 0.9000, rms radial error=167.300, avgs=0
025/300: dt: 0.9000, rms radial error=166.471, avgs=0
030/300: dt: 0.9000, rms radial error=165.608, avgs=0
035/300: dt: 0.9000, rms radial error=164.726, avgs=0
040/300: dt: 0.9000, rms radial error=163.834, avgs=0
045/300: dt: 0.9000, rms radial error=162.936, avgs=0
050/300: dt: 0.9000, rms radial error=162.036, avgs=0
055/300: dt: 0.9000, rms radial error=161.139, avgs=0
060/300: dt: 0.9000, rms radial error=160.245, avgs=0
065/300: dt: 0.9000, rms radial error=159.354, avgs=0
070/300: dt: 0.9000, rms radial error=158.467, avgs=0
075/300: dt: 0.9000, rms radial error=157.582, avgs=0
080/300: dt: 0.9000, rms radial error=156.699, avgs=0
085/300: dt: 0.9000, rms radial error=155.820, avgs=0
090/300: dt: 0.9000, rms radial error=154.944, avgs=0
095/300: dt: 0.9000, rms radial error=154.071, avgs=0
100/300: dt: 0.9000, rms radial error=153.204, avgs=0
105/300: dt: 0.9000, rms radial error=152.341, avgs=0
110/300: dt: 0.9000, rms radial error=151.481, avgs=0
115/300: dt: 0.9000, rms radial error=150.625, avgs=0
120/300: dt: 0.9000, rms radial error=149.773, avgs=0
125/300: dt: 0.9000, rms radial error=148.926, avgs=0
130/300: dt: 0.9000, rms radial error=148.082, avgs=0
135/300: dt: 0.9000, rms radial error=147.242, avgs=0
140/300: dt: 0.9000, rms radial error=146.407, avgs=0
145/300: dt: 0.9000, rms radial error=145.575, avgs=0
150/300: dt: 0.9000, rms radial error=144.748, avgs=0
155/300: dt: 0.9000, rms radial error=143.925, avgs=0
160/300: dt: 0.9000, rms radial error=143.107, avgs=0
165/300: dt: 0.9000, rms radial error=142.292, avgs=0
170/300: dt: 0.9000, rms radial error=141.482, avgs=0
175/300: dt: 0.9000, rms radial error=140.676, avgs=0
180/300: dt: 0.9000, rms radial error=139.874, avgs=0
185/300: dt: 0.9000, rms radial error=139.077, avgs=0
190/300: dt: 0.9000, rms radial error=138.284, avgs=0
195/300: dt: 0.9000, rms radial error=137.495, avgs=0
200/300: dt: 0.9000, rms radial error=136.710, avgs=0
205/300: dt: 0.9000, rms radial error=135.929, avgs=0
210/300: dt: 0.9000, rms radial error=135.152, avgs=0
215/300: dt: 0.9000, rms radial error=134.380, avgs=0
220/300: dt: 0.9000, rms radial error=133.612, avgs=0
225/300: dt: 0.9000, rms radial error=132.848, avgs=0
230/300: dt: 0.9000, rms radial error=132.089, avgs=0
235/300: dt: 0.9000, rms radial error=131.333, avgs=0
240/300: dt: 0.9000, rms radial error=130.581, avgs=0
245/300: dt: 0.9000, rms radial error=129.834, avgs=0
250/300: dt: 0.9000, rms radial error=129.091, avgs=0
255/300: dt: 0.9000, rms radial error=128.351, avgs=0
260/300: dt: 0.9000, rms radial error=127.616, avgs=0
265/300: dt: 0.9000, rms radial error=126.885, avgs=0
270/300: dt: 0.9000, rms radial error=126.158, avgs=0
275/300: dt: 0.9000, rms radial error=125.435, avgs=0
280/300: dt: 0.9000, rms radial error=124.716, avgs=0
285/300: dt: 0.9000, rms radial error=124.001, avgs=0
290/300: dt: 0.9000, rms radial error=123.290, avgs=0
295/300: dt: 0.9000, rms radial error=122.583, avgs=0
300/300: dt: 0.9000, rms radial error=121.880, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.49 +- 1.00 (0.00-->10.50) (max @ vno 22738 --> 22739)
face area 0.12 +- 0.17 (-0.55-->3.51)
epoch 1 (K=10.0), pass 1, starting sse = 4588.96
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/13 = 0.00149
epoch 2 (K=40.0), pass 1, starting sse = 712.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/14 = 0.00733
epoch 3 (K=160.0), pass 1, starting sse = 122.79
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/17 = 0.00644
epoch 4 (K=640.0), pass 1, starting sse = 34.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.18/26 = 0.00706
final distance error %100000.00
writing spherical brain to ../surf/rh.qsphere.nofix
mris_sphere utimesec    62.109533
mris_sphere stimesec    0.194862
mris_sphere ru_maxrss   464484
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   159371
mris_sphere ru_majflt   32
mris_sphere ru_nswap    0
mris_sphere ru_inblock  9136
mris_sphere ru_oublock  3888
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    54
mris_sphere ru_nivcsw   4285
spherical transformation took 0.0176 hours
FSRUNTIME@ mris_sphere  0.0176 hours 1 threads
@#@FSTIME  2020:09:22:20:29:21 mris_sphere N 9 e 63.40 S 0.21 U 62.10 P 98% M 464628 F 32 R 159373 W 0 c 4292 w 55 I 9136 O 3888 L 1.01 0.75 0.35
@#@FSLOADPOST 2020:09:22:20:30:25 mris_sphere N 9 1.24 0.87 0.42
#@# Fix Topology lh 2020��� 09��� 22��� ��������� 20:30:25 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 lh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-348 (nv=212126, nf=424948, ne=637422, g=175)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 8 iterations
marking ambiguous vertices...
418769 ambiguous faces found in tessellation
segmenting defects...
1 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
1 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -10.3751  (-5.1876)
      -vertex     loglikelihood: -10.1021  (-5.0511)
      -normal dot loglikelihood: -3.6486  (-3.6486)
      -quad curv  loglikelihood: -9.3015  (-4.6508)
      Total Loglikelihood : -33.4273
CORRECTING DEFECT 0 (vertices=211954, convex hull=172, v0=0)
error: Cannot allocate memory
error: Excessive topologic defect encountered: could not allocate -680979643 edges for retessellation
Command exited with non-zero status 254
@#@FSTIME  2020:09:22:20:30:25 mris_fix_topology N 14 e 721.06 S 0.28 U 717.03 P 99% M 778356 F 22 R 219792 W 0 c 22096 w 33 I 20056 O 4992 L 1.24 0.87 0.42
@#@FSLOADPOST 2020:09:22:20:42:26 mris_fix_topology N 14 1.00 1.00 0.76
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s monkey2 exited with ERRORS at 2020��� 09��� 22��� ��������� 20:42:26 CST

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



#New# invocation of recon-all 



2020��� 09��� 23��� ��������� 15:13:13 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        548M        1.2G         15M        194M        1.3G
Swap:          2.0G        863M        1.2G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:13-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/23-07:13:14-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 23��� ��������� 15:13:14 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:23:15:13:14 mri_mask N 5 e 2.63 S 0.03 U 2.56 P 98% M 74136 F 5 R 17268 W 0 c 154 w 11 I 7152 O 2952 L 0.10 0.20 0.18
@#@FSLOADPOST 2020:09:23:15:13:17 mri_mask N 5 0.17 0.21 0.19
#--------------------------------------------
#@# Fill 2020��� 09��� 23��� ��������� 15:13:17 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 799 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 314563 voxels filled...
filling volume: pass 2 of 3...total of 16395737 voxels filled...
filling volume: pass 3 of 3...total of 314922 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 314563 voxels filled...
filling volume: pass 2 of 3...total of 16395737 voxels filled...
filling volume: pass 3 of 3...total of 314922 voxels filled...done.
filling degenerate left hemisphere surface locations...
1039 voxels filled
35 voxels filled
2 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
1039 voxels filled
35 voxels filled
2 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16394639 voxels filled...
filling volume: pass 3 of 3...total of 316020 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16394639 voxels filled...
filling volume: pass 3 of 3...total of 316020 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  315627 ambiguous voxels remaining
9:  47551 ambiguous voxels remaining
8:  22156 ambiguous voxels remaining
7:  13089 ambiguous voxels remaining
6:  5631 ambiguous voxels remaining
5:  3520 ambiguous voxels remaining
4:  1494 ambiguous voxels remaining
3:  538 ambiguous voxels remaining
2:  106 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.5 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:23:15:13:17 mri_fill N 12 e 33.18 S 0.08 U 32.39 P 97% M 111220 F 6 R 77591 W 0 c 1728 w 8 I 2208 O 224 L 0.17 0.21 0.19
@#@FSLOADPOST 2020:09:23:15:13:50 mri_fill N 12 0.63 0.32 0.22
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 23��� ��������� 15:13:50 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  12
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  12
pass   1 (+++):   0 found -   0 modified     |    TOTAL:  12
pass   1 (+++):   0 found -   0 modified     |    TOTAL:  12
pass   1 (+++):   0 found -   0 modified     |    TOTAL:  12
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   3
pass   1 (--):   0 found -   0 modified     |    TOTAL:   3
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 18 (out of 162917: 0.011049)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:23:15:13:50 mri_pretess N 4 e 2.67 S 0.01 U 2.13 P 80% M 40268 F 16 R 8830 W 0 c 410 w 18 I 3472 O 216 L 0.63 0.32 0.22
@#@FSLOADPOST 2020:09:23:15:13:53 mri_pretess N 4 0.66 0.33 0.23

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3129 vertices, 3285 faces
slice 70: 7210 vertices, 7405 faces
slice 80: 16943 vertices, 17454 faces
slice 90: 38558 vertices, 39384 faces
slice 100: 59488 vertices, 60333 faces
slice 110: 80988 vertices, 81724 faces
slice 120: 98824 vertices, 99539 faces
slice 130: 111066 vertices, 111557 faces
slice 140: 118355 vertices, 118651 faces
slice 150: 120678 vertices, 120836 faces
slice 160: 120678 vertices, 120836 faces
slice 170: 120678 vertices, 120836 faces
slice 180: 120678 vertices, 120836 faces
slice 190: 120678 vertices, 120836 faces
slice 200: 120678 vertices, 120836 faces
slice 210: 120678 vertices, 120836 faces
slice 220: 120678 vertices, 120836 faces
slice 230: 120678 vertices, 120836 faces
slice 240: 120678 vertices, 120836 faces
slice 250: 120678 vertices, 120836 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:23:15:13:53 mri_tessellate N 3 e 2.33 S 0.01 U 2.26 P 97% M 36740 F 5 R 8195 W 0 c 107 w 9 I 1232 O 5664 L 0.66 0.33 0.23
@#@FSLOADPOST 2020:09:23:15:13:55 mri_tessellate N 3 0.66 0.33 0.23

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   120678 voxel in cpt #1: X=-158 [v=120678,e=362508,f=241672] located at (-2.566234, -28.280191, 17.872969)
For the whole surface: X=-158 [v=120678,e=362508,f=241672]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:23:15:13:55 mris_extract_main_component N 2 e 0.88 S 0.09 U 0.73 P 94% M 242288 F 17 R 66536 W 0 c 85 w 23 I 4288 O 8496 L 0.66 0.33 0.23
@#@FSLOADPOST 2020:09:23:15:13:56 mris_extract_main_component N 2 0.66 0.33 0.23
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 23��� ��������� 15:13:56 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 14 (out of 153136: 0.009142)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:23:15:13:56 mri_pretess N 4 e 3.22 S 0.01 U 2.47 P 77% M 40516 F 0 R 8848 W 0 c 563 w 1 I 0 O 216 L 0.66 0.33 0.23
@#@FSLOADPOST 2020:09:23:15:13:59 mri_pretess N 4 0.68 0.34 0.23

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2417 vertices, 2544 faces
slice 70: 6053 vertices, 6225 faces
slice 80: 13940 vertices, 14391 faces
slice 90: 32904 vertices, 33614 faces
slice 100: 53575 vertices, 54420 faces
slice 110: 75999 vertices, 76790 faces
slice 120: 94146 vertices, 94858 faces
slice 130: 107024 vertices, 107524 faces
slice 140: 115356 vertices, 115667 faces
slice 150: 117936 vertices, 118088 faces
slice 160: 117936 vertices, 118088 faces
slice 170: 117936 vertices, 118088 faces
slice 180: 117936 vertices, 118088 faces
slice 190: 117936 vertices, 118088 faces
slice 200: 117936 vertices, 118088 faces
slice 210: 117936 vertices, 118088 faces
slice 220: 117936 vertices, 118088 faces
slice 230: 117936 vertices, 118088 faces
slice 240: 117936 vertices, 118088 faces
slice 250: 117936 vertices, 118088 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:23:15:13:59 mri_tessellate N 3 e 2.39 S 0.01 U 2.33 P 97% M 36420 F 0 R 8132 W 0 c 115 w 2 I 8 O 5536 L 0.68 0.34 0.23
@#@FSLOADPOST 2020:09:23:15:14:02 mri_tessellate N 3 0.71 0.35 0.24

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   117936 voxel in cpt #1: X=-152 [v=117936,e=354264,f=236176] located at (58.545815, -26.486408, 18.658577)
For the whole surface: X=-152 [v=117936,e=354264,f=236176]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:23:15:14:02 mris_extract_main_component N 2 e 0.80 S 0.06 U 0.70 P 95% M 236548 F 0 R 64987 W 0 c 86 w 1 I 0 O 8304 L 0.71 0.35 0.24
@#@FSLOADPOST 2020:09:23:15:14:03 mris_extract_main_component N 2 0.71 0.35 0.24
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 23��� ��������� 15:14:03 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:23:15:14:03 mris_smooth N 5 e 3.44 S 0.07 U 3.29 P 97% M 195144 F 5 R 54512 W 0 c 165 w 8 I 1304 O 8496 L 0.71 0.35 0.24
@#@FSLOADPOST 2020:09:23:15:14:06 mris_smooth N 5 0.71 0.35 0.24
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 23��� ��������� 15:14:06 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:23:15:14:06 mris_smooth N 5 e 3.37 S 0.06 U 3.22 P 97% M 190528 F 0 R 53190 W 0 c 181 w 2 I 8 O 8304 L 0.71 0.35 0.24
@#@FSLOADPOST 2020:09:23:15:14:10 mris_smooth N 5 0.73 0.37 0.24
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 23��� ��������� 15:14:10 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.9 mm, total surface area = 69721 mm^2

step 000: RMS=0.139 (target=0.015)   
step 005: RMS=0.112 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.086 (target=0.015)   
step 020: RMS=0.081 (target=0.015)   
step 025: RMS=0.077 (target=0.015)   
step 030: RMS=0.074 (target=0.015)   
step 035: RMS=0.072 (target=0.015)   
step 040: RMS=0.070 (target=0.015)   
step 045: RMS=0.069 (target=0.015)   
step 050: RMS=0.069 (target=0.015)   
step 055: RMS=0.069 (target=0.015)   
step 060: RMS=0.069 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.972277
mris_inflate stimesec    0.087856
mris_inflate ru_maxrss   253552
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   74057
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4560
mris_inflate ru_oublock  8496
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    22
mris_inflate ru_nivcsw   668
@#@FSTIME  2020:09:23:15:14:10 mris_inflate N 3 e 17.23 S 0.09 U 16.97 P 99% M 253664 F 19 R 74060 W 0 c 671 w 23 I 4560 O 8496 L 0.73 0.37 0.24
@#@FSLOADPOST 2020:09:23:15:14:27 mris_inflate N 3 0.81 0.41 0.26
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 23��� ��������� 15:14:27 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.6 mm, total surface area = 68246 mm^2

step 000: RMS=0.138 (target=0.015)   
step 005: RMS=0.112 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.075 (target=0.015)   
step 030: RMS=0.072 (target=0.015)   
step 035: RMS=0.071 (target=0.015)   
step 040: RMS=0.069 (target=0.015)   
step 045: RMS=0.068 (target=0.015)   
step 050: RMS=0.066 (target=0.015)   
step 055: RMS=0.067 (target=0.015)   
step 060: RMS=0.066 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.578860
mris_inflate stimesec    0.079706
mris_inflate ru_maxrss   246868
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   67270
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8304
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   696
@#@FSTIME  2020:09:23:15:14:27 mris_inflate N 3 e 16.83 S 0.08 U 16.57 P 99% M 247064 F 0 R 67272 W 0 c 700 w 1 I 0 O 8304 L 0.81 0.41 0.26
@#@FSLOADPOST 2020:09:23:15:14:44 mris_inflate N 3 0.85 0.44 0.27
#--------------------------------------------
#@# QSphere lh 2020��� 09��� 23��� ��������� 15:14:44 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.275...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=180.308, avgs=0
005/300: dt: 0.9000, rms radial error=180.051, avgs=0
010/300: dt: 0.9000, rms radial error=179.499, avgs=0
015/300: dt: 0.9000, rms radial error=178.773, avgs=0
020/300: dt: 0.9000, rms radial error=177.946, avgs=0
025/300: dt: 0.9000, rms radial error=177.061, avgs=0
030/300: dt: 0.9000, rms radial error=176.143, avgs=0
035/300: dt: 0.9000, rms radial error=175.207, avgs=0
040/300: dt: 0.9000, rms radial error=174.262, avgs=0
045/300: dt: 0.9000, rms radial error=173.313, avgs=0
050/300: dt: 0.9000, rms radial error=172.364, avgs=0
055/300: dt: 0.9000, rms radial error=171.417, avgs=0
060/300: dt: 0.9000, rms radial error=170.472, avgs=0
065/300: dt: 0.9000, rms radial error=169.530, avgs=0
070/300: dt: 0.9000, rms radial error=168.592, avgs=0
075/300: dt: 0.9000, rms radial error=167.658, avgs=0
080/300: dt: 0.9000, rms radial error=166.730, avgs=0
085/300: dt: 0.9000, rms radial error=165.810, avgs=0
090/300: dt: 0.9000, rms radial error=164.894, avgs=0
095/300: dt: 0.9000, rms radial error=163.983, avgs=0
100/300: dt: 0.9000, rms radial error=163.076, avgs=0
105/300: dt: 0.9000, rms radial error=162.174, avgs=0
110/300: dt: 0.9000, rms radial error=161.277, avgs=0
115/300: dt: 0.9000, rms radial error=160.384, avgs=0
120/300: dt: 0.9000, rms radial error=159.496, avgs=0
125/300: dt: 0.9000, rms radial error=158.613, avgs=0
130/300: dt: 0.9000, rms radial error=157.734, avgs=0
135/300: dt: 0.9000, rms radial error=156.859, avgs=0
140/300: dt: 0.9000, rms radial error=155.989, avgs=0
145/300: dt: 0.9000, rms radial error=155.124, avgs=0
150/300: dt: 0.9000, rms radial error=154.263, avgs=0
155/300: dt: 0.9000, rms radial error=153.407, avgs=0
160/300: dt: 0.9000, rms radial error=152.555, avgs=0
165/300: dt: 0.9000, rms radial error=151.707, avgs=0
170/300: dt: 0.9000, rms radial error=150.865, avgs=0
175/300: dt: 0.9000, rms radial error=150.026, avgs=0
180/300: dt: 0.9000, rms radial error=149.192, avgs=0
185/300: dt: 0.9000, rms radial error=148.363, avgs=0
190/300: dt: 0.9000, rms radial error=147.538, avgs=0
195/300: dt: 0.9000, rms radial error=146.717, avgs=0
200/300: dt: 0.9000, rms radial error=145.901, avgs=0
205/300: dt: 0.9000, rms radial error=145.090, avgs=0
210/300: dt: 0.9000, rms radial error=144.282, avgs=0
215/300: dt: 0.9000, rms radial error=143.479, avgs=0
220/300: dt: 0.9000, rms radial error=142.681, avgs=0
225/300: dt: 0.9000, rms radial error=141.887, avgs=0
230/300: dt: 0.9000, rms radial error=141.097, avgs=0
235/300: dt: 0.9000, rms radial error=140.311, avgs=0
240/300: dt: 0.9000, rms radial error=139.530, avgs=0
245/300: dt: 0.9000, rms radial error=138.753, avgs=0
250/300: dt: 0.9000, rms radial error=137.980, avgs=0
255/300: dt: 0.9000, rms radial error=137.212, avgs=0
260/300: dt: 0.9000, rms radial error=136.447, avgs=0
265/300: dt: 0.9000, rms radial error=135.687, avgs=0
270/300: dt: 0.9000, rms radial error=134.931, avgs=0
275/300: dt: 0.9000, rms radial error=134.179, avgs=0
280/300: dt: 0.9000, rms radial error=133.432, avgs=0
285/300: dt: 0.9000, rms radial error=132.688, avgs=0
290/300: dt: 0.9000, rms radial error=131.949, avgs=0
295/300: dt: 0.9000, rms radial error=131.214, avgs=0
300/300: dt: 0.9000, rms radial error=130.482, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.09 +- 0.81 (0.00-->15.83) (max @ vno 37527 --> 39563)
face area 0.02 +- 0.04 (-0.30-->2.20)
epoch 1 (K=10.0), pass 1, starting sse = 14615.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00021
epoch 2 (K=40.0), pass 1, starting sse = 2645.12
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00009
epoch 3 (K=160.0), pass 1, starting sse = 350.26
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/13 = 0.00205
epoch 4 (K=640.0), pass 1, starting sse = 45.85
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/15 = 0.00385
final distance error %100000.00
writing spherical brain to ../surf/lh.qsphere.nofix
mris_sphere utimesec    114.641412
mris_sphere stimesec    0.375049
mris_sphere ru_maxrss   873772
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   305231
mris_sphere ru_majflt   10
mris_sphere ru_nswap    0
mris_sphere ru_inblock  3080
mris_sphere ru_oublock  8504
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    12
mris_sphere ru_nivcsw   4108
spherical transformation took 0.0322 hours
FSRUNTIME@ mris_sphere  0.0322 hours 1 threads
@#@FSTIME  2020:09:23:15:14:44 mris_sphere N 9 e 115.99 S 0.40 U 114.64 P 99% M 873972 F 10 R 305234 W 0 c 4121 w 13 I 3080 O 8504 L 0.85 0.44 0.27
@#@FSLOADPOST 2020:09:23:15:16:40 mris_sphere N 9 0.98 0.62 0.36
#--------------------------------------------
#@# QSphere rh 2020��� 09��� 23��� ��������� 15:16:40 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.275...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=180.540, avgs=0
005/300: dt: 0.9000, rms radial error=180.283, avgs=0
010/300: dt: 0.9000, rms radial error=179.733, avgs=0
015/300: dt: 0.9000, rms radial error=179.010, avgs=0
020/300: dt: 0.9000, rms radial error=178.187, avgs=0
025/300: dt: 0.9000, rms radial error=177.306, avgs=0
030/300: dt: 0.9000, rms radial error=176.392, avgs=0
035/300: dt: 0.9000, rms radial error=175.459, avgs=0
040/300: dt: 0.9000, rms radial error=174.519, avgs=0
045/300: dt: 0.9000, rms radial error=173.575, avgs=0
050/300: dt: 0.9000, rms radial error=172.632, avgs=0
055/300: dt: 0.9000, rms radial error=171.690, avgs=0
060/300: dt: 0.9000, rms radial error=170.751, avgs=0
065/300: dt: 0.9000, rms radial error=169.816, avgs=0
070/300: dt: 0.9000, rms radial error=168.884, avgs=0
075/300: dt: 0.9000, rms radial error=167.957, avgs=0
080/300: dt: 0.9000, rms radial error=167.033, avgs=0
085/300: dt: 0.9000, rms radial error=166.115, avgs=0
090/300: dt: 0.9000, rms radial error=165.200, avgs=0
095/300: dt: 0.9000, rms radial error=164.290, avgs=0
100/300: dt: 0.9000, rms radial error=163.385, avgs=0
105/300: dt: 0.9000, rms radial error=162.483, avgs=0
110/300: dt: 0.9000, rms radial error=161.587, avgs=0
115/300: dt: 0.9000, rms radial error=160.694, avgs=0
120/300: dt: 0.9000, rms radial error=159.806, avgs=0
125/300: dt: 0.9000, rms radial error=158.923, avgs=0
130/300: dt: 0.9000, rms radial error=158.044, avgs=0
135/300: dt: 0.9000, rms radial error=157.169, avgs=0
140/300: dt: 0.9000, rms radial error=156.299, avgs=0
145/300: dt: 0.9000, rms radial error=155.433, avgs=0
150/300: dt: 0.9000, rms radial error=154.572, avgs=0
155/300: dt: 0.9000, rms radial error=153.715, avgs=0
160/300: dt: 0.9000, rms radial error=152.863, avgs=0
165/300: dt: 0.9000, rms radial error=152.015, avgs=0
170/300: dt: 0.9000, rms radial error=151.172, avgs=0
175/300: dt: 0.9000, rms radial error=150.333, avgs=0
180/300: dt: 0.9000, rms radial error=149.498, avgs=0
185/300: dt: 0.9000, rms radial error=148.668, avgs=0
190/300: dt: 0.9000, rms radial error=147.842, avgs=0
195/300: dt: 0.9000, rms radial error=147.021, avgs=0
200/300: dt: 0.9000, rms radial error=146.204, avgs=0
205/300: dt: 0.9000, rms radial error=145.391, avgs=0
210/300: dt: 0.9000, rms radial error=144.582, avgs=0
215/300: dt: 0.9000, rms radial error=143.778, avgs=0
220/300: dt: 0.9000, rms radial error=142.979, avgs=0
225/300: dt: 0.9000, rms radial error=142.183, avgs=0
230/300: dt: 0.9000, rms radial error=141.392, avgs=0
235/300: dt: 0.9000, rms radial error=140.605, avgs=0
240/300: dt: 0.9000, rms radial error=139.823, avgs=0
245/300: dt: 0.9000, rms radial error=139.044, avgs=0
250/300: dt: 0.9000, rms radial error=138.270, avgs=0
255/300: dt: 0.9000, rms radial error=137.500, avgs=0
260/300: dt: 0.9000, rms radial error=136.735, avgs=0
265/300: dt: 0.9000, rms radial error=135.973, avgs=0
270/300: dt: 0.9000, rms radial error=135.216, avgs=0
275/300: dt: 0.9000, rms radial error=134.463, avgs=0
280/300: dt: 0.9000, rms radial error=133.713, avgs=0
285/300: dt: 0.9000, rms radial error=132.968, avgs=0
290/300: dt: 0.9000, rms radial error=132.228, avgs=0
295/300: dt: 0.9000, rms radial error=131.491, avgs=0
300/300: dt: 0.9000, rms radial error=130.758, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.11 +- 0.81 (0.00-->13.83) (max @ vno 31811 --> 31819)
face area 0.02 +- 0.04 (-0.21-->1.62)
epoch 1 (K=10.0), pass 1, starting sse = 14246.05
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00023
epoch 2 (K=40.0), pass 1, starting sse = 2572.82
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00011
epoch 3 (K=160.0), pass 1, starting sse = 347.06
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/13 = 0.00244
epoch 4 (K=640.0), pass 1, starting sse = 46.31
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/16 = 0.00442
final distance error %100000.00
writing spherical brain to ../surf/rh.qsphere.nofix
mris_sphere utimesec    115.672122
mris_sphere stimesec    0.338918
mris_sphere ru_maxrss   862848
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   302277
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  8
mris_sphere ru_oublock  8304
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    1
mris_sphere ru_nivcsw   4198
spherical transformation took 0.0326 hours
FSRUNTIME@ mris_sphere  0.0326 hours 1 threads
@#@FSTIME  2020:09:23:15:16:40 mris_sphere N 9 e 117.29 S 0.36 U 115.67 P 98% M 862920 F 0 R 302279 W 0 c 4206 w 2 I 8 O 8304 L 0.98 0.62 0.36
@#@FSLOADPOST 2020:09:23:15:18:37 mris_sphere N 9 1.00 0.75 0.44
#@# Fix Topology lh 2020��� 09��� 23��� ��������� 15:18:37 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 lh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-158 (nv=120678, nf=241672, ne=362508, g=80)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
25754 ambiguous faces found in tessellation
segmenting defects...
49 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 9 into 5
      -merging segment 28 into 5
      -merging segment 12 into 11
      -merging segment 38 into 30
      -merging segment 44 into 30
      -merging segment 5 into 31
      -merging segment 40 into 39
42 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7439  (-4.8720)
      -vertex     loglikelihood: -6.8581  (-3.4291)
      -normal dot loglikelihood: -3.4212  (-3.4212)
      -quad curv  loglikelihood: -5.4044  (-2.7022)
      Total Loglikelihood : -25.4276
CORRECTING DEFECT 0 (vertices=1808, convex hull=605, v0=0)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 0 (v0=0), euler #=-42 (106629,317308,210637) : difference with theory (-39) = 3 
CORRECTING DEFECT 1 (vertices=16, convex hull=24, v0=137)
After retessellation of defect 1 (v0=137), euler #=-41 (106632,317327,210654) : difference with theory (-38) = 3 
CORRECTING DEFECT 2 (vertices=648, convex hull=273, v0=541)
After retessellation of defect 2 (v0=541), euler #=-41 (106733,317768,210994) : difference with theory (-37) = 4 
CORRECTING DEFECT 3 (vertices=23, convex hull=27, v0=3951)
After retessellation of defect 3 (v0=3951), euler #=-40 (106740,317797,211017) : difference with theory (-36) = 4 
CORRECTING DEFECT 4 (vertices=20, convex hull=30, v0=4046)
After retessellation of defect 4 (v0=4046), euler #=-39 (106743,317814,211032) : difference with theory (-35) = 4 
CORRECTING DEFECT 5 (vertices=1124, convex hull=258, v0=8364)
normal vector of length zero at vertex 109793 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109963 with 4 faces
normal vector of length zero at vertex 109963 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109807 with 5 faces
normal vector of length zero at vertex 109807 with 5 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109414 with 4 faces
normal vector of length zero at vertex 109807 with 5 faces
normal vector of length zero at vertex 109963 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109831 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109806 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109806 with 3 faces
normal vector of length zero at vertex 109809 with 6 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109887 with 4 faces
normal vector of length zero at vertex 109887 with 4 faces
normal vector of length zero at vertex 109887 with 4 faces
normal vector of length zero at vertex 109887 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109809 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109862 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109814 with 5 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109814 with 3 faces
normal vector of length zero at vertex 109808 with 4 faces
normal vector of length zero at vertex 109808 with 4 faces
After retessellation of defect 5 (v0=8364), euler #=-38 (106855,318288,211395) : difference with theory (-34) = 4 
CORRECTING DEFECT 6 (vertices=31, convex hull=71, v0=11183)
After retessellation of defect 6 (v0=11183), euler #=-37 (106875,318381,211469) : difference with theory (-33) = 4 
CORRECTING DEFECT 7 (vertices=26, convex hull=51, v0=11235)
After retessellation of defect 7 (v0=11235), euler #=-36 (106888,318439,211515) : difference with theory (-32) = 4 
CORRECTING DEFECT 8 (vertices=7, convex hull=23, v0=18503)
After retessellation of defect 8 (v0=18503), euler #=-35 (106889,318449,211525) : difference with theory (-31) = 4 
CORRECTING DEFECT 9 (vertices=3808, convex hull=555, v0=18712)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 110652 with 4 faces
normal vector of length zero at vertex 110652 with 4 faces
normal vector of length zero at vertex 112364 with 4 faces
normal vector of length zero at vertex 110652 with 4 faces
normal vector of length zero at vertex 110449 with 4 faces
normal vector of length zero at vertex 110747 with 4 faces
normal vector of length zero at vertex 110652 with 4 faces
normal vector of length zero at vertex 110652 with 4 faces
normal vector of length zero at vertex 110450 with 4 faces
normal vector of length zero at vertex 113545 with 5 faces
normal vector of length zero at vertex 113545 with 8 faces
normal vector of length zero at vertex 110450 with 4 faces
normal vector of length zero at vertex 113454 with 4 faces
normal vector of length zero at vertex 113818 with 6 faces
normal vector of length zero at vertex 113454 with 4 faces
normal vector of length zero at vertex 110450 with 4 faces
normal vector of length zero at vertex 113454 with 4 faces
normal vector of length zero at vertex 113818 with 6 faces
normal vector of length zero at vertex 113454 with 4 faces
normal vector of length zero at vertex 113545 with 4 faces
normal vector of length zero at vertex 113454 with 4 faces
normal vector of length zero at vertex 113818 with 6 faces
normal vector of length zero at vertex 113454 with 4 faces
normal vector of length zero at vertex 110505 with 4 faces
normal vector of length zero at vertex 110505 with 4 faces
normal vector of length zero at vertex 110557 with 4 faces
normal vector of length zero at vertex 111596 with 4 faces
normal vector of length zero at vertex 110505 with 4 faces
normal vector of length zero at vertex 110501 with 4 faces
normal vector of length zero at vertex 110501 with 4 faces
normal vector of length zero at vertex 110652 with 4 faces
normal vector of length zero at vertex 110652 with 4 faces
After retessellation of defect 9 (v0=18712), euler #=-33 (107868,321684,213783) : difference with theory (-30) = 3 
CORRECTING DEFECT 10 (vertices=450, convex hull=342, v0=21637)
After retessellation of defect 10 (v0=21637), euler #=-32 (108061,322433,214340) : difference with theory (-29) = 3 
CORRECTING DEFECT 11 (vertices=279, convex hull=102, v0=24505)
After retessellation of defect 11 (v0=24505), euler #=-31 (108137,322709,214541) : difference with theory (-28) = 3 
CORRECTING DEFECT 12 (vertices=159, convex hull=123, v0=25351)
After retessellation of defect 12 (v0=25351), euler #=-31 (108189,322931,214711) : difference with theory (-27) = 4 
CORRECTING DEFECT 13 (vertices=28, convex hull=54, v0=25896)
After retessellation of defect 13 (v0=25896), euler #=-30 (108197,322976,214749) : difference with theory (-26) = 4 
CORRECTING DEFECT 14 (vertices=162, convex hull=119, v0=26991)
normal vector of length zero at vertex 114873 with 3 faces
normal vector of length zero at vertex 25086 with 4 faces
normal vector of length zero at vertex 25086 with 4 faces
normal vector of length zero at vertex 25086 with 4 faces
normal vector of length zero at vertex 25086 with 4 faces
normal vector of length zero at vertex 114873 with 3 faces
normal vector of length zero at vertex 114873 with 3 faces
After retessellation of defect 14 (v0=26991), euler #=-29 (108216,323091,214846) : difference with theory (-25) = 4 
CORRECTING DEFECT 15 (vertices=7, convex hull=33, v0=28353)
After retessellation of defect 15 (v0=28353), euler #=-28 (108220,323112,214864) : difference with theory (-24) = 4 
CORRECTING DEFECT 16 (vertices=183, convex hull=51, v0=31334)
After retessellation of defect 16 (v0=31334), euler #=-27 (108229,323159,214903) : difference with theory (-23) = 4 
CORRECTING DEFECT 17 (vertices=21, convex hull=18, v0=32561)
After retessellation of defect 17 (v0=32561), euler #=-26 (108232,323175,214917) : difference with theory (-22) = 4 
CORRECTING DEFECT 18 (vertices=461, convex hull=144, v0=33707)
After retessellation of defect 18 (v0=33707), euler #=-25 (108312,323485,215148) : difference with theory (-21) = 4 
CORRECTING DEFECT 19 (vertices=700, convex hull=154, v0=34065)
After retessellation of defect 19 (v0=34065), euler #=-25 (108368,323734,215341) : difference with theory (-20) = 5 
CORRECTING DEFECT 20 (vertices=26, convex hull=50, v0=34445)
After retessellation of defect 20 (v0=34445), euler #=-24 (108386,323808,215398) : difference with theory (-19) = 5 
CORRECTING DEFECT 21 (vertices=22, convex hull=30, v0=34835)
After retessellation of defect 21 (v0=34835), euler #=-23 (108388,323824,215413) : difference with theory (-18) = 5 
CORRECTING DEFECT 22 (vertices=212, convex hull=147, v0=36238)
After retessellation of defect 22 (v0=36238), euler #=-22 (108485,324180,215673) : difference with theory (-17) = 5 
CORRECTING DEFECT 23 (vertices=135, convex hull=75, v0=36390)
After retessellation of defect 23 (v0=36390), euler #=-21 (108518,324310,215771) : difference with theory (-16) = 5 
CORRECTING DEFECT 24 (vertices=135, convex hull=62, v0=38301)
After retessellation of defect 24 (v0=38301), euler #=-20 (108541,324406,215845) : difference with theory (-15) = 5 
CORRECTING DEFECT 25 (vertices=40, convex hull=48, v0=41250)
After retessellation of defect 25 (v0=41250), euler #=-19 (108570,324513,215924) : difference with theory (-14) = 5 
CORRECTING DEFECT 26 (vertices=847, convex hull=570, v0=41625)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 26 (v0=41625), euler #=-17 (108984,326092,217091) : difference with theory (-13) = 4 
CORRECTING DEFECT 27 (vertices=1970, convex hull=1026, v0=43094)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 27 (v0=43094), euler #=-13 (109615,328537,218909) : difference with theory (-12) = 1 
CORRECTING DEFECT 28 (vertices=6, convex hull=18, v0=43163)
After retessellation of defect 28 (v0=43163), euler #=-12 (109617,328548,218919) : difference with theory (-11) = 1 
CORRECTING DEFECT 29 (vertices=28, convex hull=32, v0=43528)
After retessellation of defect 29 (v0=43528), euler #=-11 (109622,328571,218938) : difference with theory (-10) = 1 
CORRECTING DEFECT 30 (vertices=8, convex hull=22, v0=45077)
After retessellation of defect 30 (v0=45077), euler #=-10 (109624,328583,218949) : difference with theory (-9) = 1 
CORRECTING DEFECT 31 (vertices=35, convex hull=55, v0=46198)
After retessellation of defect 31 (v0=46198), euler #=-9 (109634,328633,218990) : difference with theory (-8) = 1 
CORRECTING DEFECT 32 (vertices=425, convex hull=199, v0=49798)
After retessellation of defect 32 (v0=49798), euler #=-8 (109730,329012,219274) : difference with theory (-7) = 1 
CORRECTING DEFECT 33 (vertices=29, convex hull=59, v0=50367)
After retessellation of defect 33 (v0=50367), euler #=-7 (109744,329074,219323) : difference with theory (-6) = 1 
CORRECTING DEFECT 34 (vertices=37, convex hull=60, v0=58282)
After retessellation of defect 34 (v0=58282), euler #=-5 (109758,329138,219375) : difference with theory (-5) = 0 
CORRECTING DEFECT 35 (vertices=81, convex hull=71, v0=59439)
After retessellation of defect 35 (v0=59439), euler #=-4 (109773,329213,219436) : difference with theory (-4) = 0 
CORRECTING DEFECT 36 (vertices=15, convex hull=39, v0=59738)
After retessellation of defect 36 (v0=59738), euler #=-3 (109775,329232,219454) : difference with theory (-3) = 0 
CORRECTING DEFECT 37 (vertices=102, convex hull=39, v0=62637)
After retessellation of defect 37 (v0=62637), euler #=-2 (109785,329280,219493) : difference with theory (-2) = 0 
CORRECTING DEFECT 38 (vertices=66, convex hull=53, v0=68910)
After retessellation of defect 38 (v0=68910), euler #=-1 (109798,329339,219540) : difference with theory (-1) = 0 
CORRECTING DEFECT 39 (vertices=54, convex hull=32, v0=77891)
After retessellation of defect 39 (v0=77891), euler #=0 (109807,329376,219569) : difference with theory (0) = 0 
CORRECTING DEFECT 40 (vertices=69, convex hull=78, v0=82808)
After retessellation of defect 40 (v0=82808), euler #=1 (109825,329463,219639) : difference with theory (1) = 0 
CORRECTING DEFECT 41 (vertices=5, convex hull=23, v0=114105)
After retessellation of defect 41 (v0=114105), euler #=2 (109827,329475,219650) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.92 +- 0.36 (0.03-->19.56) (max @ vno 14501 --> 17833)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.92 +- 0.36 (0.03-->19.56) (max @ vno 14501 --> 17833)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
144 mutations (36.7%), 248 crossovers (63.3%), 487 vertices were eliminated
building final representation...
10851 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=109827, nf=219650, ne=329475, g=0)
writing corrected surface to /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.premesh...

0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 2000 intersecting
001: 505 intersecting
002: 123 intersecting
003: 54 intersecting
004: 49 intersecting
005: 43 intersecting
step 1 with no progress (num=43, old_num=43)
006: 43 intersecting
step 2 with no progress (num=43, old_num=43)
007: 43 intersecting
step 3 with no progress (num=43, old_num=43)
008: 43 intersecting
step 4 with no progress (num=43, old_num=43)
009: 43 intersecting
step 5 with no progress (num=43, old_num=43)
010: 43 intersecting
step 6 with no progress (num=43, old_num=43)
011: 43 intersecting
step 7 with no progress (num=43, old_num=43)
012: 43 intersecting
step 8 with no progress (num=43, old_num=43)
013: 43 intersecting
step 9 with no progress (num=43, old_num=43)
014: 43 intersecting
step 10 with no progress (num=43, old_num=43)
015: 43 intersecting
step 11 with no progress (num=43, old_num=43)
016: 43 intersecting
step 12 with no progress (num=43, old_num=43)
017: 43 intersecting
step 13 with no progress (num=43, old_num=43)
018: 43 intersecting
step 14 with no progress (num=43, old_num=43)
019: 43 intersecting
step 15 with no progress (num=43, old_num=43)
020: 43 intersecting
step 16 with no progress (num=43, old_num=43)
terminating search with 43 intersecting
topology fixing took 9.6 minutes
FSRUNTIME@ mris_fix_topology lh  0.1604 hours 1 threads
#VMPC# mris_fix_topology VmPeak  773060
@#@FSTIME  2020:09:23:15:18:37 mris_fix_topology N 14 e 577.65 S 0.31 U 573.87 P 99% M 724872 F 8 R 200603 W 0 c 17689 w 10 I 2000 O 10560 L 1.00 0.75 0.44
@#@FSLOADPOST 2020:09:23:15:28:15 mris_fix_topology N 14 1.00 0.97 0.72
#@# Fix Topology rh 2020��� 09��� 23��� ��������� 15:28:15 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 rh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-152 (nv=117936, nf=236176, ne=354264, g=77)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
25363 ambiguous faces found in tessellation
segmenting defects...
46 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 0 into 2
      -merging segment 20 into 8
      -merging segment 25 into 23
      -merging segment 34 into 28
      -merging segment 28 into 43
41 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -9.9916  (-4.9958)
      -vertex     loglikelihood: -7.0107  (-3.5054)
      -normal dot loglikelihood: -3.5054  (-3.5054)
      -quad curv  loglikelihood: -5.3990  (-2.6995)
      Total Loglikelihood : -25.9067
CORRECTING DEFECT 0 (vertices=1507, convex hull=558, v0=32)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 0 (v0=32), euler #=-33 (104133,309620,205454) : difference with theory (-38) = -5 
CORRECTING DEFECT 1 (vertices=158, convex hull=63, v0=279)
After retessellation of defect 1 (v0=279), euler #=-31 (104147,309686,205508) : difference with theory (-37) = -6 
CORRECTING DEFECT 2 (vertices=29, convex hull=33, v0=1416)
After retessellation of defect 2 (v0=1416), euler #=-30 (104151,309707,205526) : difference with theory (-36) = -6 
CORRECTING DEFECT 3 (vertices=49, convex hull=27, v0=1966)
After retessellation of defect 3 (v0=1966), euler #=-29 (104161,309746,205556) : difference with theory (-35) = -6 
CORRECTING DEFECT 4 (vertices=89, convex hull=134, v0=2207)
After retessellation of defect 4 (v0=2207), euler #=-28 (104229,310006,205749) : difference with theory (-34) = -6 
CORRECTING DEFECT 5 (vertices=14, convex hull=23, v0=2428)
After retessellation of defect 5 (v0=2428), euler #=-27 (104232,310023,205764) : difference with theory (-33) = -6 
CORRECTING DEFECT 6 (vertices=35, convex hull=27, v0=4795)
After retessellation of defect 6 (v0=4795), euler #=-26 (104239,310052,205787) : difference with theory (-32) = -6 
CORRECTING DEFECT 7 (vertices=2560, convex hull=1229, v0=6060)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 7 (v0=6060), euler #=-29 (104713,312146,207404) : difference with theory (-31) = -2 
CORRECTING DEFECT 8 (vertices=1034, convex hull=290, v0=7531)
After retessellation of defect 8 (v0=7531), euler #=-29 (104889,312831,207913) : difference with theory (-30) = -1 
CORRECTING DEFECT 9 (vertices=163, convex hull=177, v0=9930)
After retessellation of defect 9 (v0=9930), euler #=-28 (104943,313071,208100) : difference with theory (-29) = -1 
CORRECTING DEFECT 10 (vertices=21, convex hull=59, v0=9943)
After retessellation of defect 10 (v0=9943), euler #=-27 (104954,313128,208147) : difference with theory (-28) = -1 
CORRECTING DEFECT 11 (vertices=34, convex hull=60, v0=12260)
After retessellation of defect 11 (v0=12260), euler #=-26 (104975,313215,208214) : difference with theory (-27) = -1 
CORRECTING DEFECT 12 (vertices=125, convex hull=146, v0=12300)
After retessellation of defect 12 (v0=12300), euler #=-26 (105032,313462,208404) : difference with theory (-26) = 0 
CORRECTING DEFECT 13 (vertices=3483, convex hull=329, v0=15536)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 111555 with 4 faces
normal vector of length zero at vertex 19886 with 6 faces
normal vector of length zero at vertex 111555 with 4 faces
normal vector of length zero at vertex 111640 with 4 faces
normal vector of length zero at vertex 110303 with 4 faces
normal vector of length zero at vertex 111089 with 8 faces
normal vector of length zero at vertex 111302 with 6 faces
normal vector of length zero at vertex 111364 with 6 faces
normal vector of length zero at vertex 111407 with 4 faces
normal vector of length zero at vertex 111089 with 8 faces
normal vector of length zero at vertex 111302 with 6 faces
normal vector of length zero at vertex 111364 with 6 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111158 with 8 faces
normal vector of length zero at vertex 111158 with 8 faces
normal vector of length zero at vertex 109823 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111145 with 6 faces
normal vector of length zero at vertex 111284 with 8 faces
normal vector of length zero at vertex 111413 with 4 faces
normal vector of length zero at vertex 109823 with 4 faces
normal vector of length zero at vertex 111413 with 4 faces
normal vector of length zero at vertex 109823 with 4 faces
normal vector of length zero at vertex 111413 with 4 faces
normal vector of length zero at vertex 109823 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111158 with 8 faces
normal vector of length zero at vertex 111158 with 8 faces
normal vector of length zero at vertex 111088 with 4 faces
normal vector of length zero at vertex 111150 with 4 faces
normal vector of length zero at vertex 111235 with 6 faces
normal vector of length zero at vertex 111735 with 4 faces
normal vector of length zero at vertex 112296 with 6 faces
normal vector of length zero at vertex 111150 with 4 faces
normal vector of length zero at vertex 111235 with 6 faces
normal vector of length zero at vertex 111735 with 4 faces
normal vector of length zero at vertex 109787 with 6 faces
normal vector of length zero at vertex 112229 with 4 faces
normal vector of length zero at vertex 109749 with 4 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 110334 with 4 faces
normal vector of length zero at vertex 111090 with 4 faces
normal vector of length zero at vertex 109749 with 4 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 109749 with 4 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 109749 with 4 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 109749 with 4 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 109749 with 4 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 110100 with 6 faces
normal vector of length zero at vertex 19776 with 4 faces
normal vector of length zero at vertex 19776 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 110338 with 4 faces
normal vector of length zero at vertex 110991 with 4 faces
normal vector of length zero at vertex 111050 with 4 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111145 with 4 faces
normal vector of length zero at vertex 111182 with 4 faces
normal vector of length zero at vertex 111284 with 8 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111145 with 4 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111145 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111188 with 6 faces
normal vector of length zero at vertex 112237 with 4 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111188 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111358 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 112567 with 4 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111358 with 6 faces
normal vector of length zero at vertex 112567 with 4 faces
normal vector of length zero at vertex 111966 with 4 faces
normal vector of length zero at vertex 111966 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111033 with 4 faces
normal vector of length zero at vertex 110338 with 4 faces
normal vector of length zero at vertex 111083 with 4 faces
normal vector of length zero at vertex 111084 with 4 faces
normal vector of length zero at vertex 111108 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111145 with 4 faces
normal vector of length zero at vertex 111108 with 6 faces
normal vector of length zero at vertex 111145 with 4 faces
normal vector of length zero at vertex 111108 with 6 faces
normal vector of length zero at vertex 111846 with 4 faces
normal vector of length zero at vertex 111108 with 6 faces
normal vector of length zero at vertex 111846 with 4 faces
normal vector of length zero at vertex 111482 with 4 faces
normal vector of length zero at vertex 111482 with 4 faces
normal vector of length zero at vertex 111482 with 4 faces
normal vector of length zero at vertex 111482 with 4 faces
normal vector of length zero at vertex 111482 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 111110 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111736 with 3 faces
normal vector of length zero at vertex 111740 with 5 faces
normal vector of length zero at vertex 111741 with 4 faces
normal vector of length zero at vertex 111846 with 5 faces
normal vector of length zero at vertex 111847 with 4 faces
normal vector of length zero at vertex 112567 with 4 faces
normal vector of length zero at vertex 111109 with 6 faces
normal vector of length zero at vertex 111110 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111110 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 111042 with 6 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111632 with 8 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 110213 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111359 with 4 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 15695 with 4 faces
normal vector of length zero at vertex 110213 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111359 with 4 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 4 faces
normal vector of length zero at vertex 111359 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111039 with 4 faces
normal vector of length zero at vertex 111187 with 4 faces
normal vector of length zero at vertex 111232 with 4 faces
normal vector of length zero at vertex 111286 with 4 faces
normal vector of length zero at vertex 111039 with 4 faces
normal vector of length zero at vertex 111187 with 4 faces
normal vector of length zero at vertex 111232 with 4 faces
normal vector of length zero at vertex 111286 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 112293 with 4 faces
normal vector of length zero at vertex 112567 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111636 with 4 faces
normal vector of length zero at vertex 111741 with 4 faces
normal vector of length zero at vertex 112294 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111636 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111636 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111089 with 6 faces
normal vector of length zero at vertex 111302 with 4 faces
normal vector of length zero at vertex 112294 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111345 with 6 faces
normal vector of length zero at vertex 111741 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111090 with 4 faces
normal vector of length zero at vertex 111158 with 6 faces
normal vector of length zero at vertex 111636 with 4 faces
normal vector of length zero at vertex 111636 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111345 with 6 faces
normal vector of length zero at vertex 111741 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111032 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111735 with 4 faces
normal vector of length zero at vertex 111741 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111735 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111735 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111140 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111345 with 6 faces
normal vector of length zero at vertex 111485 with 4 faces
normal vector of length zero at vertex 111847 with 6 faces
normal vector of length zero at vertex 110233 with 4 faces
normal vector of length zero at vertex 111021 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111080 with 4 faces
normal vector of length zero at vertex 111284 with 4 faces
normal vector of length zero at vertex 111299 with 6 faces
normal vector of length zero at vertex 111021 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111345 with 6 faces
normal vector of length zero at vertex 111485 with 4 faces
normal vector of length zero at vertex 111847 with 6 faces
normal vector of length zero at vertex 111012 with 4 faces
normal vector of length zero at vertex 111345 with 4 faces
normal vector of length zero at vertex 112098 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111346 with 4 faces
normal vector of length zero at vertex 111346 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111348 with 4 faces
normal vector of length zero at vertex 111736 with 4 faces
normal vector of length zero at vertex 111244 with 4 faces
normal vector of length zero at vertex 111348 with 4 faces
normal vector of length zero at vertex 111023 with 6 faces
normal vector of length zero at vertex 111346 with 4 faces
normal vector of length zero at vertex 111346 with 4 faces
normal vector of length zero at vertex 110583 with 4 faces
normal vector of length zero at vertex 111020 with 4 faces
normal vector of length zero at vertex 111037 with 4 faces
normal vector of length zero at vertex 111346 with 4 faces
normal vector of length zero at vertex 110583 with 4 faces
normal vector of length zero at vertex 111020 with 4 faces
normal vector of length zero at vertex 111346 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
normal vector of length zero at vertex 111084 with 6 faces
normal vector of length zero at vertex 111109 with 4 faces
normal vector of length zero at vertex 111110 with 6 faces
normal vector of length zero at vertex 111733 with 4 faces
After retessellation of defect 13 (v0=15536), euler #=-25 (105981,316484,210478) : difference with theory (-25) = 0 
CORRECTING DEFECT 14 (vertices=32, convex hull=47, v0=16537)
After retessellation of defect 14 (v0=16537), euler #=-24 (105990,316531,210517) : difference with theory (-24) = 0 
CORRECTING DEFECT 15 (vertices=1385, convex hull=639, v0=20159)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 15 (v0=20159), euler #=-25 (106291,317770,211454) : difference with theory (-23) = 2 
CORRECTING DEFECT 16 (vertices=29, convex hull=62, v0=22840)
After retessellation of defect 16 (v0=22840), euler #=-24 (106309,317852,211519) : difference with theory (-22) = 2 
CORRECTING DEFECT 17 (vertices=66, convex hull=74, v0=24545)
After retessellation of defect 17 (v0=24545), euler #=-24 (106327,317943,211592) : difference with theory (-21) = 3 
CORRECTING DEFECT 18 (vertices=29, convex hull=43, v0=24748)
After retessellation of defect 18 (v0=24748), euler #=-23 (106330,317969,211616) : difference with theory (-20) = 3 
CORRECTING DEFECT 19 (vertices=703, convex hull=187, v0=28778)
After retessellation of defect 19 (v0=28778), euler #=-22 (106393,318255,211840) : difference with theory (-19) = 3 
CORRECTING DEFECT 20 (vertices=8, convex hull=21, v0=29414)
After retessellation of defect 20 (v0=29414), euler #=-21 (106395,318267,211851) : difference with theory (-18) = 3 
CORRECTING DEFECT 21 (vertices=372, convex hull=378, v0=30631)
After retessellation of defect 21 (v0=30631), euler #=-19 (106516,318824,212289) : difference with theory (-17) = 2 
CORRECTING DEFECT 22 (vertices=122, convex hull=66, v0=30777)
After retessellation of defect 22 (v0=30777), euler #=-18 (106530,318892,212344) : difference with theory (-16) = 2 
CORRECTING DEFECT 23 (vertices=33, convex hull=63, v0=33558)
After retessellation of defect 23 (v0=33558), euler #=-17 (106542,318954,212395) : difference with theory (-15) = 2 
CORRECTING DEFECT 24 (vertices=200, convex hull=126, v0=35931)
After retessellation of defect 24 (v0=35931), euler #=-16 (106580,319125,212529) : difference with theory (-14) = 2 
CORRECTING DEFECT 25 (vertices=89, convex hull=96, v0=37014)
After retessellation of defect 25 (v0=37014), euler #=-15 (106592,319196,212589) : difference with theory (-13) = 2 
CORRECTING DEFECT 26 (vertices=33, convex hull=65, v0=37126)
After retessellation of defect 26 (v0=37126), euler #=-14 (106612,319280,212654) : difference with theory (-12) = 2 
CORRECTING DEFECT 27 (vertices=62, convex hull=96, v0=42487)
After retessellation of defect 27 (v0=42487), euler #=-13 (106625,319359,212721) : difference with theory (-11) = 2 
CORRECTING DEFECT 28 (vertices=72, convex hull=79, v0=42928)
After retessellation of defect 28 (v0=42928), euler #=-12 (106640,319443,212791) : difference with theory (-10) = 2 
CORRECTING DEFECT 29 (vertices=161, convex hull=93, v0=47278)
After retessellation of defect 29 (v0=47278), euler #=-11 (106670,319574,212893) : difference with theory (-9) = 2 
CORRECTING DEFECT 30 (vertices=8, convex hull=27, v0=48140)
After retessellation of defect 30 (v0=48140), euler #=-10 (106673,319592,212909) : difference with theory (-8) = 2 
CORRECTING DEFECT 31 (vertices=121, convex hull=72, v0=51360)
After retessellation of defect 31 (v0=51360), euler #=-9 (106695,319688,212984) : difference with theory (-7) = 2 
CORRECTING DEFECT 32 (vertices=6, convex hull=35, v0=55611)
After retessellation of defect 32 (v0=55611), euler #=-8 (106696,319700,212996) : difference with theory (-6) = 2 
CORRECTING DEFECT 33 (vertices=58, convex hull=104, v0=56824)
After retessellation of defect 33 (v0=56824), euler #=-7 (106733,319853,213113) : difference with theory (-5) = 2 
CORRECTING DEFECT 34 (vertices=80, convex hull=47, v0=57038)
After retessellation of defect 34 (v0=57038), euler #=-6 (106743,319901,213152) : difference with theory (-4) = 2 
CORRECTING DEFECT 35 (vertices=6, convex hull=24, v0=63522)
After retessellation of defect 35 (v0=63522), euler #=-5 (106745,319914,213164) : difference with theory (-3) = 2 
CORRECTING DEFECT 36 (vertices=12, convex hull=16, v0=65725)
After retessellation of defect 36 (v0=65725), euler #=-4 (106747,319923,213172) : difference with theory (-2) = 2 
CORRECTING DEFECT 37 (vertices=60, convex hull=39, v0=70216)
After retessellation of defect 37 (v0=70216), euler #=-3 (106755,319961,213203) : difference with theory (-1) = 2 
CORRECTING DEFECT 38 (vertices=1056, convex hull=530, v0=72317)
A large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 117684 with 3 faces
After retessellation of defect 38 (v0=72317), euler #=0 (106951,320832,213881) : difference with theory (0) = 0 
CORRECTING DEFECT 39 (vertices=7, convex hull=12, v0=72594)
After retessellation of defect 39 (v0=72594), euler #=1 (106952,320837,213886) : difference with theory (1) = 0 
CORRECTING DEFECT 40 (vertices=39, convex hull=36, v0=74816)
After retessellation of defect 40 (v0=74816), euler #=2 (106963,320883,213922) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.92 +- 0.39 (0.04-->22.34) (max @ vno 23360 --> 112006)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.92 +- 0.39 (0.04-->22.34) (max @ vno 23360 --> 112006)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
137 mutations (36.0%), 244 crossovers (64.0%), 1380 vertices were eliminated
building final representation...
10973 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=106963, nf=213922, ne=320883, g=0)
writing corrected surface to /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.premesh...

0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 2193 intersecting
001: 562 intersecting
002: 216 intersecting
003: 144 intersecting
004: 126 intersecting
005: 112 intersecting
006: 110 intersecting
step 1 with no progress (num=110, old_num=110)
007: 110 intersecting
step 2 with no progress (num=110, old_num=110)
008: 110 intersecting
step 3 with no progress (num=110, old_num=110)
009: 110 intersecting
step 4 with no progress (num=110, old_num=110)
010: 110 intersecting
step 5 with no progress (num=110, old_num=110)
011: 110 intersecting
step 6 with no progress (num=110, old_num=110)
012: 110 intersecting
step 7 with no progress (num=110, old_num=110)
013: 110 intersecting
step 8 with no progress (num=110, old_num=110)
014: 110 intersecting
step 9 with no progress (num=110, old_num=110)
015: 110 intersecting
step 10 with no progress (num=110, old_num=110)
016: 110 intersecting
step 11 with no progress (num=110, old_num=110)
017: 110 intersecting
step 12 with no progress (num=110, old_num=110)
018: 110 intersecting
step 13 with no progress (num=110, old_num=110)
019: 110 intersecting
step 14 with no progress (num=110, old_num=110)
020: 110 intersecting
step 15 with no progress (num=110, old_num=110)
021: 110 intersecting
step 16 with no progress (num=110, old_num=110)
terminating search with 110 intersecting
topology fixing took 33.4 minutes
FSRUNTIME@ mris_fix_topology rh  0.5572 hours 1 threads
#VMPC# mris_fix_topology VmPeak  770204
@#@FSTIME  2020:09:23:15:28:15 mris_fix_topology N 14 e 2006.13 S 1.32 U 1991.04 P 99% M 722240 F 0 R 199592 W 0 c 21964 w 2 I 200 O 10312 L 1.00 0.97 0.72
@#@FSLOADPOST 2020:09:23:16:01:41 mris_fix_topology N 14 1.07 1.07 1.00

 mris_euler_number ../surf/lh.orig.premesh 

euler # = v-e+f = 2g-2: 109827 - 329475 + 219650 = 2 --> 0 holes
      F =2V-4:          219650 = 219654-4 (0)
      2E=3F:            658950 = 658950 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig.premesh 

euler # = v-e+f = 2g-2: 106963 - 320883 + 213922 = 2 --> 0 holes
      F =2V-4:          213922 = 213926-4 (0)
      2E=3F:            641766 = 641766 (0)

total defect index = 0
2020��� 09��� 23��� ��������� 16:01:42 CST

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer/subjects/monkey2/scripts
/usr/local/freesurfer/bin/defect2seg --s monkey2

freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
defect2seg 7.1.0
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
pid 21438
mri_label2vol --defects /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz 1000 0 /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mri_label2vol supposed to be reproducible but seed not set
Changing input type 0 to MRI_INT
Converting defects to volume: offset=1000, merge=0
Writing to /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mris_defects_pointset -s /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix -d /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels -o /usr/local/freesurfer/subjects/monkey2/surf/lh.defects.pointset
Reading in surface /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix
Reading in defect segmentation /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels
#VMPC# mris_defects_pointset 176348
mris_defects_pointset done
mri_label2vol --defects /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz 2000 1 /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mri_label2vol supposed to be reproducible but seed not set
Converting defects to volume: offset=2000, merge=1
Writing to /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mris_defects_pointset -s /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix -d /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels -o /usr/local/freesurfer/subjects/monkey2/surf/rh.defects.pointset
Reading in surface /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix
Reading in defect segmentation /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels
#VMPC# mris_defects_pointset 173076
mris_defects_pointset done
 
Started at 2020��� 09��� 23��� ��������� 16:01:42 CST 
Ended   at 2020��� 09��� 23��� ��������� 16:01:50 CST
Defect2seg-Run-Time-Sec 8
Defect2seg-Run-Time-Min 0.16
Defect2seg-Run-Time-Hours 0.00
 
tkmeditfv monkey2 orig.mgz -defect -c /usr/local/freesurfer/subjects/monkey2/surf/?h.defects.pointset
defect2seg Done
@#@FSTIME  2020:09:23:16:01:42 defect2seg N 2 e 7.59 S 0.27 U 6.93 P 95% M 228784 F 34 R 213844 W 0 c 697 w 275 I 16592 O 456 L 1.07 1.07 1.00
@#@FSLOADPOST 2020:09:23:16:01:50 defect2seg N 2 1.06 1.06 1.00

 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.premesh --output /usr/local/freesurfer/subjects/monkey2/surf/lh.orig 

iters = 3
standard remeshing without target
   adjusted l: 0.735472
remeshing to edge length 0.735472 with 3 iterations

avg qual before   : 0.876294  after: 0.970671

Removing intersections
removing intersecting faces
000: 137 intersecting
001: 10 intersecting
step 1 with no progress (num=11, old_num=10)
002: 11 intersecting
003: 8 intersecting
step 1 with no progress (num=8, old_num=8)
004: 8 intersecting
step 2 with no progress (num=8, old_num=8)
005: 8 intersecting
step 3 with no progress (num=8, old_num=8)
006: 8 intersecting
step 4 with no progress (num=8, old_num=8)
007: 8 intersecting
step 5 with no progress (num=8, old_num=8)
008: 8 intersecting
step 6 with no progress (num=8, old_num=8)
009: 8 intersecting
step 7 with no progress (num=8, old_num=8)
010: 8 intersecting
step 8 with no progress (num=8, old_num=8)
011: 8 intersecting
step 9 with no progress (num=8, old_num=8)
012: 8 intersecting
step 10 with no progress (num=8, old_num=8)
013: 8 intersecting
step 11 with no progress (num=8, old_num=8)
014: 8 intersecting
step 12 with no progress (num=8, old_num=8)
015: 8 intersecting
step 13 with no progress (num=8, old_num=8)
016: 8 intersecting
step 14 with no progress (num=8, old_num=8)
017: 8 intersecting
step 15 with no progress (num=8, old_num=8)
018: 8 intersecting
step 16 with no progress (num=8, old_num=8)
terminating search with 8 intersecting
Remeshed surface quality stats nv0 = 109827  nv = 112248  1.02204
Area    224492  0.32191  0.03726 0.000356   0.5638
Corner  673476 60.00000  9.00516 0.114106 179.5238
Edge    336738  0.87052  0.08699 0.027454   1.6839
Hinge   336738  8.11054 11.23550 0.000000 178.7060
mris_remesh done
@#@FSTIME  2020:09:23:16:01:50 mris_remesh N 7 e 65.45 S 0.34 U 63.38 P 97% M 782336 F 19 R 262912 W 0 c 3423 w 22 I 4248 O 7896 L 1.06 1.06 1.00
@#@FSLOADPOST 2020:09:23:16:02:55 mris_remesh N 7 1.06 1.06 1.00

 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.premesh --output /usr/local/freesurfer/subjects/monkey2/surf/rh.orig 

iters = 3
standard remeshing without target
   adjusted l: 0.736595
remeshing to edge length 0.736595 with 3 iterations

avg qual before   : 0.880002  after: 0.971253

Removing intersections
removing intersecting faces
000: 382 intersecting
001: 108 intersecting
002: 75 intersecting
003: 70 intersecting
004: 63 intersecting
005: 61 intersecting
step 1 with no progress (num=61, old_num=61)
006: 61 intersecting
step 2 with no progress (num=61, old_num=61)
007: 61 intersecting
step 3 with no progress (num=61, old_num=61)
008: 61 intersecting
step 4 with no progress (num=61, old_num=61)
009: 61 intersecting
step 5 with no progress (num=61, old_num=61)
010: 61 intersecting
step 6 with no progress (num=61, old_num=61)
011: 61 intersecting
step 7 with no progress (num=61, old_num=61)
012: 61 intersecting
step 8 with no progress (num=61, old_num=61)
013: 61 intersecting
step 9 with no progress (num=61, old_num=61)
014: 61 intersecting
step 10 with no progress (num=61, old_num=61)
015: 61 intersecting
step 11 with no progress (num=61, old_num=61)
016: 61 intersecting
step 12 with no progress (num=61, old_num=61)
017: 61 intersecting
step 13 with no progress (num=61, old_num=61)
018: 61 intersecting
step 14 with no progress (num=61, old_num=61)
019: 61 intersecting
step 15 with no progress (num=61, old_num=61)
020: 61 intersecting
step 16 with no progress (num=61, old_num=61)
terminating search with 61 intersecting
Remeshed surface quality stats nv0 = 106963  nv = 108743  1.01664
Area    217482  0.32214  0.03688 0.003928   0.5984
Corner  652446 60.00000  8.88576 2.026629 171.5179
Edge    326223  0.87077  0.08669 0.039895   1.5074
Hinge   326223  7.94140 10.95924 0.000000 179.5362
mris_remesh done
@#@FSTIME  2020:09:23:16:02:55 mris_remesh N 7 e 68.90 S 0.34 U 66.49 P 97% M 770756 F 0 R 253301 W 0 c 3465 w 1 I 0 O 7648 L 1.06 1.06 1.00
@#@FSLOADPOST 2020:09:23:16:04:04 mris_remesh N 7 1.02 1.05 1.00
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.01 hours
removing intersecting faces
000: 8 intersecting
step 1 with no progress (num=8, old_num=8)
001: 8 intersecting
step 2 with no progress (num=8, old_num=8)
002: 8 intersecting
step 3 with no progress (num=8, old_num=8)
003: 8 intersecting
step 4 with no progress (num=8, old_num=8)
004: 8 intersecting
step 5 with no progress (num=8, old_num=8)
005: 8 intersecting
step 6 with no progress (num=8, old_num=8)
006: 8 intersecting
step 7 with no progress (num=8, old_num=8)
007: 8 intersecting
step 8 with no progress (num=8, old_num=8)
008: 8 intersecting
step 9 with no progress (num=8, old_num=8)
009: 8 intersecting
step 10 with no progress (num=8, old_num=8)
010: 8 intersecting
step 11 with no progress (num=8, old_num=8)
011: 8 intersecting
step 12 with no progress (num=8, old_num=8)
012: 8 intersecting
step 13 with no progress (num=8, old_num=8)
013: 8 intersecting
step 14 with no progress (num=8, old_num=8)
014: 8 intersecting
step 15 with no progress (num=8, old_num=8)
015: 8 intersecting
step 16 with no progress (num=8, old_num=8)
terminating search with 8 intersecting
writing corrected surface to ../surf/lh.orig
@#@FSTIME  2020:09:23:16:04:04 mris_remove_intersection N 2 e 30.75 S 0.08 U 30.45 P 99% M 296052 F 18 R 89486 W 0 c 930 w 21 I 3952 O 7896 L 1.02 1.05 1.00
@#@FSLOADPOST 2020:09:23:16:04:35 mris_remove_intersection N 2 1.01 1.04 1.00

 rm ../surf/lh.inflated 

rm: cannot remove '../surf/lh.inflated': No such file or directory
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.01 hours
removing intersecting faces
000: 61 intersecting
step 1 with no progress (num=61, old_num=61)
001: 61 intersecting
step 2 with no progress (num=61, old_num=61)
002: 61 intersecting
step 3 with no progress (num=61, old_num=61)
003: 61 intersecting
step 4 with no progress (num=61, old_num=61)
004: 61 intersecting
step 5 with no progress (num=61, old_num=61)
005: 61 intersecting
step 6 with no progress (num=61, old_num=61)
006: 61 intersecting
step 7 with no progress (num=61, old_num=61)
007: 61 intersecting
step 8 with no progress (num=61, old_num=61)
008: 61 intersecting
step 9 with no progress (num=61, old_num=61)
009: 61 intersecting
step 10 with no progress (num=61, old_num=61)
010: 61 intersecting
step 11 with no progress (num=61, old_num=61)
011: 61 intersecting
step 12 with no progress (num=61, old_num=61)
012: 61 intersecting
step 13 with no progress (num=61, old_num=61)
013: 61 intersecting
step 14 with no progress (num=61, old_num=61)
014: 61 intersecting
step 15 with no progress (num=61, old_num=61)
015: 61 intersecting
step 16 with no progress (num=61, old_num=61)
terminating search with 61 intersecting
writing corrected surface to ../surf/rh.orig
@#@FSTIME  2020:09:23:16:04:35 mris_remove_intersection N 2 e 29.28 S 0.10 U 29.04 P 99% M 288948 F 0 R 87470 W 0 c 876 w 1 I 0 O 7648 L 1.01 1.04 1.00
@#@FSLOADPOST 2020:09:23:16:05:05 mris_remove_intersection N 2 1.00 1.04 1.00

 rm ../surf/rh.inflated 

rm: cannot remove '../surf/rh.inflated': No such file or directory
#--------------------------------------------
#@# AutoDetGWStats lh 2020��� 09��� 23��� ��������� 16:05:05 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 

border white:    205386 voxels (1.22%)
border gray      252828 voxels (1.51%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/lh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=28949, wmmin=5, clip=110 
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (100.0): 99.6 +- 9.4 [70.0 --> 110.0]
CCS GM (71.0) : 70.9 +- 13.2 [30.0 --> 110.0]
white_mean = 99.5525 +/- 9.4499, gray_mean = 70.8991 +/- 13.1999
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=255 nbins=256
intensity peaks found at WM=107+-6.1,    GM=70+-7.8
white_mode = 107, gray_mode = 70
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 56.8 (was 70.000000)
setting MAX_BORDER_WHITE to 116.4 (was 105.000000)
setting MIN_BORDER_WHITE to 70.0 (was 85.000000)
setting MAX_CSF to 43.6 (was 40.000000)
setting MAX_GRAY to 97.6 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 56.8 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 30.4 (was 40.000000)
When placing the white surface
  white_border_hi   = 116.45;
  white_border_low  = 70;
  white_outside_low = 56.8001;
  white_inside_hi   = 120;
  white_outside_hi  = 116.45;
When placing the pial surface
  pial_border_hi   = 56.8001;
  pial_border_low  = 30.4004;
  pial_outside_low = 10;
  pial_inside_hi   = 97.5501;
  pial_outside_hi  = 50.2002;
#VMPC# mris_autodet_gwstats VmPeak  245076
mris_autodet_gwstats done
@#@FSTIME  2020:09:23:16:05:05 mris_autodet_gwstats N 8 e 11.86 S 0.09 U 11.67 P 99% M 209464 F 17 R 61612 W 0 c 390 w 20 I 4288 O 8 L 1.00 1.04 1.00
@#@FSLOADPOST 2020:09:23:16:05:16 mris_autodet_gwstats N 8 1.00 1.03 1.00
#--------------------------------------------
#@# AutoDetGWStats rh 2020��� 09��� 23��� ��������� 16:05:16 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 

border white:    205386 voxels (1.22%)
border gray      252828 voxels (1.51%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/rh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=28949, wmmin=5, clip=110 
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (100.0): 99.6 +- 9.4 [70.0 --> 110.0]
CCS GM (71.0) : 70.9 +- 13.2 [30.0 --> 110.0]
white_mean = 99.5525 +/- 9.4499, gray_mean = 70.8991 +/- 13.1999
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=255 nbins=256
intensity peaks found at WM=107+-6.1,    GM=65+-8.7
white_mode = 107, gray_mode = 65
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 51.8 (was 70.000000)
setting MAX_BORDER_WHITE to 116.4 (was 105.000000)
setting MIN_BORDER_WHITE to 65.0 (was 85.000000)
setting MAX_CSF to 38.6 (was 40.000000)
setting MAX_GRAY to 97.6 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 51.8 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 25.4 (was 40.000000)
When placing the white surface
  white_border_hi   = 116.45;
  white_border_low  = 65;
  white_outside_low = 51.8001;
  white_inside_hi   = 120;
  white_outside_hi  = 116.45;
When placing the pial surface
  pial_border_hi   = 51.8001;
  pial_border_low  = 25.4004;
  pial_outside_low = 10;
  pial_inside_hi   = 97.5501;
  pial_outside_hi  = 45.2002;
#VMPC# mris_autodet_gwstats VmPeak  241004
mris_autodet_gwstats done
@#@FSTIME  2020:09:23:16:05:16 mris_autodet_gwstats N 8 e 11.78 S 0.07 U 11.65 P 99% M 205144 F 0 R 60424 W 0 c 378 w 1 I 0 O 8 L 1.00 1.03 1.00
@#@FSLOADPOST 2020:09:23:16:05:28 mris_autodet_gwstats N 8 1.00 1.03 1.00
#--------------------------------------------
#@# WhitePreAparc lh 2020��� 09��� 23��� ��������� 16:05:28 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5
7.1.0
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 

Reading in input surface ../surf/lh.orig
Smoothing surface with 5 iterations
removing intersecting faces
000: 63 intersecting
001: 62 intersecting
step 1 with no progress (num=65, old_num=62)
002: 65 intersecting
003: 61 intersecting
004: 55 intersecting
step 1 with no progress (num=59, old_num=55)
005: 59 intersecting
006: 41 intersecting
step 1 with no progress (num=55, old_num=41)
007: 55 intersecting
008: 48 intersecting
009: 42 intersecting
010: 39 intersecting
step 1 with no progress (num=54, old_num=39)
011: 54 intersecting
012: 52 intersecting
013: 44 intersecting
014: 42 intersecting
step 1 with no progress (num=50, old_num=42)
015: 50 intersecting
step 2 with no progress (num=60, old_num=50)
016: 60 intersecting
017: 47 intersecting
step 1 with no progress (num=49, old_num=47)
018: 49 intersecting
step 2 with no progress (num=49, old_num=49)
019: 49 intersecting
step 3 with no progress (num=53, old_num=49)
020: 53 intersecting
021: 43 intersecting
step 1 with no progress (num=46, old_num=43)
022: 46 intersecting
step 2 with no progress (num=57, old_num=46)
023: 57 intersecting
024: 43 intersecting
step 1 with no progress (num=53, old_num=43)
025: 53 intersecting
step 2 with no progress (num=53, old_num=53)
026: 53 intersecting
027: 50 intersecting
step 1 with no progress (num=56, old_num=50)
028: 56 intersecting
029: 48 intersecting
step 1 with no progress (num=50, old_num=48)
030: 50 intersecting
031: 49 intersecting
032: 47 intersecting
step 1 with no progress (num=56, old_num=47)
033: 56 intersecting
034: 54 intersecting
035: 52 intersecting
step 1 with no progress (num=55, old_num=52)
036: 55 intersecting
037: 49 intersecting
step 1 with no progress (num=49, old_num=49)
038: 49 intersecting
step 2 with no progress (num=49, old_num=49)
039: 49 intersecting
step 3 with no progress (num=49, old_num=49)
040: 49 intersecting
step 4 with no progress (num=49, old_num=49)
041: 49 intersecting
step 5 with no progress (num=49, old_num=49)
042: 49 intersecting
step 6 with no progress (num=49, old_num=49)
043: 49 intersecting
step 7 with no progress (num=49, old_num=49)
044: 49 intersecting
step 8 with no progress (num=49, old_num=49)
045: 49 intersecting
step 9 with no progress (num=49, old_num=49)
046: 49 intersecting
step 10 with no progress (num=49, old_num=49)
047: 49 intersecting
step 11 with no progress (num=49, old_num=49)
048: 49 intersecting
step 12 with no progress (num=49, old_num=49)
049: 49 intersecting
step 13 with no progress (num=49, old_num=49)
050: 49 intersecting
step 14 with no progress (num=49, old_num=49)
051: 49 intersecting
step 15 with no progress (num=49, old_num=49)
052: 49 intersecting
step 16 with no progress (num=49, old_num=49)
terminating search with 39 intersecting
Area    224492  0.29432  0.07098 0.000000   0.6487
Corner  673476 60.00000  9.85633 0.000088 179.9997
Edge    336738  0.82752  0.12372 0.000136   1.5928
Hinge   336738  4.98185  7.05352 0.000000 179.9822
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=28949, wmmin=5, clip=110 
MRIfindBrightNonWM(): 3333 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
ERROR: need seg for ripping
Command exited with non-zero status 1
@#@FSTIME  2020:09:23:16:05:28 mris_place_surface N 14 e 94.99 S 0.21 U 94.27 P 99% M 593624 F 13 R 165867 W 0 c 2763 w 14 I 2456 O 0 L 1.00 1.03 1.00
@#@FSLOADPOST 2020:09:23:16:07:03 mris_place_surface N 14 1.00 1.02 1.00
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s monkey2 exited with ERRORS at 2020��� 09��� 23��� ��������� 16:07:03 CST

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



#New# invocation of recon-all 



2020��� 09��� 24��� ��������� 10:34:07 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        735M        241M         19M        1.0G        1.0G
Swap:          2.0G        778M        1.2G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-02:34:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-117-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 24��� ��������� 10:34:07 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 415 control points...
only using 415 control points from file, mean 82.6, scaling by 1.33...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 111
gm peak at 66 (66), valley at 26 (26)
csf peak at 33, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 22 (22)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 7 minutes and 13 seconds.
@#@FSTIME  2020:09:24:10:34:08 mri_normalize N 7 e 434.79 S 0.46 U 347.61 P 80% M 583580 F 5 R 316392 W 0 c 36650 w 10 I 4408 O 3024 L 0.15 0.08 0.02
@#@FSLOADPOST 2020:09:24:10:41:22 mri_normalize N 7 1.41 1.23 0.60
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 24��� ��������� 10:41:22 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:24:10:41:22 mri_mask N 5 e 2.64 S 0.02 U 2.59 P 98% M 74208 F 16 R 17264 W 0 c 99 w 18 I 3488 O 2952 L 1.41 1.23 0.60
@#@FSLOADPOST 2020:09:24:10:41:25 mri_mask N 5 1.38 1.22 0.61
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 24��� ��������� 10:41:25 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:24:10:41:32 AntsDenoiseImageFs N 4 e 62.01 S 0.11 U 61.57 P 99% M 350640 F 18 R 86503 W 0 c 1832 w 21 I 4320 O 3000 L 1.35 1.22 0.61
@#@FSLOADPOST 2020:09:24:10:42:34 AntsDenoiseImageFs N 4 1.12 1.17 0.64

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 104.9 +- 6.1 [79.0 --> 125.0]
CCS GM (71.0) : 69.4 +- 10.4 [30.0 --> 95.0]
 white_mean 104.875
 white_sigma 6.12543
 gray_mean 69.3848
 gray_sigma 10.4182
setting bottom of white matter range wm_low to 79.8
setting top of gray matter range gray_hi to 90.2
 wm_low 79.803
 wm_hi  125
 gray_low 30
 gray_hi  90.2211
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.803
 wm_hi  125
 gray_low 30
 gray_hi  90.2211
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.2211, wm_low = 79.803
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.2211, wmlow=79.803
    125413 voxels processed (0.75%)
     54080 voxels white (0.32%)
     71333 voxels non-white (0.43%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.803, gray_hi=90.2211, wsize=13
    212188 voxels tested (1.26%)
     47610 voxels changed (0.28%)
     53604 multi-scale searches  (0.32%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.803
 wm_hi 125
 slack 6.12543
 pct_thresh 0.33
 intensity_thresh 131.125
 nvox_thresh 8.58
      908 voxels tested (0.01%)
      698 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.803, hithr=90.2211
  smoothing input volume with sigma = 0.250
    72680 voxels tested (0.43%)
    13567 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 6598 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3427 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3532 filled
MRIfindBrightNonWM(): 1928 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.7 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:24:10:42:34 mri_segment N 6 e 222.48 S 0.20 U 220.39 P 99% M 147676 F 16 R 137422 W 0 c 6750 w 18 I 3640 O 648 L 1.12 1.17 0.64
@#@FSLOADPOST 2020:09:24:10:46:16 mri_segment N 6 1.00 1.08 0.73

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  86 found -  86 modified     |    TOTAL:  86
pass   2 (xy+):   0 found -  86 modified     |    TOTAL:  86
pass   1 (xy-):  93 found -  93 modified     |    TOTAL: 179
pass   2 (xy-):   0 found -  93 modified     |    TOTAL: 179
pass   1 (yz+): 180 found - 180 modified     |    TOTAL: 359
pass   2 (yz+):   0 found - 180 modified     |    TOTAL: 359
pass   1 (yz-):  70 found -  70 modified     |    TOTAL: 429
pass   2 (yz-):   0 found -  70 modified     |    TOTAL: 429
pass   1 (xz+): 141 found - 141 modified     |    TOTAL: 570
pass   2 (xz+):   0 found - 141 modified     |    TOTAL: 570
pass   1 (xz-):  92 found -  92 modified     |    TOTAL: 662
pass   2 (xz-):   0 found -  92 modified     |    TOTAL: 662
Iteration Number : 1
pass   1 (+++):  69 found -  69 modified     |    TOTAL:  69
pass   2 (+++):   0 found -  69 modified     |    TOTAL:  69
pass   1 (+++):  30 found -  30 modified     |    TOTAL:  99
pass   2 (+++):   0 found -  30 modified     |    TOTAL:  99
pass   1 (+++):  39 found -  39 modified     |    TOTAL: 138
pass   2 (+++):   0 found -  39 modified     |    TOTAL: 138
pass   1 (+++):  25 found -  25 modified     |    TOTAL: 163
pass   2 (+++):   0 found -  25 modified     |    TOTAL: 163
Iteration Number : 1
pass   1 (++): 160 found - 160 modified     |    TOTAL: 160
pass   2 (++):   0 found - 160 modified     |    TOTAL: 160
pass   1 (+-): 242 found - 242 modified     |    TOTAL: 402
pass   2 (+-):   0 found - 242 modified     |    TOTAL: 402
pass   1 (--): 195 found - 195 modified     |    TOTAL: 597
pass   2 (--):   0 found - 195 modified     |    TOTAL: 597
pass   1 (-+): 234 found - 234 modified     |    TOTAL: 831
pass   2 (-+):   0 found - 234 modified     |    TOTAL: 831
Iteration Number : 2
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:  11
pass   1 (yz+):  18 found -  18 modified     |    TOTAL:  29
pass   2 (yz+):   0 found -  18 modified     |    TOTAL:  29
pass   1 (yz-):  12 found -  12 modified     |    TOTAL:  41
pass   2 (yz-):   0 found -  12 modified     |    TOTAL:  41
pass   1 (xz+):  16 found -  16 modified     |    TOTAL:  57
pass   2 (xz+):   0 found -  16 modified     |    TOTAL:  57
pass   1 (xz-):  12 found -  12 modified     |    TOTAL:  69
pass   2 (xz-):   0 found -  12 modified     |    TOTAL:  69
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   8
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  12
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  12
Iteration Number : 2
pass   1 (++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+-):  12 found -  12 modified     |    TOTAL:  20
pass   2 (+-):   0 found -  12 modified     |    TOTAL:  20
pass   1 (--):   2 found -   2 modified     |    TOTAL:  22
pass   2 (--):   0 found -   2 modified     |    TOTAL:  22
pass   1 (-+):   6 found -   6 modified     |    TOTAL:  28
pass   2 (-+):   0 found -   6 modified     |    TOTAL:  28
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   5
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   6
Iteration Number : 3
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   4
pass   1 (--):   0 found -   0 modified     |    TOTAL:   4
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 4
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1782 (out of 318090: 0.560219)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:24:10:46:16 mri_pretess N 5 e 5.89 S 0.01 U 5.61 P 95% M 57204 F 16 R 17108 W 0 c 530 w 18 I 3472 O 640 L 1.00 1.08 0.73
@#@FSLOADPOST 2020:09:24:10:46:22 mri_pretess N 5 1.00 1.07 0.73
#--------------------------------------------
#@# Fill 2020��� 09��� 24��� ��������� 10:46:22 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 799 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 315414 voxels filled...
filling volume: pass 2 of 3...total of 16394885 voxels filled...
filling volume: pass 3 of 3...total of 315774 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 315414 voxels filled...
filling volume: pass 2 of 3...total of 16394885 voxels filled...
filling volume: pass 3 of 3...total of 315774 voxels filled...done.
filling degenerate left hemisphere surface locations...
394 voxels filled
11 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
394 voxels filled
11 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16394469 voxels filled...
filling volume: pass 3 of 3...total of 316190 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16394469 voxels filled...
filling volume: pass 3 of 3...total of 316190 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  315797 ambiguous voxels remaining
9:  47784 ambiguous voxels remaining
8:  22378 ambiguous voxels remaining
7:  13234 ambiguous voxels remaining
6:  4986 ambiguous voxels remaining
5:  3426 ambiguous voxels remaining
4:  1548 ambiguous voxels remaining
3:  555 ambiguous voxels remaining
2:  154 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:24:10:46:22 mri_fill N 12 e 38.22 S 0.11 U 37.70 P 98% M 111436 F 17 R 77588 W 0 c 1501 w 19 I 4064 O 224 L 1.00 1.07 0.73
@#@FSLOADPOST 2020:09:24:10:47:01 mri_fill N 12 1.00 1.06 0.74
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 24��� ��������� 10:47:01 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 162983: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:24:10:47:01 mri_pretess N 4 e 1.77 S 0.00 U 1.71 P 97% M 40524 F 0 R 8847 W 0 c 121 w 1 I 0 O 216 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:02 mri_pretess N 4 1.00 1.06 0.74

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3249 vertices, 3405 faces
slice 70: 7384 vertices, 7572 faces
slice 80: 17117 vertices, 17620 faces
slice 90: 38734 vertices, 39552 faces
slice 100: 59702 vertices, 60541 faces
slice 110: 81195 vertices, 81925 faces
slice 120: 99028 vertices, 99737 faces
slice 130: 111270 vertices, 111755 faces
slice 140: 118559 vertices, 118849 faces
slice 150: 120882 vertices, 121034 faces
slice 160: 120882 vertices, 121034 faces
slice 170: 120882 vertices, 121034 faces
slice 180: 120882 vertices, 121034 faces
slice 190: 120882 vertices, 121034 faces
slice 200: 120882 vertices, 121034 faces
slice 210: 120882 vertices, 121034 faces
slice 220: 120882 vertices, 121034 faces
slice 230: 120882 vertices, 121034 faces
slice 240: 120882 vertices, 121034 faces
slice 250: 120882 vertices, 121034 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:24:10:47:03 mri_tessellate N 3 e 2.71 S 0.01 U 2.65 P 98% M 36880 F 16 R 8194 W 0 c 105 w 19 I 3736 O 5672 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:05 mri_tessellate N 3 1.00 1.06 0.74

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   120882 voxel in cpt #1: X=-152 [v=120882,e=363102,f=242068] located at (-2.573750, -28.344444, 17.880495)
For the whole surface: X=-152 [v=120882,e=363102,f=242068]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:24:10:47:05 mris_extract_main_component N 2 e 1.06 S 0.10 U 0.92 P 96% M 242880 F 17 R 66642 W 0 c 75 w 24 I 4256 O 8512 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:06 mris_extract_main_component N 2 1.00 1.06 0.74
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 24��� ��������� 10:47:06 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 6 (out of 153214: 0.003916)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:24:10:47:06 mri_pretess N 4 e 2.50 S 0.01 U 2.38 P 95% M 40516 F 0 R 8847 W 0 c 231 w 1 I 0 O 216 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:09 mri_pretess N 4 1.00 1.06 0.74

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2603 vertices, 2726 faces
slice 70: 6253 vertices, 6421 faces
slice 80: 14141 vertices, 14591 faces
slice 90: 33080 vertices, 33790 faces
slice 100: 53732 vertices, 54571 faces
slice 110: 76161 vertices, 76946 faces
slice 120: 94308 vertices, 95014 faces
slice 130: 107184 vertices, 107678 faces
slice 140: 115524 vertices, 115829 faces
slice 150: 118104 vertices, 118250 faces
slice 160: 118104 vertices, 118250 faces
slice 170: 118104 vertices, 118250 faces
slice 180: 118104 vertices, 118250 faces
slice 190: 118104 vertices, 118250 faces
slice 200: 118104 vertices, 118250 faces
slice 210: 118104 vertices, 118250 faces
slice 220: 118104 vertices, 118250 faces
slice 230: 118104 vertices, 118250 faces
slice 240: 118104 vertices, 118250 faces
slice 250: 118104 vertices, 118250 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:24:10:47:09 mri_tessellate N 3 e 2.68 S 0.01 U 2.59 P 97% M 36480 F 0 R 8139 W 0 c 105 w 2 I 8 O 5544 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:12 mri_tessellate N 3 1.00 1.06 0.74

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   118104 voxel in cpt #1: X=-146 [v=118104,e=354750,f=236500] located at (58.553581, -26.559237, 18.670908)
For the whole surface: X=-146 [v=118104,e=354750,f=236500]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:24:10:47:12 mris_extract_main_component N 2 e 0.92 S 0.09 U 0.80 P 97% M 237096 F 0 R 65091 W 0 c 76 w 3 I 16 O 8320 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:13 mris_extract_main_component N 2 1.00 1.06 0.74
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 24��� ��������� 10:47:13 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:24:10:47:13 mris_smooth N 5 e 4.07 S 0.09 U 3.83 P 96% M 196052 F 17 R 54723 W 0 c 146 w 24 I 4072 O 8512 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:17 mris_smooth N 5 1.00 1.06 0.74
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 24��� ��������� 10:47:17 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:24:10:47:17 mris_smooth N 5 e 3.96 S 0.06 U 3.86 P 99% M 191868 F 0 R 53481 W 0 c 152 w 2 I 8 O 8320 L 1.00 1.06 0.74
@#@FSLOADPOST 2020:09:24:10:47:21 mris_smooth N 5 1.00 1.06 0.75
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 24��� ��������� 10:47:21 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.9 mm, total surface area = 69824 mm^2

step 000: RMS=0.139 (target=0.015)   
step 005: RMS=0.111 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.086 (target=0.015)   
step 020: RMS=0.081 (target=0.015)   
step 025: RMS=0.077 (target=0.015)   
step 030: RMS=0.075 (target=0.015)   
step 035: RMS=0.073 (target=0.015)   
step 040: RMS=0.071 (target=0.015)   
step 045: RMS=0.070 (target=0.015)   
step 050: RMS=0.068 (target=0.015)   
step 055: RMS=0.069 (target=0.015)   
step 060: RMS=0.070 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.4 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    21.267017
mris_inflate stimesec    0.071821
mris_inflate ru_maxrss   253200
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   68995
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4560
mris_inflate ru_oublock  8512
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    22
mris_inflate ru_nivcsw   701
@#@FSTIME  2020:09:24:10:47:21 mris_inflate N 3 e 21.51 S 0.08 U 21.26 P 99% M 253384 F 19 R 68997 W 0 c 705 w 23 I 4560 O 8512 L 1.00 1.06 0.75
@#@FSLOADPOST 2020:09:24:10:47:42 mris_inflate N 3 1.00 1.05 0.75
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 24��� ��������� 10:47:42 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.7 mm, total surface area = 68305 mm^2

step 000: RMS=0.137 (target=0.015)   
step 005: RMS=0.110 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.078 (target=0.015)   
step 025: RMS=0.074 (target=0.015)   
step 030: RMS=0.071 (target=0.015)   
step 035: RMS=0.069 (target=0.015)   
step 040: RMS=0.068 (target=0.015)   
step 045: RMS=0.066 (target=0.015)   
step 050: RMS=0.066 (target=0.015)   
step 055: RMS=0.066 (target=0.015)   
step 060: RMS=0.065 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.4 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    25.752495
mris_inflate stimesec    0.107851
mris_inflate ru_maxrss   248368
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   72412
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8320
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   867
@#@FSTIME  2020:09:24:10:47:42 mris_inflate N 3 e 26.07 S 0.11 U 25.75 P 99% M 248536 F 0 R 72414 W 0 c 870 w 1 I 0 O 8320 L 1.00 1.05 0.75
@#@FSLOADPOST 2020:09:24:10:48:08 mris_inflate N 3 1.00 1.05 0.76

Started at 2020��� 09��� 24��� ��������� 10:34:07 CST 
Ended   at 2020��� 09��� 24��� ��������� 10:48:08 CST
#@#%# recon-all-run-time-hours 0.234
recon-all -s monkey2 finished without error at 2020��� 09��� 24��� ��������� 10:48:09 CST



#New# invocation of recon-all 



2020��� 09��� 24��� ��������� 20:51:06 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        1.5G         68M         22M        399M        298M
Swap:          2.0G         51M        2.0G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:06-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:06-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-12:51:07-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 24��� ��������� 20:51:07 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 90 control points...
only using 90 control points from file, mean 87.0, scaling by 1.26...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 111
gm peak at 63 (63), valley at 19 (19)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 61 (61), valley at 19 (19)
csf peak at 31, setting threshold to 51
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 21 seconds.
@#@FSTIME  2020:09:24:20:51:07 mri_normalize N 7 e 382.67 S 0.56 U 377.46 P 98% M 577404 F 108 R 312395 W 0 c 15031 w 124 I 27288 O 3024 L 0.57 0.27 0.19
@#@FSLOADPOST 2020:09:24:20:57:30 mri_normalize N 7 1.03 0.82 0.48
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 24��� ��������� 20:57:30 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:24:20:57:30 mri_mask N 5 e 2.94 S 0.03 U 2.84 P 98% M 74144 F 32 R 17254 W 0 c 148 w 48 I 9832 O 2952 L 1.03 0.82 0.48
@#@FSLOADPOST 2020:09:24:20:57:33 mri_mask N 5 1.03 0.82 0.48
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 24��� ��������� 20:57:33 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:24:20:57:41 AntsDenoiseImageFs N 4 e 64.60 S 0.07 U 64.23 P 99% M 350668 F 18 R 86509 W 0 c 2111 w 21 I 4320 O 2992 L 1.02 0.83 0.49
@#@FSLOADPOST 2020:09:24:20:58:45 AntsDenoiseImageFs N 4 1.01 0.86 0.53

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.6 +- 5.9 [79.0 --> 125.0]
CCS GM (71.0) : 69.7 +- 10.9 [30.0 --> 95.0]
 white_mean 104.575
 white_sigma 5.92544
 gray_mean 69.7323
 gray_sigma 10.8657
setting bottom of white matter range wm_low to 80.6
setting top of gray matter range gray_hi to 91.5
 wm_low 80.598
 wm_hi  125
 gray_low 30
 gray_hi  91.4636
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.598
 wm_hi  125
 gray_low 30
 gray_hi  91.4636
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 91.4636, wm_low = 80.598
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.4636, wmlow=80.598
    106116 voxels processed (0.63%)
     49804 voxels white (0.30%)
     56312 voxels non-white (0.34%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.598, gray_hi=91.4636, wsize=13
    177372 voxels tested (1.06%)
     43996 voxels changed (0.26%)
     34654 multi-scale searches  (0.21%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.598
 wm_hi 125
 slack 5.92544
 pct_thresh 0.33
 intensity_thresh 130.925
 nvox_thresh 8.58
      803 voxels tested (0.00%)
      681 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.598, hithr=91.4636
  smoothing input volume with sigma = 0.250
    76452 voxels tested (0.46%)
    12543 voxels changed (0.07%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 4943 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3182 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 2883 filled
MRIfindBrightNonWM(): 1098 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.4 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:24:20:58:45 mri_segment N 6 e 202.93 S 0.27 U 197.78 P 97% M 147144 F 17 R 218321 W 0 c 10343 w 19 I 3824 O 592 L 1.01 0.86 0.53
@#@FSLOADPOST 2020:09:24:21:02:08 mri_segment N 6 1.02 0.97 0.65

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  93 found -  93 modified     |    TOTAL:  93
pass   2 (xy+):   0 found -  93 modified     |    TOTAL:  93
pass   1 (xy-):  91 found -  91 modified     |    TOTAL: 184
pass   2 (xy-):   0 found -  91 modified     |    TOTAL: 184
pass   1 (yz+): 165 found - 165 modified     |    TOTAL: 349
pass   2 (yz+):   0 found - 165 modified     |    TOTAL: 349
pass   1 (yz-):  52 found -  52 modified     |    TOTAL: 401
pass   2 (yz-):   0 found -  52 modified     |    TOTAL: 401
pass   1 (xz+): 119 found - 119 modified     |    TOTAL: 520
pass   2 (xz+):   0 found - 119 modified     |    TOTAL: 520
pass   1 (xz-):  93 found -  93 modified     |    TOTAL: 613
pass   2 (xz-):   0 found -  93 modified     |    TOTAL: 613
Iteration Number : 1
pass   1 (+++):  78 found -  78 modified     |    TOTAL:  78
pass   2 (+++):   0 found -  78 modified     |    TOTAL:  78
pass   1 (+++):  31 found -  31 modified     |    TOTAL: 109
pass   2 (+++):   0 found -  31 modified     |    TOTAL: 109
pass   1 (+++):  42 found -  42 modified     |    TOTAL: 151
pass   2 (+++):   0 found -  42 modified     |    TOTAL: 151
pass   1 (+++):  26 found -  26 modified     |    TOTAL: 177
pass   2 (+++):   0 found -  26 modified     |    TOTAL: 177
Iteration Number : 1
pass   1 (++): 187 found - 187 modified     |    TOTAL: 187
pass   2 (++):   0 found - 187 modified     |    TOTAL: 187
pass   1 (+-): 228 found - 228 modified     |    TOTAL: 415
pass   2 (+-):   0 found - 228 modified     |    TOTAL: 415
pass   1 (--): 206 found - 206 modified     |    TOTAL: 621
pass   2 (--):   0 found - 206 modified     |    TOTAL: 621
pass   1 (-+): 203 found - 203 modified     |    TOTAL: 824
pass   2 (-+):   0 found - 203 modified     |    TOTAL: 824
Iteration Number : 2
pass   1 (xy+):  15 found -  15 modified     |    TOTAL:  15
pass   2 (xy+):   0 found -  15 modified     |    TOTAL:  15
pass   1 (xy-):   8 found -   8 modified     |    TOTAL:  23
pass   2 (xy-):   0 found -   8 modified     |    TOTAL:  23
pass   1 (yz+):  29 found -  29 modified     |    TOTAL:  52
pass   2 (yz+):   0 found -  29 modified     |    TOTAL:  52
pass   1 (yz-):  11 found -  11 modified     |    TOTAL:  63
pass   2 (yz-):   0 found -  11 modified     |    TOTAL:  63
pass   1 (xz+):  20 found -  20 modified     |    TOTAL:  83
pass   2 (xz+):   0 found -  20 modified     |    TOTAL:  83
pass   1 (xz-):  14 found -  14 modified     |    TOTAL:  97
pass   2 (xz-):   0 found -  14 modified     |    TOTAL:  97
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+-):  16 found -  16 modified     |    TOTAL:  22
pass   2 (+-):   0 found -  16 modified     |    TOTAL:  22
pass   1 (--):   6 found -   6 modified     |    TOTAL:  28
pass   2 (--):   0 found -   6 modified     |    TOTAL:  28
pass   1 (-+):   6 found -   6 modified     |    TOTAL:  34
pass   2 (-+):   0 found -   6 modified     |    TOTAL:  34
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1752 (out of 290468: 0.603165)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:24:21:02:08 mri_pretess N 5 e 5.09 S 0.01 U 4.52 P 89% M 57004 F 16 R 17100 W 0 c 707 w 18 I 3472 O 584 L 1.02 0.97 0.65
@#@FSLOADPOST 2020:09:24:21:02:13 mri_pretess N 5 1.02 0.98 0.65
#--------------------------------------------
#@# Fill 2020��� 09��� 24��� ��������� 21:02:13 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 768 (min = 350, max = 1400), aspect = 4.64 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 287208 voxels filled...
filling volume: pass 2 of 3...total of 16423008 voxels filled...
filling volume: pass 3 of 3...total of 287651 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 287208 voxels filled...
filling volume: pass 2 of 3...total of 16423008 voxels filled...
filling volume: pass 3 of 3...total of 287651 voxels filled...done.
filling degenerate left hemisphere surface locations...
374 voxels filled
10 voxels filled
1 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
374 voxels filled
10 voxels filled
1 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16422584 voxels filled...
filling volume: pass 3 of 3...total of 288075 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16422584 voxels filled...
filling volume: pass 3 of 3...total of 288075 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  287682 ambiguous voxels remaining
9:  37817 ambiguous voxels remaining
8:  20376 ambiguous voxels remaining
7:  13157 ambiguous voxels remaining
6:  6611 ambiguous voxels remaining
5:  3538 ambiguous voxels remaining
4:  1825 ambiguous voxels remaining
3:  880 ambiguous voxels remaining
2:  180 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:24:21:02:14 mri_fill N 12 e 36.31 S 0.16 U 33.88 P 93% M 111084 F 17 R 77584 W 0 c 2652 w 19 I 4072 O 208 L 1.02 0.98 0.65
@#@FSLOADPOST 2020:09:24:21:02:50 mri_fill N 12 1.43 1.09 0.70
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 24��� ��������� 21:02:50 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 163410: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:24:21:02:50 mri_pretess N 4 e 1.43 S 0.03 U 1.31 P 93% M 40412 F 0 R 8846 W 0 c 151 w 1 I 0 O 200 L 1.43 1.09 0.70
@#@FSLOADPOST 2020:09:24:21:02:51 mri_pretess N 4 1.43 1.09 0.70

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3262 vertices, 3438 faces
slice 70: 7218 vertices, 7411 faces
slice 80: 16116 vertices, 16580 faces
slice 90: 34581 vertices, 35248 faces
slice 100: 53643 vertices, 54520 faces
slice 110: 76037 vertices, 76823 faces
slice 120: 94978 vertices, 95777 faces
slice 130: 108355 vertices, 108910 faces
slice 140: 116208 vertices, 116551 faces
slice 150: 118622 vertices, 118814 faces
slice 160: 118622 vertices, 118814 faces
slice 170: 118622 vertices, 118814 faces
slice 180: 118622 vertices, 118814 faces
slice 190: 118622 vertices, 118814 faces
slice 200: 118622 vertices, 118814 faces
slice 210: 118622 vertices, 118814 faces
slice 220: 118622 vertices, 118814 faces
slice 230: 118622 vertices, 118814 faces
slice 240: 118622 vertices, 118814 faces
slice 250: 118622 vertices, 118814 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:24:21:02:51 mri_tessellate N 3 e 2.43 S 0.01 U 2.31 P 95% M 36528 F 16 R 8143 W 0 c 118 w 20 I 3744 O 5568 L 1.43 1.09 0.70
@#@FSLOADPOST 2020:09:24:21:02:54 mri_tessellate N 3 1.43 1.09 0.70

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   118622 voxel in cpt #1: X=-192 [v=118622,e=356442,f=237628] located at (-2.886463, -27.014002, 13.488932)
For the whole surface: X=-192 [v=118622,e=356442,f=237628]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:24:21:02:54 mris_extract_main_component N 2 e 0.90 S 0.10 U 0.77 P 96% M 238564 F 17 R 65436 W 0 c 76 w 31 I 4296 O 8352 L 1.43 1.09 0.70
@#@FSLOADPOST 2020:09:24:21:02:55 mris_extract_main_component N 2 1.39 1.09 0.71
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 24��� ��������� 21:02:55 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 3 (out of 124669: 0.002406)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:24:21:02:55 mri_pretess N 4 e 1.86 S 0.00 U 1.67 P 89% M 40304 F 0 R 8843 W 0 c 256 w 1 I 0 O 200 L 1.39 1.09 0.71
@#@FSLOADPOST 2020:09:24:21:02:57 mri_pretess N 4 1.39 1.09 0.71

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 22 vertices, 28 faces
slice 80: 2783 vertices, 3048 faces
slice 90: 16450 vertices, 16955 faces
slice 100: 30131 vertices, 30855 faces
slice 110: 51110 vertices, 51860 faces
slice 120: 68655 vertices, 69347 faces
slice 130: 81176 vertices, 81654 faces
slice 140: 89294 vertices, 89591 faces
slice 150: 91824 vertices, 91964 faces
slice 160: 91824 vertices, 91964 faces
slice 170: 91824 vertices, 91964 faces
slice 180: 91824 vertices, 91964 faces
slice 190: 91824 vertices, 91964 faces
slice 200: 91824 vertices, 91964 faces
slice 210: 91824 vertices, 91964 faces
slice 220: 91824 vertices, 91964 faces
slice 230: 91824 vertices, 91964 faces
slice 240: 91824 vertices, 91964 faces
slice 250: 91824 vertices, 91964 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:24:21:02:57 mri_tessellate N 3 e 2.34 S 0.01 U 2.26 P 97% M 34088 F 0 R 7562 W 0 c 108 w 3 I 16 O 4312 L 1.39 1.09 0.71
@#@FSLOADPOST 2020:09:24:21:02:59 mri_tessellate N 3 1.39 1.09 0.71

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   91824 voxel in cpt #1: X=-140 [v=91824,e=275892,f=183928] located at (56.544117, -20.971151, 12.860439)
For the whole surface: X=-140 [v=91824,e=275892,f=183928]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:24:21:02:59 mris_extract_main_component N 2 e 0.75 S 0.06 U 0.61 P 90% M 185864 F 0 R 50684 W 0 c 88 w 2 I 8 O 6464 L 1.39 1.09 0.71
@#@FSLOADPOST 2020:09:24:21:03:00 mris_extract_main_component N 2 1.36 1.08 0.71
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 24��� ��������� 21:03:00 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:24:21:03:00 mris_smooth N 5 e 3.63 S 0.06 U 3.28 P 92% M 192120 F 17 R 53584 W 0 c 230 w 24 I 4072 O 8352 L 1.36 1.08 0.71
@#@FSLOADPOST 2020:09:24:21:03:04 mris_smooth N 5 1.36 1.08 0.71
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 24��� ��������� 21:03:04 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:24:21:03:04 mris_smooth N 5 e 3.04 S 0.06 U 2.54 P 85% M 150248 F 0 R 41509 W 0 c 259 w 1 I 0 O 6472 L 1.36 1.08 0.71
@#@FSLOADPOST 2020:09:24:21:03:07 mris_smooth N 5 1.33 1.08 0.71
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 24��� ��������� 21:03:07 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.2 mm, total surface area = 68187 mm^2

step 000: RMS=0.143 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.088 (target=0.015)   
step 025: RMS=0.085 (target=0.015)   
step 030: RMS=0.081 (target=0.015)   
step 035: RMS=0.079 (target=0.015)   
step 040: RMS=0.078 (target=0.015)   
step 045: RMS=0.077 (target=0.015)   
step 050: RMS=0.077 (target=0.015)   
step 055: RMS=0.078 (target=0.015)   
step 060: RMS=0.078 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.238863
mris_inflate stimesec    0.083126
mris_inflate ru_maxrss   249664
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   72806
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  8360
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   1197
@#@FSTIME  2020:09:24:21:03:07 mris_inflate N 3 e 18.13 S 0.09 U 17.23 P 95% M 249812 F 19 R 72808 W 0 c 1200 w 22 I 4552 O 8360 L 1.33 1.08 0.71
@#@FSLOADPOST 2020:09:24:21:03:25 mris_inflate N 3 1.40 1.11 0.73
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 24��� ��������� 21:03:25 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 42.2 mm, total surface area = 52184 mm^2

step 000: RMS=0.148 (target=0.015)   
step 005: RMS=0.120 (target=0.015)   
step 010: RMS=0.102 (target=0.015)   
step 015: RMS=0.095 (target=0.015)   
step 020: RMS=0.090 (target=0.015)   
step 025: RMS=0.085 (target=0.015)   
step 030: RMS=0.082 (target=0.015)   
step 035: RMS=0.081 (target=0.015)   
step 040: RMS=0.080 (target=0.015)   
step 045: RMS=0.080 (target=0.015)   
step 050: RMS=0.079 (target=0.015)   
step 055: RMS=0.080 (target=0.015)   
step 060: RMS=0.080 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    13.168118
mris_inflate stimesec    0.079565
mris_inflate ru_maxrss   194284
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   52470
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  6472
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   688
@#@FSTIME  2020:09:24:21:03:25 mris_inflate N 3 e 13.52 S 0.08 U 13.17 P 97% M 194372 F 0 R 52472 W 0 c 691 w 1 I 0 O 6472 L 1.40 1.11 0.73
@#@FSLOADPOST 2020:09:24:21:03:38 mris_inflate N 3 1.34 1.11 0.73

Started at 2020��� 09��� 24��� ��������� 20:51:06 CST 
Ended   at 2020��� 09��� 24��� ��������� 21:03:39 CST
#@#%# recon-all-run-time-hours 0.209
recon-all -s monkey2 finished without error at 2020��� 09��� 24��� ��������� 21:03:39 CST



#New# invocation of recon-all 



2020��� 09��� 24��� ��������� 22:00:29 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        523M        1.2G        8.3M        211M        1.3G
Swap:          2.0G        701M        1.3G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:29-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/24-14:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 24��� ��������� 22:00:30 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 612 control points...
only using 612 control points from file, mean 94.3, scaling by 1.17...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 113
gm peak at 65 (65), valley at 21 (21)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 62 (62), valley at 21 (21)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 10 seconds.
@#@FSTIME  2020:09:24:22:00:30 mri_normalize N 7 e 371.31 S 0.42 U 369.17 P 99% M 583264 F 5 R 312310 W 0 c 4983 w 11 I 4464 O 3016 L 0.43 0.35 0.23
@#@FSLOADPOST 2020:09:24:22:06:42 mri_normalize N 7 1.00 0.83 0.50
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 24��� ��������� 22:06:42 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:24:22:06:42 mri_mask N 5 e 2.77 S 0.04 U 2.72 P 99% M 74164 F 5 R 17272 W 0 c 48 w 6 I 1064 O 2936 L 1.00 0.83 0.50
@#@FSLOADPOST 2020:09:24:22:06:44 mri_mask N 5 1.00 0.83 0.51
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 24��� ��������� 22:06:44 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:24:22:06:52 AntsDenoiseImageFs N 4 e 70.94 S 0.12 U 70.66 P 99% M 350604 F 18 R 86502 W 0 c 705 w 22 I 4328 O 2992 L 1.00 0.83 0.51
@#@FSLOADPOST 2020:09:24:22:08:03 AntsDenoiseImageFs N 4 1.00 0.87 0.55

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.2 +- 5.8 [79.0 --> 125.0]
CCS GM (71.0) : 69.0 +- 10.3 [30.0 --> 95.0]
 white_mean 104.232
 white_sigma 5.77399
 gray_mean 69.0101
 gray_sigma 10.3025
setting bottom of white matter range wm_low to 79.3
setting top of gray matter range gray_hi to 89.6
 wm_low 79.3126
 wm_hi  125
 gray_low 30
 gray_hi  89.6152
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.3126
 wm_hi  125
 gray_low 30
 gray_hi  89.6152
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 89.6152, wm_low = 79.3126
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=89.6152, wmlow=79.3126
    105304 voxels processed (0.63%)
     47282 voxels white (0.28%)
     58022 voxels non-white (0.35%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.3126, gray_hi=89.6152, wsize=13
    185853 voxels tested (1.11%)
     41817 voxels changed (0.25%)
     45016 multi-scale searches  (0.27%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.3126
 wm_hi 125
 slack 5.77399
 pct_thresh 0.33
 intensity_thresh 130.774
 nvox_thresh 8.58
      232 voxels tested (0.00%)
       97 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.3126, hithr=89.6152
  smoothing input volume with sigma = 0.250
    65936 voxels tested (0.39%)
    13289 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 5974 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3221 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3363 filled
MRIfindBrightNonWM(): 1864 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.5 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:24:22:08:03 mri_segment N 6 e 209.98 S 0.08 U 209.60 P 99% M 147096 F 5 R 54165 W 0 c 2195 w 6 I 1024 O 640 L 1.00 0.87 0.55
@#@FSLOADPOST 2020:09:24:22:11:33 mri_segment N 6 1.00 0.96 0.66

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  87 found -  87 modified     |    TOTAL:  87
pass   2 (xy+):   0 found -  87 modified     |    TOTAL:  87
pass   1 (xy-):  90 found -  90 modified     |    TOTAL: 177
pass   2 (xy-):   0 found -  90 modified     |    TOTAL: 177
pass   1 (yz+): 129 found - 129 modified     |    TOTAL: 306
pass   2 (yz+):   0 found - 129 modified     |    TOTAL: 306
pass   1 (yz-):  71 found -  71 modified     |    TOTAL: 377
pass   2 (yz-):   0 found -  71 modified     |    TOTAL: 377
pass   1 (xz+): 116 found - 116 modified     |    TOTAL: 493
pass   2 (xz+):   0 found - 116 modified     |    TOTAL: 493
pass   1 (xz-):  95 found -  95 modified     |    TOTAL: 588
pass   2 (xz-):   0 found -  95 modified     |    TOTAL: 588
Iteration Number : 1
pass   1 (+++):  52 found -  52 modified     |    TOTAL:  52
pass   2 (+++):   0 found -  52 modified     |    TOTAL:  52
pass   1 (+++):  23 found -  23 modified     |    TOTAL:  75
pass   2 (+++):   0 found -  23 modified     |    TOTAL:  75
pass   1 (+++):  61 found -  61 modified     |    TOTAL: 136
pass   2 (+++):   0 found -  61 modified     |    TOTAL: 136
pass   1 (+++):  32 found -  32 modified     |    TOTAL: 168
pass   2 (+++):   0 found -  32 modified     |    TOTAL: 168
Iteration Number : 1
pass   1 (++): 143 found - 143 modified     |    TOTAL: 143
pass   2 (++):   0 found - 143 modified     |    TOTAL: 143
pass   1 (+-): 209 found - 209 modified     |    TOTAL: 352
pass   2 (+-):   0 found - 209 modified     |    TOTAL: 352
pass   1 (--): 179 found - 179 modified     |    TOTAL: 531
pass   2 (--):   2 found - 181 modified     |    TOTAL: 533
pass   3 (--):   0 found - 181 modified     |    TOTAL: 533
pass   1 (-+): 193 found - 193 modified     |    TOTAL: 726
pass   2 (-+):   0 found - 193 modified     |    TOTAL: 726
Iteration Number : 2
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):  10 found -  10 modified     |    TOTAL:  17
pass   2 (xy-):   0 found -  10 modified     |    TOTAL:  17
pass   1 (yz+):  16 found -  16 modified     |    TOTAL:  33
pass   2 (yz+):   0 found -  16 modified     |    TOTAL:  33
pass   1 (yz-):  10 found -  10 modified     |    TOTAL:  43
pass   2 (yz-):   0 found -  10 modified     |    TOTAL:  43
pass   1 (xz+):  16 found -  16 modified     |    TOTAL:  59
pass   2 (xz+):   0 found -  16 modified     |    TOTAL:  59
pass   1 (xz-):  10 found -  10 modified     |    TOTAL:  69
pass   2 (xz-):   0 found -  10 modified     |    TOTAL:  69
Iteration Number : 2
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   8
pass   1 (+++):   3 found -   3 modified     |    TOTAL:  11
pass   2 (+++):   0 found -   3 modified     |    TOTAL:  11
Iteration Number : 2
pass   1 (++):  10 found -  10 modified     |    TOTAL:  10
pass   2 (++):   0 found -  10 modified     |    TOTAL:  10
pass   1 (+-):  11 found -  11 modified     |    TOTAL:  21
pass   2 (+-):   0 found -  11 modified     |    TOTAL:  21
pass   1 (--):   3 found -   3 modified     |    TOTAL:  24
pass   2 (--):   0 found -   3 modified     |    TOTAL:  24
pass   1 (-+):   3 found -   3 modified     |    TOTAL:  27
pass   2 (-+):   0 found -   3 modified     |    TOTAL:  27
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   4
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:   9
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:   9
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   9
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   4 modified     |    TOTAL:   4
pass   1 (--):   1 found -   1 modified     |    TOTAL:   5
pass   2 (--):   0 found -   1 modified     |    TOTAL:   5
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   7
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   7
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1606 (out of 320828: 0.500580)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:24:22:11:33 mri_pretess N 5 e 5.45 S 0.03 U 5.33 P 98% M 57168 F 16 R 17106 W 0 c 374 w 18 I 3472 O 640 L 1.00 0.96 0.66
@#@FSLOADPOST 2020:09:24:22:11:38 mri_pretess N 5 1.00 0.96 0.66
#--------------------------------------------
#@# Fill 2020��� 09��� 24��� ��������� 22:11:38 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 793 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 316976 voxels filled...
filling volume: pass 2 of 3...total of 16393377 voxels filled...
filling volume: pass 3 of 3...total of 317282 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 316976 voxels filled...
filling volume: pass 2 of 3...total of 16393377 voxels filled...
filling volume: pass 3 of 3...total of 317282 voxels filled...done.
filling degenerate left hemisphere surface locations...
389 voxels filled
6 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
389 voxels filled
6 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16392931 voxels filled...
filling volume: pass 3 of 3...total of 317728 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16392931 voxels filled...
filling volume: pass 3 of 3...total of 317728 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  317334 ambiguous voxels remaining
9:  45890 ambiguous voxels remaining
8:  22435 ambiguous voxels remaining
7:  12634 ambiguous voxels remaining
6:  5296 ambiguous voxels remaining
5:  3590 ambiguous voxels remaining
4:  1676 ambiguous voxels remaining
3:  713 ambiguous voxels remaining
2:  226 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:24:22:11:38 mri_fill N 12 e 35.70 S 0.05 U 35.54 P 99% M 111480 F 6 R 77595 W 0 c 726 w 7 I 1568 O 224 L 1.00 0.96 0.66
@#@FSLOADPOST 2020:09:24:22:12:14 mri_fill N 12 1.00 0.97 0.68
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 24��� ��������� 22:12:14 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 2 (out of 167141: 0.001197)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:24:22:12:14 mri_pretess N 4 e 1.80 S 0.00 U 1.77 P 98% M 40388 F 0 R 8846 W 0 c 116 w 1 I 0 O 216 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:16 mri_pretess N 4 1.00 0.97 0.68

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3187 vertices, 3341 faces
slice 70: 7340 vertices, 7532 faces
slice 80: 17181 vertices, 17667 faces
slice 90: 38464 vertices, 39260 faces
slice 100: 59340 vertices, 60217 faces
slice 110: 81109 vertices, 81891 faces
slice 120: 99363 vertices, 100133 faces
slice 130: 112221 vertices, 112743 faces
slice 140: 119669 vertices, 120001 faces
slice 150: 122068 vertices, 122256 faces
slice 160: 122068 vertices, 122256 faces
slice 170: 122068 vertices, 122256 faces
slice 180: 122068 vertices, 122256 faces
slice 190: 122068 vertices, 122256 faces
slice 200: 122068 vertices, 122256 faces
slice 210: 122068 vertices, 122256 faces
slice 220: 122068 vertices, 122256 faces
slice 230: 122068 vertices, 122256 faces
slice 240: 122068 vertices, 122256 faces
slice 250: 122068 vertices, 122256 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:24:22:12:16 mri_tessellate N 3 e 2.44 S 0.01 U 2.42 P 99% M 36844 F 5 R 8223 W 0 c 37 w 9 I 1232 O 5736 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:18 mri_tessellate N 3 1.00 0.97 0.68

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   122068 voxel in cpt #1: X=-188 [v=122068,e=366768,f=244512] located at (-2.630468, -28.038586, 17.108267)
For the whole surface: X=-188 [v=122068,e=366768,f=244512]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:24:22:12:18 mris_extract_main_component N 2 e 0.91 S 0.07 U 0.81 P 97% M 245076 F 16 R 67291 W 0 c 54 w 22 I 4184 O 8600 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:19 mris_extract_main_component N 2 1.00 0.97 0.68
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 24��� ��������� 22:12:19 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1 (out of 150591: 0.000664)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:24:22:12:19 mri_pretess N 4 e 1.82 S 0.01 U 1.79 P 98% M 40424 F 0 R 8847 W 0 c 108 w 1 I 0 O 216 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:21 mri_pretess N 4 1.00 0.97 0.68

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2568 vertices, 2685 faces
slice 70: 5721 vertices, 5900 faces
slice 80: 13122 vertices, 13554 faces
slice 90: 31213 vertices, 31907 faces
slice 100: 50950 vertices, 51800 faces
slice 110: 73456 vertices, 74241 faces
slice 120: 91616 vertices, 92330 faces
slice 130: 104456 vertices, 104953 faces
slice 140: 112592 vertices, 112905 faces
slice 150: 115074 vertices, 115228 faces
slice 160: 115074 vertices, 115228 faces
slice 170: 115074 vertices, 115228 faces
slice 180: 115074 vertices, 115228 faces
slice 190: 115074 vertices, 115228 faces
slice 200: 115074 vertices, 115228 faces
slice 210: 115074 vertices, 115228 faces
slice 220: 115074 vertices, 115228 faces
slice 230: 115074 vertices, 115228 faces
slice 240: 115074 vertices, 115228 faces
slice 250: 115074 vertices, 115228 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:24:22:12:21 mri_tessellate N 3 e 2.43 S 0.01 U 2.41 P 99% M 36264 F 0 R 8074 W 0 c 43 w 2 I 8 O 5400 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:24 mri_tessellate N 3 1.00 0.97 0.68

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   115074 voxel in cpt #1: X=-154 [v=115074,e=345684,f=230456] located at (58.487034, -26.180815, 17.561213)
For the whole surface: X=-154 [v=115074,e=345684,f=230456]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:24:22:12:24 mris_extract_main_component N 2 e 0.80 S 0.07 U 0.72 P 99% M 231340 F 0 R 63435 W 0 c 53 w 2 I 8 O 8104 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:24 mris_extract_main_component N 2 1.00 0.97 0.68
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 24��� ��������� 22:12:24 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:24:22:12:25 mris_smooth N 5 e 3.68 S 0.08 U 3.58 P 99% M 197500 F 5 R 55142 W 0 c 70 w 9 I 1312 O 8600 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:28 mris_smooth N 5 1.00 0.97 0.68
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 24��� ��������� 22:12:28 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:24:22:12:28 mris_smooth N 5 e 3.41 S 0.07 U 3.32 P 99% M 186316 F 0 R 51922 W 0 c 66 w 2 I 8 O 8104 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:32 mris_smooth N 5 1.00 0.97 0.68
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 24��� ��������� 22:12:32 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.8 mm, total surface area = 70489 mm^2

step 000: RMS=0.141 (target=0.015)   
step 005: RMS=0.114 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.089 (target=0.015)   
step 020: RMS=0.084 (target=0.015)   
step 025: RMS=0.081 (target=0.015)   
step 030: RMS=0.078 (target=0.015)   
step 035: RMS=0.076 (target=0.015)   
step 040: RMS=0.074 (target=0.015)   
step 045: RMS=0.074 (target=0.015)   
step 050: RMS=0.074 (target=0.015)   
step 055: RMS=0.074 (target=0.015)   
step 060: RMS=0.074 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    19.317143
mris_inflate stimesec    0.088023
mris_inflate ru_maxrss   256668
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   74933
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  8600
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   274
@#@FSTIME  2020:09:24:22:12:32 mris_inflate N 3 e 19.45 S 0.09 U 19.31 P 99% M 256832 F 19 R 74935 W 0 c 279 w 22 I 4552 O 8600 L 1.00 0.97 0.68
@#@FSLOADPOST 2020:09:24:22:12:51 mris_inflate N 3 1.00 0.97 0.69
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 24��� ��������� 22:12:51 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.5 mm, total surface area = 66226 mm^2

step 000: RMS=0.138 (target=0.015)   
step 005: RMS=0.112 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.085 (target=0.015)   
step 020: RMS=0.080 (target=0.015)   
step 025: RMS=0.076 (target=0.015)   
step 030: RMS=0.073 (target=0.015)   
step 035: RMS=0.071 (target=0.015)   
step 040: RMS=0.069 (target=0.015)   
step 045: RMS=0.068 (target=0.015)   
step 050: RMS=0.067 (target=0.015)   
step 055: RMS=0.068 (target=0.015)   
step 060: RMS=0.068 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    18.118766
mris_inflate stimesec    0.083938
mris_inflate ru_maxrss   241072
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   65657
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8104
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   255
@#@FSTIME  2020:09:24:22:12:51 mris_inflate N 3 e 18.24 S 0.09 U 18.11 P 99% M 241376 F 0 R 65659 W 0 c 257 w 1 I 0 O 8104 L 1.00 0.97 0.69
@#@FSLOADPOST 2020:09:24:22:13:09 mris_inflate N 3 1.00 0.97 0.70

Started at 2020��� 09��� 24��� ��������� 22:00:29 CST 
Ended   at 2020��� 09��� 24��� ��������� 22:13:09 CST
#@#%# recon-all-run-time-hours 0.211
recon-all -s monkey2 finished without error at 2020��� 09��� 24��� ��������� 22:13:09 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 12:56:46 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        647M        242M        9.0M        1.1G        1.1G
Swap:          2.0G        616M        1.4G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:46-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-04:56:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 12:56:47 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 11 control points...
only using 11 control points from file, mean 87.6, scaling by 1.26...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 42 (42)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 62 (62), valley at 18 (18)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 54 seconds.
@#@FSTIME  2020:09:25:12:56:47 mri_normalize N 7 e 415.15 S 0.43 U 410.18 P 98% M 583288 F 1 R 312311 W 0 c 6799 w 6 I 536 O 3040 L 0.06 0.08 0.02
@#@FSLOADPOST 2020:09:25:13:03:42 mri_normalize N 7 1.00 0.78 0.39
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 13:03:42 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:13:03:42 mri_mask N 5 e 2.65 S 0.02 U 2.58 P 98% M 74288 F 19 R 17261 W 0 c 72 w 30 I 6720 O 2968 L 1.00 0.78 0.39
@#@FSLOADPOST 2020:09:25:13:03:45 mri_mask N 5 1.00 0.78 0.39
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 13:03:45 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:13:03:52 AntsDenoiseImageFs N 4 e 61.88 S 0.09 U 61.70 P 99% M 350736 F 18 R 86509 W 0 c 620 w 23 I 4592 O 2992 L 1.00 0.79 0.40
@#@FSLOADPOST 2020:09:25:13:04:54 AntsDenoiseImageFs N 4 1.00 0.83 0.44

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.4 +- 6.0 [79.0 --> 125.0]
CCS GM (71.0) : 69.8 +- 10.7 [30.0 --> 95.0]
 white_mean 104.375
 white_sigma 5.9639
 gray_mean 69.7731
 gray_sigma 10.718
setting bottom of white matter range wm_low to 80.5
setting top of gray matter range gray_hi to 91.2
 wm_low 80.4911
 wm_hi  125
 gray_low 30
 gray_hi  91.2091
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.4911
 wm_hi  125
 gray_low 30
 gray_hi  91.2091
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 91.2091, wm_low = 80.4911
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.2091, wmlow=80.4911
    109997 voxels processed (0.66%)
     52027 voxels white (0.31%)
     57970 voxels non-white (0.35%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.4911, gray_hi=91.2091, wsize=13
    183091 voxels tested (1.09%)
     44826 voxels changed (0.27%)
     36869 multi-scale searches  (0.22%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.4911
 wm_hi 125
 slack 5.9639
 pct_thresh 0.33
 intensity_thresh 130.964
 nvox_thresh 8.58
      780 voxels tested (0.00%)
      659 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.4911, hithr=91.2091
  smoothing input volume with sigma = 0.250
    78557 voxels tested (0.47%)
    13159 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 4873 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3579 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3077 filled
MRIfindBrightNonWM(): 1099 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.4 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:13:04:54 mri_segment N 6 e 203.46 S 0.23 U 199.00 P 97% M 146852 F 16 R 206913 W 0 c 5176 w 18 I 3480 O 600 L 1.00 0.83 0.44
@#@FSLOADPOST 2020:09:25:13:08:17 mri_segment N 6 1.06 0.94 0.56

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  93 found -  93 modified     |    TOTAL:  93
pass   2 (xy+):   0 found -  93 modified     |    TOTAL:  93
pass   1 (xy-):  93 found -  93 modified     |    TOTAL: 186
pass   2 (xy-):   0 found -  93 modified     |    TOTAL: 186
pass   1 (yz+): 163 found - 163 modified     |    TOTAL: 349
pass   2 (yz+):   0 found - 163 modified     |    TOTAL: 349
pass   1 (yz-):  65 found -  65 modified     |    TOTAL: 414
pass   2 (yz-):   0 found -  65 modified     |    TOTAL: 414
pass   1 (xz+): 123 found - 123 modified     |    TOTAL: 537
pass   2 (xz+):   0 found - 123 modified     |    TOTAL: 537
pass   1 (xz-):  89 found -  89 modified     |    TOTAL: 626
pass   2 (xz-):   0 found -  89 modified     |    TOTAL: 626
Iteration Number : 1
pass   1 (+++):  62 found -  62 modified     |    TOTAL:  62
pass   2 (+++):   0 found -  62 modified     |    TOTAL:  62
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  78
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  78
pass   1 (+++):  39 found -  39 modified     |    TOTAL: 117
pass   2 (+++):   0 found -  39 modified     |    TOTAL: 117
pass   1 (+++):  25 found -  25 modified     |    TOTAL: 142
pass   2 (+++):   0 found -  25 modified     |    TOTAL: 142
Iteration Number : 1
pass   1 (++): 174 found - 174 modified     |    TOTAL: 174
pass   2 (++):   0 found - 174 modified     |    TOTAL: 174
pass   1 (+-): 248 found - 248 modified     |    TOTAL: 422
pass   2 (+-):   0 found - 248 modified     |    TOTAL: 422
pass   1 (--): 206 found - 206 modified     |    TOTAL: 628
pass   2 (--):   0 found - 206 modified     |    TOTAL: 628
pass   1 (-+): 217 found - 217 modified     |    TOTAL: 845
pass   2 (-+):   0 found - 217 modified     |    TOTAL: 845
Iteration Number : 2
pass   1 (xy+):   9 found -   9 modified     |    TOTAL:   9
pass   2 (xy+):   0 found -   9 modified     |    TOTAL:   9
pass   1 (xy-):   7 found -   7 modified     |    TOTAL:  16
pass   2 (xy-):   0 found -   7 modified     |    TOTAL:  16
pass   1 (yz+):  22 found -  22 modified     |    TOTAL:  38
pass   2 (yz+):   0 found -  22 modified     |    TOTAL:  38
pass   1 (yz-):  13 found -  13 modified     |    TOTAL:  51
pass   2 (yz-):   0 found -  13 modified     |    TOTAL:  51
pass   1 (xz+):  17 found -  17 modified     |    TOTAL:  68
pass   2 (xz+):   0 found -  17 modified     |    TOTAL:  68
pass   1 (xz-):  11 found -  11 modified     |    TOTAL:  79
pass   2 (xz-):   0 found -  11 modified     |    TOTAL:  79
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   3
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   5
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 2
pass   1 (++):   7 found -   7 modified     |    TOTAL:   7
pass   2 (++):   0 found -   7 modified     |    TOTAL:   7
pass   1 (+-):  15 found -  15 modified     |    TOTAL:  22
pass   2 (+-):   0 found -  15 modified     |    TOTAL:  22
pass   1 (--):   2 found -   2 modified     |    TOTAL:  24
pass   2 (--):   0 found -   2 modified     |    TOTAL:  24
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  28
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  28
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   7
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (--):   2 found -   2 modified     |    TOTAL:   5
pass   2 (--):   0 found -   2 modified     |    TOTAL:   5
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1738 (out of 290968: 0.597317)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:13:08:17 mri_pretess N 5 e 6.33 S 0.02 U 4.70 P 74% M 57144 F 16 R 17104 W 0 c 799 w 18 I 3472 O 592 L 1.06 0.94 0.56
@#@FSLOADPOST 2020:09:25:13:08:24 mri_pretess N 5 1.14 0.96 0.57
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 13:08:24 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 771 (min = 350, max = 1400), aspect = 4.64 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 287654 voxels filled...
filling volume: pass 2 of 3...total of 16422582 voxels filled...
filling volume: pass 3 of 3...total of 288077 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 287654 voxels filled...
filling volume: pass 2 of 3...total of 16422582 voxels filled...
filling volume: pass 3 of 3...total of 288077 voxels filled...done.
filling degenerate left hemisphere surface locations...
401 voxels filled
10 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
401 voxels filled
10 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16422117 voxels filled...
filling volume: pass 3 of 3...total of 288542 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16422117 voxels filled...
filling volume: pass 3 of 3...total of 288542 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  288149 ambiguous voxels remaining
9:  38698 ambiguous voxels remaining
8:  20410 ambiguous voxels remaining
7:  12972 ambiguous voxels remaining
6:  6280 ambiguous voxels remaining
5:  3394 ambiguous voxels remaining
4:  1773 ambiguous voxels remaining
3:  924 ambiguous voxels remaining
2:  71 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:13:08:24 mri_fill N 12 e 34.58 S 0.09 U 33.57 P 97% M 111216 F 18 R 77586 W 0 c 1267 w 21 I 4040 O 208 L 1.14 0.96 0.57
@#@FSLOADPOST 2020:09:25:13:08:58 mri_fill N 12 1.08 0.96 0.59
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 13:08:58 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 8 (out of 162423: 0.004925)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:13:08:58 mri_pretess N 4 e 3.11 S 0.00 U 2.20 P 70% M 40404 F 0 R 8848 W 0 c 439 w 1 I 0 O 200 L 1.08 0.96 0.59
@#@FSLOADPOST 2020:09:25:13:09:01 mri_pretess N 4 1.15 0.98 0.60

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3275 vertices, 3451 faces
slice 70: 7229 vertices, 7425 faces
slice 80: 16380 vertices, 16847 faces
slice 90: 35071 vertices, 35770 faces
slice 100: 54030 vertices, 54901 faces
slice 110: 76256 vertices, 77019 faces
slice 120: 95139 vertices, 95913 faces
slice 130: 108425 vertices, 108961 faces
slice 140: 116178 vertices, 116495 faces
slice 150: 118374 vertices, 118552 faces
slice 160: 118374 vertices, 118552 faces
slice 170: 118374 vertices, 118552 faces
slice 180: 118374 vertices, 118552 faces
slice 190: 118374 vertices, 118552 faces
slice 200: 118374 vertices, 118552 faces
slice 210: 118374 vertices, 118552 faces
slice 220: 118374 vertices, 118552 faces
slice 230: 118374 vertices, 118552 faces
slice 240: 118374 vertices, 118552 faces
slice 250: 118374 vertices, 118552 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:13:09:01 mri_tessellate N 3 e 2.47 S 0.00 U 2.32 P 94% M 36388 F 16 R 8130 W 0 c 244 w 19 I 3736 O 5560 L 1.15 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:04 mri_tessellate N 3 1.15 0.98 0.60

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   118374 voxel in cpt #1: X=-178 [v=118374,e=355656,f=237104] located at (-2.869380, -27.247663, 12.740323)
For the whole surface: X=-178 [v=118374,e=355656,f=237104]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:13:09:04 mris_extract_main_component N 2 e 0.96 S 0.06 U 0.81 P 91% M 238032 F 17 R 65281 W 0 c 84 w 24 I 4584 O 8336 L 1.15 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:05 mris_extract_main_component N 2 1.15 0.98 0.60
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 13:09:05 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 2 (out of 126130: 0.001586)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:13:09:05 mri_pretess N 4 e 2.28 S 0.01 U 1.72 P 76% M 40352 F 0 R 8844 W 0 c 315 w 1 I 0 O 200 L 1.15 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:07 mri_pretess N 4 1.14 0.98 0.60

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 35 vertices, 46 faces
slice 80: 4609 vertices, 4983 faces
slice 90: 19600 vertices, 20138 faces
slice 100: 34159 vertices, 34831 faces
slice 110: 55309 vertices, 56052 faces
slice 120: 72660 vertices, 73326 faces
slice 130: 84843 vertices, 85299 faces
slice 140: 92588 vertices, 92870 faces
slice 150: 94320 vertices, 94448 faces
slice 160: 94320 vertices, 94448 faces
slice 170: 94320 vertices, 94448 faces
slice 180: 94320 vertices, 94448 faces
slice 190: 94320 vertices, 94448 faces
slice 200: 94320 vertices, 94448 faces
slice 210: 94320 vertices, 94448 faces
slice 220: 94320 vertices, 94448 faces
slice 230: 94320 vertices, 94448 faces
slice 240: 94320 vertices, 94448 faces
slice 250: 94320 vertices, 94448 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:13:09:07 mri_tessellate N 3 e 2.42 S 0.01 U 2.26 P 93% M 34268 F 0 R 7611 W 0 c 86 w 2 I 8 O 4432 L 1.14 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:10 mri_tessellate N 3 1.14 0.98 0.60

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   94320 voxel in cpt #1: X=-128 [v=94320,e=283344,f=188896] located at (57.259075, -22.562872, 10.265691)
For the whole surface: X=-128 [v=94320,e=283344,f=188896]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:13:09:10 mris_extract_main_component N 2 e 0.75 S 0.09 U 0.61 P 93% M 191092 F 0 R 52070 W 0 c 66 w 1 I 0 O 6640 L 1.14 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:11 mris_extract_main_component N 2 1.14 0.98 0.60
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 13:09:11 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:13:09:11 mris_smooth N 5 e 3.64 S 0.07 U 3.47 P 97% M 192720 F 17 R 53699 W 0 c 109 w 20 I 4032 O 8336 L 1.13 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:14 mris_smooth N 5 1.13 0.98 0.60
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 13:09:14 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:13:09:14 mris_smooth N 5 e 2.82 S 0.05 U 2.69 P 97% M 154940 F 0 R 42824 W 0 c 94 w 2 I 8 O 6640 L 1.13 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:17 mris_smooth N 5 1.12 0.98 0.60
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 13:09:17 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.0 mm, total surface area = 67995 mm^2

step 000: RMS=0.144 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.101 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.089 (target=0.015)   
step 025: RMS=0.085 (target=0.015)   
step 030: RMS=0.082 (target=0.015)   
step 035: RMS=0.080 (target=0.015)   
step 040: RMS=0.078 (target=0.015)   
step 045: RMS=0.077 (target=0.015)   
step 050: RMS=0.077 (target=0.015)   
step 055: RMS=0.077 (target=0.015)   
step 060: RMS=0.078 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.906459
mris_inflate stimesec    0.119932
mris_inflate ru_maxrss   249000
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   72634
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  8336
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   462
@#@FSTIME  2020:09:25:13:09:17 mris_inflate N 3 e 17.26 S 0.12 U 16.90 P 98% M 249180 F 19 R 72636 W 0 c 466 w 22 I 4552 O 8336 L 1.12 0.98 0.60
@#@FSLOADPOST 2020:09:25:13:09:35 mris_inflate N 3 1.09 0.98 0.61
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 13:09:35 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 42.1 mm, total surface area = 53619 mm^2

step 000: RMS=0.145 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.090 (target=0.015)   
step 020: RMS=0.084 (target=0.015)   
step 025: RMS=0.081 (target=0.015)   
step 030: RMS=0.078 (target=0.015)   
step 035: RMS=0.077 (target=0.015)   
step 040: RMS=0.075 (target=0.015)   
step 045: RMS=0.075 (target=0.015)   
step 050: RMS=0.075 (target=0.015)   
step 055: RMS=0.074 (target=0.015)   
step 060: RMS=0.075 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    13.750778
mris_inflate stimesec    0.068212
mris_inflate ru_maxrss   199096
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   53896
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  8
mris_inflate ru_oublock  6648
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1
mris_inflate ru_nivcsw   339
@#@FSTIME  2020:09:25:13:09:35 mris_inflate N 3 e 13.95 S 0.07 U 13.75 P 99% M 199268 F 0 R 53898 W 0 c 342 w 2 I 8 O 6648 L 1.09 0.98 0.61
@#@FSLOADPOST 2020:09:25:13:09:49 mris_inflate N 3 1.07 0.98 0.62

Started at 2020��� 09��� 25��� ��������� 12:56:46 CST 
Ended   at 2020��� 09��� 25��� ��������� 13:09:49 CST
#@#%# recon-all-run-time-hours 0.218
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 13:09:49 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 13:14:47 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        612M        459M        9.0M        921M        1.2G
Swap:          2.0G        614M        1.4G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:47-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:14:48-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 13:14:48 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 4 control points...
only using 4 control points from file, mean 91.5, scaling by 1.20...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 61 (61), valley at 19 (19)
csf peak at 31, setting threshold to 51
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 19 (19)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 30 seconds.
@#@FSTIME  2020:09:25:13:14:48 mri_normalize N 7 e 391.16 S 0.44 U 388.99 P 99% M 583396 F 0 R 312313 W 0 c 4571 w 1 I 0 O 3016 L 0.02 0.41 0.47
@#@FSLOADPOST 2020:09:25:13:21:19 mri_normalize N 7 1.00 0.85 0.67
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 13:21:19 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:13:21:19 mri_mask N 5 e 2.73 S 0.01 U 2.68 P 98% M 74188 F 0 R 17278 W 0 c 73 w 1 I 0 O 2944 L 1.00 0.85 0.67
@#@FSLOADPOST 2020:09:25:13:21:22 mri_mask N 5 1.00 0.85 0.67
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 13:21:22 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:13:21:29 AntsDenoiseImageFs N 4 e 64.47 S 0.10 U 64.30 P 99% M 350708 F 0 R 86511 W 0 c 620 w 1 I 0 O 2984 L 1.00 0.86 0.67
@#@FSLOADPOST 2020:09:25:13:22:33 AntsDenoiseImageFs N 4 1.00 0.89 0.70

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.6 +- 5.9 [79.0 --> 125.0]
CCS GM (71.0) : 69.6 +- 10.9 [30.0 --> 95.0]
 white_mean 104.566
 white_sigma 5.90636
 gray_mean 69.5659
 gray_sigma 10.9199
setting bottom of white matter range wm_low to 80.5
setting top of gray matter range gray_hi to 91.4
 wm_low 80.4858
 wm_hi  125
 gray_low 30
 gray_hi  91.4057
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.4858
 wm_hi  125
 gray_low 30
 gray_hi  91.4057
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 91.4057, wm_low = 80.4858
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.4057, wmlow=80.4858
    105610 voxels processed (0.63%)
     50124 voxels white (0.30%)
     55486 voxels non-white (0.33%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.4858, gray_hi=91.4057, wsize=13
    176870 voxels tested (1.05%)
     43871 voxels changed (0.26%)
     35372 multi-scale searches  (0.21%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.4858
 wm_hi 125
 slack 5.90636
 pct_thresh 0.33
 intensity_thresh 130.906
 nvox_thresh 8.58
      771 voxels tested (0.00%)
      652 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.4858, hithr=91.4057
  smoothing input volume with sigma = 0.250
    76393 voxels tested (0.46%)
    12581 voxels changed (0.07%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 5020 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3235 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 2927 filled
MRIfindBrightNonWM(): 1157 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.2 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:13:22:33 mri_segment N 6 e 192.44 S 0.06 U 191.22 P 99% M 147156 F 0 R 54349 W 0 c 3268 w 1 I 0 O 600 L 1.00 0.89 0.70
@#@FSLOADPOST 2020:09:25:13:25:46 mri_segment N 6 1.00 0.95 0.76

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+): 100 found - 100 modified     |    TOTAL: 100
pass   2 (xy+):   0 found - 100 modified     |    TOTAL: 100
pass   1 (xy-):  94 found -  94 modified     |    TOTAL: 194
pass   2 (xy-):   0 found -  94 modified     |    TOTAL: 194
pass   1 (yz+): 174 found - 174 modified     |    TOTAL: 368
pass   2 (yz+):   0 found - 174 modified     |    TOTAL: 368
pass   1 (yz-):  53 found -  53 modified     |    TOTAL: 421
pass   2 (yz-):   0 found -  53 modified     |    TOTAL: 421
pass   1 (xz+): 117 found - 117 modified     |    TOTAL: 538
pass   2 (xz+):   0 found - 117 modified     |    TOTAL: 538
pass   1 (xz-):  91 found -  91 modified     |    TOTAL: 629
pass   2 (xz-):   0 found -  91 modified     |    TOTAL: 629
Iteration Number : 1
pass   1 (+++):  89 found -  89 modified     |    TOTAL:  89
pass   2 (+++):   0 found -  89 modified     |    TOTAL:  89
pass   1 (+++):  26 found -  26 modified     |    TOTAL: 115
pass   2 (+++):   0 found -  26 modified     |    TOTAL: 115
pass   1 (+++):  50 found -  50 modified     |    TOTAL: 165
pass   2 (+++):   0 found -  50 modified     |    TOTAL: 165
pass   1 (+++):  24 found -  24 modified     |    TOTAL: 189
pass   2 (+++):   0 found -  24 modified     |    TOTAL: 189
Iteration Number : 1
pass   1 (++): 192 found - 192 modified     |    TOTAL: 192
pass   2 (++):   0 found - 192 modified     |    TOTAL: 192
pass   1 (+-): 248 found - 248 modified     |    TOTAL: 440
pass   2 (+-):   0 found - 248 modified     |    TOTAL: 440
pass   1 (--): 216 found - 216 modified     |    TOTAL: 656
pass   2 (--):   0 found - 216 modified     |    TOTAL: 656
pass   1 (-+): 189 found - 189 modified     |    TOTAL: 845
pass   2 (-+):   0 found - 189 modified     |    TOTAL: 845
Iteration Number : 2
pass   1 (xy+):  16 found -  16 modified     |    TOTAL:  16
pass   2 (xy+):   0 found -  16 modified     |    TOTAL:  16
pass   1 (xy-):   6 found -   6 modified     |    TOTAL:  22
pass   2 (xy-):   0 found -   6 modified     |    TOTAL:  22
pass   1 (yz+):  25 found -  25 modified     |    TOTAL:  47
pass   2 (yz+):   0 found -  25 modified     |    TOTAL:  47
pass   1 (yz-):  11 found -  11 modified     |    TOTAL:  58
pass   2 (yz-):   0 found -  11 modified     |    TOTAL:  58
pass   1 (xz+):  17 found -  17 modified     |    TOTAL:  75
pass   2 (xz+):   0 found -  17 modified     |    TOTAL:  75
pass   1 (xz-):  14 found -  14 modified     |    TOTAL:  89
pass   2 (xz-):   0 found -  14 modified     |    TOTAL:  89
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   8
Iteration Number : 2
pass   1 (++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+-):  10 found -  10 modified     |    TOTAL:  16
pass   2 (+-):   0 found -  10 modified     |    TOTAL:  16
pass   1 (--):   8 found -   8 modified     |    TOTAL:  24
pass   2 (--):   0 found -   8 modified     |    TOTAL:  24
pass   1 (-+):   8 found -   8 modified     |    TOTAL:  32
pass   2 (-+):   0 found -   8 modified     |    TOTAL:  32
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (--):   1 found -   1 modified     |    TOTAL:   4
pass   2 (--):   0 found -   1 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1802 (out of 296029: 0.608724)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:13:25:46 mri_pretess N 5 e 4.71 S 0.01 U 4.54 P 96% M 57164 F 0 R 17118 W 0 c 610 w 2 I 0 O 600 L 1.00 0.95 0.76
@#@FSLOADPOST 2020:09:25:13:25:51 mri_pretess N 5 1.00 0.95 0.76
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 13:25:51 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 788 (min = 350, max = 1400), aspect = 4.43 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 292690 voxels filled...
filling volume: pass 2 of 3...total of 16417584 voxels filled...
filling volume: pass 3 of 3...total of 293075 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 292690 voxels filled...
filling volume: pass 2 of 3...total of 16417584 voxels filled...
filling volume: pass 3 of 3...total of 293075 voxels filled...done.
filling degenerate left hemisphere surface locations...
379 voxels filled
8 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
379 voxels filled
8 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16417179 voxels filled...
filling volume: pass 3 of 3...total of 293480 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16417179 voxels filled...
filling volume: pass 3 of 3...total of 293480 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  293087 ambiguous voxels remaining
9:  40630 ambiguous voxels remaining
8:  22002 ambiguous voxels remaining
7:  14162 ambiguous voxels remaining
6:  6492 ambiguous voxels remaining
5:  3337 ambiguous voxels remaining
4:  1909 ambiguous voxels remaining
3:  633 ambiguous voxels remaining
2:  250 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:13:25:51 mri_fill N 12 e 36.82 S 0.10 U 34.01 P 92% M 111276 F 0 R 77596 W 0 c 2100 w 1 I 0 O 208 L 1.00 0.95 0.76
@#@FSLOADPOST 2020:09:25:13:26:28 mri_fill N 12 1.07 0.97 0.78
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 13:26:28 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 164878: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:13:26:28 mri_pretess N 4 e 1.78 S 0.02 U 1.42 P 80% M 40516 F 0 R 8848 W 0 c 162 w 1 I 0 O 200 L 1.07 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:29 mri_pretess N 4 1.07 0.97 0.78

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3252 vertices, 3426 faces
slice 70: 7229 vertices, 7422 faces
slice 80: 16166 vertices, 16634 faces
slice 90: 35561 vertices, 36314 faces
slice 100: 55786 vertices, 56665 faces
slice 110: 77964 vertices, 78720 faces
slice 120: 96874 vertices, 97647 faces
slice 130: 110205 vertices, 110739 faces
slice 140: 117987 vertices, 118299 faces
slice 150: 120252 vertices, 120424 faces
slice 160: 120252 vertices, 120424 faces
slice 170: 120252 vertices, 120424 faces
slice 180: 120252 vertices, 120424 faces
slice 190: 120252 vertices, 120424 faces
slice 200: 120252 vertices, 120424 faces
slice 210: 120252 vertices, 120424 faces
slice 220: 120252 vertices, 120424 faces
slice 230: 120252 vertices, 120424 faces
slice 240: 120252 vertices, 120424 faces
slice 250: 120252 vertices, 120424 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:13:26:29 mri_tessellate N 3 e 2.43 S 0.02 U 2.35 P 97% M 36564 F 0 R 8183 W 0 c 80 w 1 I 0 O 5648 L 1.07 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:32 mri_tessellate N 3 1.07 0.97 0.78

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   120252 voxel in cpt #1: X=-172 [v=120252,e=361272,f=240848] located at (-2.879553, -27.311022, 14.327321)
For the whole surface: X=-172 [v=120252,e=361272,f=240848]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:13:26:32 mris_extract_main_component N 2 e 0.95 S 0.09 U 0.81 P 94% M 241844 F 0 R 66325 W 0 c 66 w 1 I 0 O 8472 L 1.07 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:33 mris_extract_main_component N 2 1.07 0.97 0.78
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 13:26:33 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 10 (out of 128613: 0.007775)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:13:26:33 mri_pretess N 4 e 3.04 S 0.00 U 2.20 P 72% M 40468 F 0 R 8846 W 0 c 413 w 1 I 0 O 200 L 1.07 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:36 mri_pretess N 4 1.07 0.97 0.78

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 14 vertices, 20 faces
slice 80: 2990 vertices, 3279 faces
slice 90: 17388 vertices, 17967 faces
slice 100: 33702 vertices, 34429 faces
slice 110: 55237 vertices, 56008 faces
slice 120: 73210 vertices, 73911 faces
slice 130: 85831 vertices, 86310 faces
slice 140: 93656 vertices, 93955 faces
slice 150: 95528 vertices, 95672 faces
slice 160: 95528 vertices, 95672 faces
slice 170: 95528 vertices, 95672 faces
slice 180: 95528 vertices, 95672 faces
slice 190: 95528 vertices, 95672 faces
slice 200: 95528 vertices, 95672 faces
slice 210: 95528 vertices, 95672 faces
slice 220: 95528 vertices, 95672 faces
slice 230: 95528 vertices, 95672 faces
slice 240: 95528 vertices, 95672 faces
slice 250: 95528 vertices, 95672 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:13:26:36 mri_tessellate N 3 e 2.39 S 0.01 U 2.31 P 97% M 34484 F 0 R 7650 W 0 c 88 w 1 I 0 O 4488 L 1.07 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:38 mri_tessellate N 3 1.06 0.97 0.78

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   95528 voxel in cpt #1: X=-144 [v=95528,e=287016,f=191344] located at (56.386181, -21.879711, 15.277458)
For the whole surface: X=-144 [v=95528,e=287016,f=191344]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:13:26:39 mris_extract_main_component N 2 e 0.77 S 0.06 U 0.66 P 94% M 193180 F 0 R 52733 W 0 c 63 w 1 I 0 O 6728 L 1.06 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:39 mris_extract_main_component N 2 1.06 0.97 0.78
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 13:26:39 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:13:26:39 mris_smooth N 5 e 3.67 S 0.07 U 3.51 P 97% M 195440 F 0 R 54514 W 0 c 107 w 1 I 0 O 8472 L 1.06 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:43 mris_smooth N 5 1.06 0.97 0.78
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 13:26:43 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:13:26:43 mris_smooth N 5 e 2.97 S 0.08 U 2.82 P 97% M 157488 F 0 R 43559 W 0 c 99 w 1 I 0 O 6728 L 1.06 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:26:46 mris_smooth N 5 1.06 0.97 0.78
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 13:26:46 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.4 mm, total surface area = 69064 mm^2

step 000: RMS=0.142 (target=0.015)   
step 005: RMS=0.116 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.091 (target=0.015)   
step 020: RMS=0.086 (target=0.015)   
step 025: RMS=0.082 (target=0.015)   
step 030: RMS=0.080 (target=0.015)   
step 035: RMS=0.078 (target=0.015)   
step 040: RMS=0.076 (target=0.015)   
step 045: RMS=0.075 (target=0.015)   
step 050: RMS=0.074 (target=0.015)   
step 055: RMS=0.076 (target=0.015)   
step 060: RMS=0.076 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    18.239384
mris_inflate stimesec    0.092118
mris_inflate ru_maxrss   252696
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   73814
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8472
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   377
@#@FSTIME  2020:09:25:13:26:46 mris_inflate N 3 e 18.51 S 0.10 U 18.24 P 99% M 252900 F 0 R 73816 W 0 c 380 w 1 I 0 O 8472 L 1.06 0.97 0.78
@#@FSLOADPOST 2020:09:25:13:27:05 mris_inflate N 3 1.04 0.97 0.79
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 13:27:05 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 43.6 mm, total surface area = 54318 mm^2

step 000: RMS=0.147 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.087 (target=0.015)   
step 025: RMS=0.082 (target=0.015)   
step 030: RMS=0.080 (target=0.015)   
step 035: RMS=0.079 (target=0.015)   
step 040: RMS=0.079 (target=0.015)   
step 045: RMS=0.078 (target=0.015)   
step 050: RMS=0.078 (target=0.015)   
step 055: RMS=0.078 (target=0.015)   
step 060: RMS=0.078 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    13.824947
mris_inflate stimesec    0.072004
mris_inflate ru_maxrss   202260
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   58278
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  6728
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   334
@#@FSTIME  2020:09:25:13:27:05 mris_inflate N 3 e 14.03 S 0.07 U 13.82 P 99% M 202444 F 0 R 58280 W 0 c 337 w 1 I 0 O 6728 L 1.04 0.97 0.79
@#@FSLOADPOST 2020:09:25:13:27:19 mris_inflate N 3 1.03 0.98 0.79

Started at 2020��� 09��� 25��� ��������� 13:14:47 CST 
Ended   at 2020��� 09��� 25��� ��������� 13:27:19 CST
#@#%# recon-all-run-time-hours 0.209
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 13:27:19 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 13:32:40 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        615M        627M        9.0M        750M        1.2G
Swap:          2.0G        611M        1.4G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:40-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-05:32:41-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 13:32:41 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 5 control points...
only using 5 control points from file, mean 94.0, scaling by 1.17...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 111
gm peak at 61 (61), valley at 19 (19)
csf peak at 31, setting threshold to 51
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 19 (19)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 25 seconds.
@#@FSTIME  2020:09:25:13:32:41 mri_normalize N 7 e 386.17 S 0.42 U 384.99 P 99% M 583228 F 0 R 312307 W 0 c 4183 w 1 I 0 O 3016 L 0.02 0.35 0.56
@#@FSLOADPOST 2020:09:25:13:39:07 mri_normalize N 7 1.00 0.83 0.73
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 13:39:07 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:13:39:07 mri_mask N 5 e 2.79 S 0.02 U 2.63 P 95% M 74036 F 0 R 17272 W 0 c 134 w 1 I 0 O 2944 L 1.00 0.83 0.73
@#@FSLOADPOST 2020:09:25:13:39:10 mri_mask N 5 1.00 0.83 0.73
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 13:39:10 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:13:39:17 AntsDenoiseImageFs N 4 e 63.09 S 0.09 U 62.92 P 99% M 350800 F 0 R 86513 W 0 c 606 w 1 I 0 O 2984 L 1.00 0.84 0.73
@#@FSLOADPOST 2020:09:25:13:40:20 AntsDenoiseImageFs N 4 1.00 0.87 0.75

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 104.6 +- 5.9 [79.0 --> 125.0]
CCS GM (71.0) : 69.6 +- 10.9 [30.0 --> 95.0]
 white_mean 104.625
 white_sigma 5.89886
 gray_mean 69.6119
 gray_sigma 10.9407
setting bottom of white matter range wm_low to 80.6
setting top of gray matter range gray_hi to 91.5
 wm_low 80.5526
 wm_hi  125
 gray_low 30
 gray_hi  91.4933
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.5526
 wm_hi  125
 gray_low 30
 gray_hi  91.4933
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 91.4933, wm_low = 80.5526
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=91.4933, wmlow=80.5526
    105998 voxels processed (0.63%)
     49624 voxels white (0.30%)
     56374 voxels non-white (0.34%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.5526, gray_hi=91.4933, wsize=13
    177610 voxels tested (1.06%)
     44214 voxels changed (0.26%)
     35673 multi-scale searches  (0.21%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.5526
 wm_hi 125
 slack 5.89886
 pct_thresh 0.33
 intensity_thresh 130.899
 nvox_thresh 8.58
      781 voxels tested (0.00%)
      663 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.5526, hithr=91.4933
  smoothing input volume with sigma = 0.250
    75836 voxels tested (0.45%)
    12451 voxels changed (0.07%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 5110 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3266 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 2929 filled
MRIfindBrightNonWM(): 1152 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.2 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:13:40:20 mri_segment N 6 e 194.26 S 0.20 U 193.45 P 99% M 147096 F 0 R 167320 W 0 c 2323 w 1 I 0 O 600 L 1.00 0.87 0.75
@#@FSLOADPOST 2020:09:25:13:43:34 mri_segment N 6 1.00 0.94 0.81

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  94 found -  94 modified     |    TOTAL:  94
pass   2 (xy+):   0 found -  94 modified     |    TOTAL:  94
pass   1 (xy-):  91 found -  91 modified     |    TOTAL: 185
pass   2 (xy-):   0 found -  91 modified     |    TOTAL: 185
pass   1 (yz+): 173 found - 173 modified     |    TOTAL: 358
pass   2 (yz+):   0 found - 173 modified     |    TOTAL: 358
pass   1 (yz-):  55 found -  55 modified     |    TOTAL: 413
pass   2 (yz-):   0 found -  55 modified     |    TOTAL: 413
pass   1 (xz+): 113 found - 113 modified     |    TOTAL: 526
pass   2 (xz+):   0 found - 113 modified     |    TOTAL: 526
pass   1 (xz-):  87 found -  87 modified     |    TOTAL: 613
pass   2 (xz-):   0 found -  87 modified     |    TOTAL: 613
Iteration Number : 1
pass   1 (+++):  75 found -  75 modified     |    TOTAL:  75
pass   2 (+++):   0 found -  75 modified     |    TOTAL:  75
pass   1 (+++):  22 found -  22 modified     |    TOTAL:  97
pass   2 (+++):   0 found -  22 modified     |    TOTAL:  97
pass   1 (+++):  48 found -  48 modified     |    TOTAL: 145
pass   2 (+++):   0 found -  48 modified     |    TOTAL: 145
pass   1 (+++):  27 found -  27 modified     |    TOTAL: 172
pass   2 (+++):   0 found -  27 modified     |    TOTAL: 172
Iteration Number : 1
pass   1 (++): 177 found - 177 modified     |    TOTAL: 177
pass   2 (++):   0 found - 177 modified     |    TOTAL: 177
pass   1 (+-): 238 found - 238 modified     |    TOTAL: 415
pass   2 (+-):   0 found - 238 modified     |    TOTAL: 415
pass   1 (--): 212 found - 212 modified     |    TOTAL: 627
pass   2 (--):   0 found - 212 modified     |    TOTAL: 627
pass   1 (-+): 205 found - 205 modified     |    TOTAL: 832
pass   2 (-+):   0 found - 205 modified     |    TOTAL: 832
Iteration Number : 2
pass   1 (xy+):  17 found -  17 modified     |    TOTAL:  17
pass   2 (xy+):   0 found -  17 modified     |    TOTAL:  17
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:  19
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:  19
pass   1 (yz+):  25 found -  25 modified     |    TOTAL:  44
pass   2 (yz+):   0 found -  25 modified     |    TOTAL:  44
pass   1 (yz-):  11 found -  11 modified     |    TOTAL:  55
pass   2 (yz-):   0 found -  11 modified     |    TOTAL:  55
pass   1 (xz+):  19 found -  19 modified     |    TOTAL:  74
pass   2 (xz+):   0 found -  19 modified     |    TOTAL:  74
pass   1 (xz-):   9 found -   9 modified     |    TOTAL:  83
pass   2 (xz-):   0 found -   9 modified     |    TOTAL:  83
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):  10 found -  10 modified     |    TOTAL:  12
pass   2 (+-):   0 found -  10 modified     |    TOTAL:  12
pass   1 (--):   9 found -   9 modified     |    TOTAL:  21
pass   2 (--):   0 found -   9 modified     |    TOTAL:  21
pass   1 (-+):   3 found -   3 modified     |    TOTAL:  24
pass   2 (-+):   0 found -   3 modified     |    TOTAL:  24
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (--):   1 found -   1 modified     |    TOTAL:   4
pass   2 (--):   0 found -   1 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1734 (out of 295931: 0.585947)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:13:43:35 mri_pretess N 5 e 6.36 S 0.03 U 4.68 P 74% M 57232 F 0 R 17119 W 0 c 778 w 1 I 0 O 600 L 1.00 0.94 0.81
@#@FSLOADPOST 2020:09:25:13:43:41 mri_pretess N 5 1.00 0.94 0.81
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 13:43:41 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 786 (min = 350, max = 1400), aspect = 4.43 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 292545 voxels filled...
filling volume: pass 2 of 3...total of 16417789 voxels filled...
filling volume: pass 3 of 3...total of 292870 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 292545 voxels filled...
filling volume: pass 2 of 3...total of 16417789 voxels filled...
filling volume: pass 3 of 3...total of 292870 voxels filled...done.
filling degenerate left hemisphere surface locations...
391 voxels filled
13 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
391 voxels filled
13 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16417367 voxels filled...
filling volume: pass 3 of 3...total of 293292 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16417367 voxels filled...
filling volume: pass 3 of 3...total of 293292 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  292899 ambiguous voxels remaining
9:  40143 ambiguous voxels remaining
8:  22210 ambiguous voxels remaining
7:  14308 ambiguous voxels remaining
6:  5622 ambiguous voxels remaining
5:  3276 ambiguous voxels remaining
4:  1718 ambiguous voxels remaining
3:  511 ambiguous voxels remaining
2:  145 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:13:43:41 mri_fill N 12 e 38.20 S 0.07 U 35.37 P 92% M 111216 F 0 R 77594 W 0 c 1741 w 1 I 0 O 208 L 1.00 0.94 0.81
@#@FSLOADPOST 2020:09:25:13:44:19 mri_fill N 12 1.00 0.95 0.82
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 13:44:19 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 164420: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:13:44:19 mri_pretess N 4 e 1.58 S 0.01 U 1.33 P 84% M 40356 F 0 R 8844 W 0 c 141 w 1 I 0 O 200 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:21 mri_pretess N 4 1.00 0.95 0.82

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3252 vertices, 3426 faces
slice 70: 7238 vertices, 7434 faces
slice 80: 16129 vertices, 16595 faces
slice 90: 35412 vertices, 36174 faces
slice 100: 55726 vertices, 56629 faces
slice 110: 78177 vertices, 78962 faces
slice 120: 97076 vertices, 97873 faces
slice 130: 110393 vertices, 110953 faces
slice 140: 118175 vertices, 118514 faces
slice 150: 120440 vertices, 120638 faces
slice 160: 120440 vertices, 120638 faces
slice 170: 120440 vertices, 120638 faces
slice 180: 120440 vertices, 120638 faces
slice 190: 120440 vertices, 120638 faces
slice 200: 120440 vertices, 120638 faces
slice 210: 120440 vertices, 120638 faces
slice 220: 120440 vertices, 120638 faces
slice 230: 120440 vertices, 120638 faces
slice 240: 120440 vertices, 120638 faces
slice 250: 120440 vertices, 120638 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:13:44:21 mri_tessellate N 3 e 2.44 S 0.02 U 2.31 P 95% M 36468 F 0 R 8185 W 0 c 91 w 1 I 0 O 5656 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:23 mri_tessellate N 3 1.00 0.95 0.82

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   120440 voxel in cpt #1: X=-198 [v=120440,e=361914,f=241276] located at (-2.822866, -27.290651, 14.188700)
For the whole surface: X=-198 [v=120440,e=361914,f=241276]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:13:44:23 mris_extract_main_component N 2 e 0.94 S 0.09 U 0.80 P 95% M 242300 F 0 R 66446 W 0 c 61 w 1 I 0 O 8480 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:24 mris_extract_main_component N 2 1.00 0.95 0.82
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 13:44:24 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 128873: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:13:44:24 mri_pretess N 4 e 1.61 S 0.01 U 1.33 P 83% M 40452 F 0 R 8848 W 0 c 165 w 1 I 0 O 200 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:26 mri_pretess N 4 1.00 0.95 0.82

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 26 vertices, 33 faces
slice 80: 3236 vertices, 3512 faces
slice 90: 17807 vertices, 18373 faces
slice 100: 33922 vertices, 34662 faces
slice 110: 55479 vertices, 56262 faces
slice 120: 73490 vertices, 74200 faces
slice 130: 86075 vertices, 86564 faces
slice 140: 93871 vertices, 94181 faces
slice 150: 95730 vertices, 95886 faces
slice 160: 95730 vertices, 95886 faces
slice 170: 95730 vertices, 95886 faces
slice 180: 95730 vertices, 95886 faces
slice 190: 95730 vertices, 95886 faces
slice 200: 95730 vertices, 95886 faces
slice 210: 95730 vertices, 95886 faces
slice 220: 95730 vertices, 95886 faces
slice 230: 95730 vertices, 95886 faces
slice 240: 95730 vertices, 95886 faces
slice 250: 95730 vertices, 95886 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:13:44:26 mri_tessellate N 3 e 2.32 S 0.01 U 2.25 P 97% M 34456 F 0 R 7655 W 0 c 78 w 1 I 0 O 4496 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:28 mri_tessellate N 3 1.00 0.95 0.82

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   95730 voxel in cpt #1: X=-156 [v=95730,e=287658,f=191772] located at (56.619232, -22.003395, 15.177353)
For the whole surface: X=-156 [v=95730,e=287658,f=191772]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:13:44:28 mris_extract_main_component N 2 e 0.78 S 0.05 U 0.68 P 93% M 193696 F 0 R 52829 W 0 c 69 w 1 I 0 O 6744 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:29 mris_extract_main_component N 2 1.00 0.95 0.82
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 13:44:29 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:13:44:29 mris_smooth N 5 e 3.56 S 0.07 U 3.40 P 97% M 195668 F 0 R 54566 W 0 c 117 w 1 I 0 O 8480 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:33 mris_smooth N 5 1.00 0.95 0.82
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 13:44:33 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:13:44:33 mris_smooth N 5 e 2.83 S 0.05 U 2.70 P 97% M 156848 F 0 R 43388 W 0 c 90 w 1 I 0 O 6744 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:36 mris_smooth N 5 1.00 0.95 0.82
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 13:44:36 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.3 mm, total surface area = 69141 mm^2

step 000: RMS=0.144 (target=0.015)   
step 005: RMS=0.118 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.088 (target=0.015)   
step 025: RMS=0.085 (target=0.015)   
step 030: RMS=0.082 (target=0.015)   
step 035: RMS=0.080 (target=0.015)   
step 040: RMS=0.078 (target=0.015)   
step 045: RMS=0.077 (target=0.015)   
step 050: RMS=0.076 (target=0.015)   
step 055: RMS=0.076 (target=0.015)   
step 060: RMS=0.076 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.313030
mris_inflate stimesec    0.080171
mris_inflate ru_maxrss   252192
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   68787
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8488
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   367
@#@FSTIME  2020:09:25:13:44:36 mris_inflate N 3 e 17.53 S 0.08 U 17.31 P 99% M 252544 F 0 R 68789 W 0 c 370 w 1 I 0 O 8488 L 1.00 0.95 0.82
@#@FSLOADPOST 2020:09:25:13:44:53 mris_inflate N 3 1.00 0.96 0.83
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 13:44:53 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 43.4 mm, total surface area = 54719 mm^2

step 000: RMS=0.147 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.094 (target=0.015)   
step 020: RMS=0.088 (target=0.015)   
step 025: RMS=0.082 (target=0.015)   
step 030: RMS=0.081 (target=0.015)   
step 035: RMS=0.080 (target=0.015)   
step 040: RMS=0.078 (target=0.015)   
step 045: RMS=0.077 (target=0.015)   
step 050: RMS=0.076 (target=0.015)   
step 055: RMS=0.077 (target=0.015)   
step 060: RMS=0.077 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    13.823377
mris_inflate stimesec    0.052042
mris_inflate ru_maxrss   201720
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   54691
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  6744
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   343
@#@FSTIME  2020:09:25:13:44:53 mris_inflate N 3 e 14.03 S 0.05 U 13.82 P 98% M 201980 F 0 R 54693 W 0 c 346 w 1 I 0 O 6744 L 1.00 0.96 0.83
@#@FSLOADPOST 2020:09:25:13:45:07 mris_inflate N 3 1.00 0.96 0.83

Started at 2020��� 09��� 25��� ��������� 13:32:40 CST 
Ended   at 2020��� 09��� 25��� ��������� 13:45:08 CST
#@#%# recon-all-run-time-hours 0.208
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 13:45:08 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 14:00:30 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        619M        632M        9.0M        741M        1.2G
Swap:          2.0G        611M        1.4G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:00:30-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 14:00:30 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 3 control points...
only using 3 control points from file, mean 125.3, scaling by 0.88...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 19 (19)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 58 (58), valley at 19 (19)
csf peak at 29, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 13 seconds.
@#@FSTIME  2020:09:25:14:00:30 mri_normalize N 7 e 374.66 S 0.40 U 373.07 P 99% M 583420 F 0 R 312313 W 0 c 3799 w 1 I 0 O 3024 L 0.02 0.06 0.29
@#@FSLOADPOST 2020:09:25:14:06:45 mri_normalize N 7 1.00 0.74 0.54
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 14:06:45 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:14:06:45 mri_mask N 5 e 2.64 S 0.01 U 2.60 P 99% M 74108 F 0 R 17275 W 0 c 63 w 1 I 0 O 2952 L 1.00 0.74 0.54
@#@FSLOADPOST 2020:09:25:14:06:48 mri_mask N 5 1.00 0.74 0.54
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 14:06:48 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:14:06:55 AntsDenoiseImageFs N 4 e 64.41 S 0.10 U 63.74 P 99% M 350864 F 0 R 86518 W 0 c 721 w 1 I 0 O 2984 L 1.00 0.75 0.55
@#@FSLOADPOST 2020:09:25:14:07:59 AntsDenoiseImageFs N 4 1.00 0.80 0.58

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.1 +- 5.8 [79.0 --> 125.0]
CCS GM (71.0) : 69.6 +- 10.6 [30.0 --> 95.0]
 white_mean 104.116
 white_sigma 5.82132
 gray_mean 69.6186
 gray_sigma 10.5894
setting bottom of white matter range wm_low to 80.2
setting top of gray matter range gray_hi to 90.8
 wm_low 80.208
 wm_hi  125
 gray_low 30
 gray_hi  90.7975
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 80.208
 wm_hi  125
 gray_low 30
 gray_hi  90.7975
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.7975, wm_low = 80.208
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.7975, wmlow=80.208
     97992 voxels processed (0.58%)
     46483 voxels white (0.28%)
     51509 voxels non-white (0.31%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=75.208, gray_hi=90.7975, wsize=13
    167032 voxels tested (1.00%)
     42425 voxels changed (0.25%)
     35593 multi-scale searches  (0.21%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 80.208
 wm_hi 125
 slack 5.82132
 pct_thresh 0.33
 intensity_thresh 130.821
 nvox_thresh 8.58
      204 voxels tested (0.00%)
       94 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=75.208, hithr=90.7975
  smoothing input volume with sigma = 0.250
    73177 voxels tested (0.44%)
    12030 voxels changed (0.07%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 4811 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3005 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3509 filled
MRIfindBrightNonWM(): 965 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.3 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:14:07:59 mri_segment N 6 e 198.64 S 0.08 U 194.96 P 98% M 146776 F 0 R 62867 W 0 c 4385 w 1 I 0 O 584 L 1.00 0.80 0.58
@#@FSLOADPOST 2020:09:25:14:11:18 mri_segment N 6 1.00 0.90 0.67

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  97 found -  97 modified     |    TOTAL:  97
pass   2 (xy+):   0 found -  97 modified     |    TOTAL:  97
pass   1 (xy-): 103 found - 103 modified     |    TOTAL: 200
pass   2 (xy-):   0 found - 103 modified     |    TOTAL: 200
pass   1 (yz+): 170 found - 170 modified     |    TOTAL: 370
pass   2 (yz+):   0 found - 170 modified     |    TOTAL: 370
pass   1 (yz-):  50 found -  50 modified     |    TOTAL: 420
pass   2 (yz-):   0 found -  50 modified     |    TOTAL: 420
pass   1 (xz+): 115 found - 115 modified     |    TOTAL: 535
pass   2 (xz+):   0 found - 115 modified     |    TOTAL: 535
pass   1 (xz-):  91 found -  91 modified     |    TOTAL: 626
pass   2 (xz-):   0 found -  91 modified     |    TOTAL: 626
Iteration Number : 1
pass   1 (+++):  67 found -  67 modified     |    TOTAL:  67
pass   2 (+++):   0 found -  67 modified     |    TOTAL:  67
pass   1 (+++):  24 found -  24 modified     |    TOTAL:  91
pass   2 (+++):   0 found -  24 modified     |    TOTAL:  91
pass   1 (+++):  43 found -  43 modified     |    TOTAL: 134
pass   2 (+++):   0 found -  43 modified     |    TOTAL: 134
pass   1 (+++):  25 found -  25 modified     |    TOTAL: 159
pass   2 (+++):   0 found -  25 modified     |    TOTAL: 159
Iteration Number : 1
pass   1 (++): 144 found - 144 modified     |    TOTAL: 144
pass   2 (++):   0 found - 144 modified     |    TOTAL: 144
pass   1 (+-): 233 found - 233 modified     |    TOTAL: 377
pass   2 (+-):   0 found - 233 modified     |    TOTAL: 377
pass   1 (--): 204 found - 204 modified     |    TOTAL: 581
pass   2 (--):   0 found - 204 modified     |    TOTAL: 581
pass   1 (-+): 171 found - 171 modified     |    TOTAL: 752
pass   2 (-+):   0 found - 171 modified     |    TOTAL: 752
Iteration Number : 2
pass   1 (xy+):  10 found -  10 modified     |    TOTAL:  10
pass   2 (xy+):   0 found -  10 modified     |    TOTAL:  10
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  15
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  15
pass   1 (yz+):  14 found -  14 modified     |    TOTAL:  29
pass   2 (yz+):   0 found -  14 modified     |    TOTAL:  29
pass   1 (yz-):   9 found -   9 modified     |    TOTAL:  38
pass   2 (yz-):   0 found -   9 modified     |    TOTAL:  38
pass   1 (xz+):  13 found -  13 modified     |    TOTAL:  51
pass   2 (xz+):   0 found -  13 modified     |    TOTAL:  51
pass   1 (xz-):  13 found -  13 modified     |    TOTAL:  64
pass   2 (xz-):   0 found -  13 modified     |    TOTAL:  64
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   7 found -   7 modified     |    TOTAL:   9
pass   2 (+-):   0 found -   7 modified     |    TOTAL:   9
pass   1 (--):   3 found -   3 modified     |    TOTAL:  12
pass   2 (--):   0 found -   3 modified     |    TOTAL:  12
pass   1 (-+):   7 found -   7 modified     |    TOTAL:  19
pass   2 (-+):   0 found -   7 modified     |    TOTAL:  19
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   3
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1630 (out of 285478: 0.570972)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:14:11:18 mri_pretess N 5 e 6.93 S 0.01 U 5.03 P 72% M 57032 F 0 R 17113 W 0 c 877 w 1 I 0 O 584 L 1.00 0.90 0.67
@#@FSLOADPOST 2020:09:25:14:11:25 mri_pretess N 5 1.00 0.91 0.67
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 14:11:25 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 774 (min = 350, max = 1400), aspect = 4.64 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 282132 voxels filled...
filling volume: pass 2 of 3...total of 16428244 voxels filled...
filling volume: pass 3 of 3...total of 282415 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 282132 voxels filled...
filling volume: pass 2 of 3...total of 16428244 voxels filled...
filling volume: pass 3 of 3...total of 282415 voxels filled...done.
filling degenerate left hemisphere surface locations...
359 voxels filled
4 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
359 voxels filled
4 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16427878 voxels filled...
filling volume: pass 3 of 3...total of 282781 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16427878 voxels filled...
filling volume: pass 3 of 3...total of 282781 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  282388 ambiguous voxels remaining
9:  40027 ambiguous voxels remaining
8:  20874 ambiguous voxels remaining
7:  13794 ambiguous voxels remaining
6:  5556 ambiguous voxels remaining
5:  3320 ambiguous voxels remaining
4:  1809 ambiguous voxels remaining
3:  579 ambiguous voxels remaining
2:  150 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.5 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:14:11:25 mri_fill N 12 e 32.37 S 0.09 U 31.49 P 97% M 111296 F 0 R 77591 W 0 c 1059 w 1 I 0 O 200 L 1.00 0.91 0.67
@#@FSLOADPOST 2020:09:25:14:11:57 mri_fill N 12 1.00 0.92 0.68
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 14:11:57 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1 (out of 157152: 0.000636)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:14:11:57 mri_pretess N 4 e 2.31 S 0.01 U 1.70 P 74% M 40352 F 0 R 8844 W 0 c 274 w 1 I 0 O 192 L 1.00 0.92 0.68
@#@FSLOADPOST 2020:09:25:14:11:59 mri_pretess N 4 1.16 0.95 0.70

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3254 vertices, 3427 faces
slice 70: 7240 vertices, 7434 faces
slice 80: 16342 vertices, 16810 faces
slice 90: 34836 vertices, 35513 faces
slice 100: 53341 vertices, 54185 faces
slice 110: 75124 vertices, 75902 faces
slice 120: 93548 vertices, 94306 faces
slice 130: 106331 vertices, 106836 faces
slice 140: 113614 vertices, 113927 faces
slice 150: 115816 vertices, 115994 faces
slice 160: 115816 vertices, 115994 faces
slice 170: 115816 vertices, 115994 faces
slice 180: 115816 vertices, 115994 faces
slice 190: 115816 vertices, 115994 faces
slice 200: 115816 vertices, 115994 faces
slice 210: 115816 vertices, 115994 faces
slice 220: 115816 vertices, 115994 faces
slice 230: 115816 vertices, 115994 faces
slice 240: 115816 vertices, 115994 faces
slice 250: 115816 vertices, 115994 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:14:12:00 mri_tessellate N 3 e 2.41 S 0.01 U 2.31 P 96% M 36296 F 0 R 8087 W 0 c 87 w 1 I 0 O 5440 L 1.16 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:02 mri_tessellate N 3 1.16 0.95 0.70

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   115816 voxel in cpt #1: X=-178 [v=115816,e=347982,f=231988] located at (-2.860529, -27.474684, 14.966352)
For the whole surface: X=-178 [v=115816,e=347982,f=231988]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:14:12:02 mris_extract_main_component N 2 e 0.90 S 0.09 U 0.76 P 94% M 233164 F 0 R 63903 W 0 c 68 w 1 I 0 O 8160 L 1.16 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:03 mris_extract_main_component N 2 1.16 0.95 0.70
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 14:12:03 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 4 (out of 125635: 0.003184)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:14:12:03 mri_pretess N 4 e 2.27 S 0.00 U 1.73 P 76% M 40436 F 0 R 8847 W 0 c 265 w 1 I 0 O 192 L 1.16 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:05 mri_pretess N 4 1.15 0.95 0.70

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 28 vertices, 36 faces
slice 80: 3158 vertices, 3458 faces
slice 90: 17183 vertices, 17691 faces
slice 100: 31419 vertices, 32107 faces
slice 110: 52153 vertices, 52924 faces
slice 120: 69951 vertices, 70655 faces
slice 130: 82516 vertices, 83004 faces
slice 140: 90403 vertices, 90709 faces
slice 150: 92306 vertices, 92460 faces
slice 160: 92306 vertices, 92460 faces
slice 170: 92306 vertices, 92460 faces
slice 180: 92306 vertices, 92460 faces
slice 190: 92306 vertices, 92460 faces
slice 200: 92306 vertices, 92460 faces
slice 210: 92306 vertices, 92460 faces
slice 220: 92306 vertices, 92460 faces
slice 230: 92306 vertices, 92460 faces
slice 240: 92306 vertices, 92460 faces
slice 250: 92306 vertices, 92460 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:14:12:05 mri_tessellate N 3 e 2.34 S 0.02 U 2.26 P 97% M 34132 F 0 R 7573 W 0 c 73 w 1 I 0 O 4336 L 1.15 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:08 mri_tessellate N 3 1.15 0.95 0.70

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   92306 voxel in cpt #1: X=-154 [v=92306,e=277380,f=184920] located at (56.918304, -21.554644, 14.689836)
For the whole surface: X=-154 [v=92306,e=277380,f=184920]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:14:12:08 mris_extract_main_component N 2 e 0.70 S 0.08 U 0.57 P 93% M 186992 F 0 R 50958 W 0 c 68 w 1 I 0 O 6504 L 1.15 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:08 mris_extract_main_component N 2 1.15 0.95 0.70
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 14:12:08 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:14:12:08 mris_smooth N 5 e 3.40 S 0.07 U 3.22 P 97% M 188668 F 0 R 52538 W 0 c 105 w 1 I 0 O 8160 L 1.15 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:12 mris_smooth N 5 1.13 0.95 0.70
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 14:12:12 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:14:12:12 mris_smooth N 5 e 2.72 S 0.03 U 2.62 P 97% M 151532 F 0 R 41875 W 0 c 105 w 1 I 0 O 6504 L 1.13 0.95 0.70
@#@FSLOADPOST 2020:09:25:14:12:15 mris_smooth N 5 1.12 0.96 0.70
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 14:12:15 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.6 mm, total surface area = 66627 mm^2

step 000: RMS=0.143 (target=0.015)   
step 005: RMS=0.116 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.090 (target=0.015)   
step 020: RMS=0.084 (target=0.015)   
step 025: RMS=0.082 (target=0.015)   
step 030: RMS=0.078 (target=0.015)   
step 035: RMS=0.076 (target=0.015)   
step 040: RMS=0.075 (target=0.015)   
step 045: RMS=0.074 (target=0.015)   
step 050: RMS=0.073 (target=0.015)   
step 055: RMS=0.075 (target=0.015)   
step 060: RMS=0.075 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.752738
mris_inflate stimesec    0.083923
mris_inflate ru_maxrss   244044
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   71053
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8160
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   362
@#@FSTIME  2020:09:25:14:12:15 mris_inflate N 3 e 17.02 S 0.09 U 16.75 P 98% M 244212 F 0 R 71056 W 0 c 365 w 1 I 0 O 8160 L 1.12 0.96 0.70
@#@FSLOADPOST 2020:09:25:14:12:32 mris_inflate N 3 1.16 0.97 0.71
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 14:12:32 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 42.4 mm, total surface area = 52457 mm^2

step 000: RMS=0.148 (target=0.015)   
step 005: RMS=0.120 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.089 (target=0.015)   
step 025: RMS=0.084 (target=0.015)   
step 030: RMS=0.081 (target=0.015)   
step 035: RMS=0.081 (target=0.015)   
step 040: RMS=0.080 (target=0.015)   
step 045: RMS=0.079 (target=0.015)   
step 050: RMS=0.078 (target=0.015)   
step 055: RMS=0.079 (target=0.015)   
step 060: RMS=0.080 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    13.009887
mris_inflate stimesec    0.043911
mris_inflate ru_maxrss   195840
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   56240
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  6504
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   324
@#@FSTIME  2020:09:25:14:12:32 mris_inflate N 3 e 13.24 S 0.05 U 13.00 P 98% M 195932 F 0 R 56242 W 0 c 328 w 1 I 0 O 6504 L 1.16 0.97 0.71
@#@FSLOADPOST 2020:09:25:14:12:45 mris_inflate N 3 1.13 0.98 0.72

Started at 2020��� 09��� 25��� ��������� 14:00:30 CST 
Ended   at 2020��� 09��� 25��� ��������� 14:12:45 CST
#@#%# recon-all-run-time-hours 0.204
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 14:12:45 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 14:55:26 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        499M        1.3G        6.4M        176M        1.3G
Swap:          2.0G        709M        1.3G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-06:55:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 14:55:27 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 60 control points...
only using 60 control points from file, mean 93.6, scaling by 1.17...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 111
gm peak at 62 (62), valley at 20 (20)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 19 (19)
csf peak at 31, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 41 seconds.
@#@FSTIME  2020:09:25:14:55:27 mri_normalize N 7 e 342.36 S 0.37 U 341.12 P 99% M 583376 F 7 R 312317 W 0 c 3566 w 12 I 4840 O 3016 L 0.20 0.16 0.15
@#@FSLOADPOST 2020:09:25:15:01:09 mri_normalize N 7 1.00 0.74 0.42
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 15:01:09 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:15:01:09 mri_mask N 5 e 2.63 S 0.01 U 2.57 P 98% M 74256 F 5 R 17272 W 0 c 65 w 6 I 1064 O 2944 L 1.00 0.74 0.42
@#@FSLOADPOST 2020:09:25:15:01:12 mri_mask N 5 1.00 0.74 0.43
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 15:01:12 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:15:01:19 AntsDenoiseImageFs N 4 e 61.80 S 0.09 U 61.61 P 99% M 350572 F 18 R 86503 W 0 c 566 w 21 I 4320 O 2984 L 1.00 0.75 0.43
@#@FSLOADPOST 2020:09:25:15:02:21 AntsDenoiseImageFs N 4 1.00 0.80 0.47

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.1 +- 5.6 [79.0 --> 125.0]
CCS GM (71.0) : 69.6 +- 10.4 [30.0 --> 95.0]
 white_mean 104.055
 white_sigma 5.60875
 gray_mean 69.6283
 gray_sigma 10.3554
setting bottom of white matter range wm_low to 80.0
setting top of gray matter range gray_hi to 90.3
 wm_low 79.9838
 wm_hi  125
 gray_low 30
 gray_hi  90.3392
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.9838
 wm_hi  125
 gray_low 30
 gray_hi  90.3392
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.3392, wm_low = 79.9838
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.3392, wmlow=79.9838
    110865 voxels processed (0.66%)
     49222 voxels white (0.29%)
     61643 voxels non-white (0.37%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.9838, gray_hi=90.3392, wsize=13
    192729 voxels tested (1.15%)
     43434 voxels changed (0.26%)
     40565 multi-scale searches  (0.24%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.9838
 wm_hi 125
 slack 5.60875
 pct_thresh 0.33
 intensity_thresh 130.609
 nvox_thresh 8.58
      185 voxels tested (0.00%)
       73 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.9838, hithr=90.3392
  smoothing input volume with sigma = 0.250
    72336 voxels tested (0.43%)
    12396 voxels changed (0.07%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 5305 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3016 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3894 filled
MRIfindBrightNonWM(): 1502 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.5 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:15:02:21 mri_segment N 6 e 209.10 S 0.31 U 205.56 P 98% M 147028 F 5 R 293808 W 0 c 3997 w 6 I 1024 O 616 L 1.00 0.80 0.47
@#@FSLOADPOST 2020:09:25:15:05:50 mri_segment N 6 1.09 0.96 0.61

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  87 found -  87 modified     |    TOTAL:  87
pass   2 (xy+):   0 found -  87 modified     |    TOTAL:  87
pass   1 (xy-):  85 found -  85 modified     |    TOTAL: 172
pass   2 (xy-):   0 found -  85 modified     |    TOTAL: 172
pass   1 (yz+): 154 found - 154 modified     |    TOTAL: 326
pass   2 (yz+):   0 found - 154 modified     |    TOTAL: 326
pass   1 (yz-):  60 found -  60 modified     |    TOTAL: 386
pass   2 (yz-):   0 found -  60 modified     |    TOTAL: 386
pass   1 (xz+): 116 found - 116 modified     |    TOTAL: 502
pass   2 (xz+):   0 found - 116 modified     |    TOTAL: 502
pass   1 (xz-):  80 found -  80 modified     |    TOTAL: 582
pass   2 (xz-):   0 found -  80 modified     |    TOTAL: 582
Iteration Number : 1
pass   1 (+++):  57 found -  57 modified     |    TOTAL:  57
pass   2 (+++):   0 found -  57 modified     |    TOTAL:  57
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  69
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  69
pass   1 (+++):  54 found -  54 modified     |    TOTAL: 123
pass   2 (+++):   0 found -  54 modified     |    TOTAL: 123
pass   1 (+++):  19 found -  19 modified     |    TOTAL: 142
pass   2 (+++):   0 found -  19 modified     |    TOTAL: 142
Iteration Number : 1
pass   1 (++): 135 found - 135 modified     |    TOTAL: 135
pass   2 (++):   0 found - 135 modified     |    TOTAL: 135
pass   1 (+-): 260 found - 260 modified     |    TOTAL: 395
pass   2 (+-):   0 found - 260 modified     |    TOTAL: 395
pass   1 (--): 203 found - 203 modified     |    TOTAL: 598
pass   2 (--):   0 found - 203 modified     |    TOTAL: 598
pass   1 (-+): 209 found - 209 modified     |    TOTAL: 807
pass   2 (-+):   0 found - 209 modified     |    TOTAL: 807
Iteration Number : 2
pass   1 (xy+):   8 found -   8 modified     |    TOTAL:   8
pass   2 (xy+):   0 found -   8 modified     |    TOTAL:   8
pass   1 (xy-):  11 found -  11 modified     |    TOTAL:  19
pass   2 (xy-):   0 found -  11 modified     |    TOTAL:  19
pass   1 (yz+):  18 found -  18 modified     |    TOTAL:  37
pass   2 (yz+):   0 found -  18 modified     |    TOTAL:  37
pass   1 (yz-):   7 found -   7 modified     |    TOTAL:  44
pass   2 (yz-):   0 found -   7 modified     |    TOTAL:  44
pass   1 (xz+):  13 found -  13 modified     |    TOTAL:  57
pass   2 (xz+):   0 found -  13 modified     |    TOTAL:  57
pass   1 (xz-):  10 found -  10 modified     |    TOTAL:  67
pass   2 (xz-):   0 found -  10 modified     |    TOTAL:  67
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+-):  11 found -  11 modified     |    TOTAL:  15
pass   2 (+-):   0 found -  11 modified     |    TOTAL:  15
pass   1 (--):   6 found -   6 modified     |    TOTAL:  21
pass   2 (--):   0 found -   6 modified     |    TOTAL:  21
pass   1 (-+):   6 found -   6 modified     |    TOTAL:  27
pass   2 (-+):   0 found -   6 modified     |    TOTAL:  27
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1637 (out of 302097: 0.541879)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:15:05:50 mri_pretess N 5 e 6.70 S 0.03 U 4.93 P 74% M 57144 F 16 R 17105 W 0 c 887 w 18 I 3472 O 608 L 1.09 0.96 0.61
@#@FSLOADPOST 2020:09:25:15:05:57 mri_pretess N 5 1.08 0.96 0.61
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 15:05:57 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 789 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 298524 voxels filled...
filling volume: pass 2 of 3...total of 16411900 voxels filled...
filling volume: pass 3 of 3...total of 298759 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 298524 voxels filled...
filling volume: pass 2 of 3...total of 16411900 voxels filled...
filling volume: pass 3 of 3...total of 298759 voxels filled...done.
filling degenerate left hemisphere surface locations...
327 voxels filled
6 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
327 voxels filled
6 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16411566 voxels filled...
filling volume: pass 3 of 3...total of 299093 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16411566 voxels filled...
filling volume: pass 3 of 3...total of 299093 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  298700 ambiguous voxels remaining
9:  44531 ambiguous voxels remaining
8:  21441 ambiguous voxels remaining
7:  12925 ambiguous voxels remaining
6:  5430 ambiguous voxels remaining
5:  3603 ambiguous voxels remaining
4:  1855 ambiguous voxels remaining
3:  611 ambiguous voxels remaining
2:  115 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.5 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:15:05:57 mri_fill N 12 e 32.03 S 0.06 U 31.17 P 97% M 111348 F 6 R 77595 W 0 c 1104 w 7 I 1568 O 216 L 1.08 0.96 0.61
@#@FSLOADPOST 2020:09:25:15:06:29 mri_fill N 12 1.05 0.97 0.63
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 15:06:29 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 158031: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:15:06:29 mri_pretess N 4 e 1.64 S 0.01 U 1.35 P 83% M 40420 F 0 R 8846 W 0 c 152 w 1 I 0 O 208 L 1.05 0.97 0.63
@#@FSLOADPOST 2020:09:25:15:06:31 mri_pretess N 4 1.05 0.97 0.63

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3260 vertices, 3425 faces
slice 70: 7313 vertices, 7514 faces
slice 80: 16700 vertices, 17168 faces
slice 90: 36539 vertices, 37276 faces
slice 100: 55841 vertices, 56669 faces
slice 110: 77578 vertices, 78296 faces
slice 120: 95697 vertices, 96408 faces
slice 130: 108077 vertices, 108537 faces
slice 140: 115215 vertices, 115486 faces
slice 150: 117464 vertices, 117598 faces
slice 160: 117464 vertices, 117598 faces
slice 170: 117464 vertices, 117598 faces
slice 180: 117464 vertices, 117598 faces
slice 190: 117464 vertices, 117598 faces
slice 200: 117464 vertices, 117598 faces
slice 210: 117464 vertices, 117598 faces
slice 220: 117464 vertices, 117598 faces
slice 230: 117464 vertices, 117598 faces
slice 240: 117464 vertices, 117598 faces
slice 250: 117464 vertices, 117598 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:15:06:31 mri_tessellate N 3 e 2.36 S 0.00 U 2.28 P 96% M 36396 F 5 R 8111 W 0 c 80 w 7 I 1216 O 5512 L 1.05 0.97 0.63
@#@FSLOADPOST 2020:09:25:15:06:33 mri_tessellate N 3 1.04 0.97 0.63

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   117464 voxel in cpt #1: X=-134 [v=117464,e=352794,f=235196] located at (-3.011178, -27.918810, 16.426521)
For the whole surface: X=-134 [v=117464,e=352794,f=235196]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:15:06:33 mris_extract_main_component N 2 e 0.87 S 0.08 U 0.73 P 93% M 236308 F 18 R 64774 W 0 c 74 w 23 I 4312 O 8272 L 1.04 0.97 0.63
@#@FSLOADPOST 2020:09:25:15:06:34 mris_extract_main_component N 2 1.04 0.97 0.63
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 15:06:34 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 8 (out of 141071: 0.005671)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:15:06:34 mri_pretess N 4 e 2.46 S 0.02 U 1.81 P 74% M 40440 F 0 R 8845 W 0 c 296 w 1 I 0 O 208 L 1.04 0.97 0.63
@#@FSLOADPOST 2020:09:25:15:06:37 mri_pretess N 4 1.20 1.00 0.64

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 1374 vertices, 1481 faces
slice 80: 8552 vertices, 8919 faces
slice 90: 25757 vertices, 26337 faces
slice 100: 43602 vertices, 44322 faces
slice 110: 65358 vertices, 66085 faces
slice 120: 83379 vertices, 84034 faces
slice 130: 95989 vertices, 96423 faces
slice 140: 103875 vertices, 104128 faces
slice 150: 105894 vertices, 105994 faces
slice 160: 105894 vertices, 105994 faces
slice 170: 105894 vertices, 105994 faces
slice 180: 105894 vertices, 105994 faces
slice 190: 105894 vertices, 105994 faces
slice 200: 105894 vertices, 105994 faces
slice 210: 105894 vertices, 105994 faces
slice 220: 105894 vertices, 105994 faces
slice 230: 105894 vertices, 105994 faces
slice 240: 105894 vertices, 105994 faces
slice 250: 105894 vertices, 105994 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:15:06:37 mri_tessellate N 3 e 2.31 S 0.00 U 2.25 P 97% M 35304 F 0 R 7864 W 0 c 75 w 1 I 0 O 4968 L 1.20 1.00 0.64
@#@FSLOADPOST 2020:09:25:15:06:39 mri_tessellate N 3 1.20 1.00 0.64

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   105894 voxel in cpt #1: X=-100 [v=105894,e=317982,f=211988] located at (58.050343, -24.378548, 16.543846)
For the whole surface: X=-100 [v=105894,e=317982,f=211988]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:15:06:39 mris_extract_main_component N 2 e 0.83 S 0.07 U 0.70 P 93% M 213280 F 0 R 58384 W 0 c 67 w 1 I 0 O 7456 L 1.20 1.00 0.64
@#@FSLOADPOST 2020:09:25:15:06:40 mris_extract_main_component N 2 1.20 1.00 0.64
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 15:06:40 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:15:06:40 mris_smooth N 5 e 3.49 S 0.05 U 3.29 P 95% M 190864 F 5 R 53227 W 0 c 101 w 8 I 1304 O 8272 L 1.20 1.00 0.64
@#@FSLOADPOST 2020:09:25:15:06:43 mris_smooth N 5 1.18 1.00 0.65
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 15:06:43 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:15:06:43 mris_smooth N 5 e 3.10 S 0.05 U 2.96 P 97% M 172696 F 0 R 47953 W 0 c 112 w 1 I 0 O 7456 L 1.18 1.00 0.65
@#@FSLOADPOST 2020:09:25:15:06:47 mris_smooth N 5 1.17 1.00 0.65
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 15:06:47 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.5 mm, total surface area = 67471 mm^2

step 000: RMS=0.141 (target=0.015)   
step 005: RMS=0.114 (target=0.015)   
step 010: RMS=0.097 (target=0.015)   
step 015: RMS=0.088 (target=0.015)   
step 020: RMS=0.083 (target=0.015)   
step 025: RMS=0.080 (target=0.015)   
step 030: RMS=0.075 (target=0.015)   
step 035: RMS=0.073 (target=0.015)   
step 040: RMS=0.072 (target=0.015)   
step 045: RMS=0.072 (target=0.015)   
step 050: RMS=0.071 (target=0.015)   
step 055: RMS=0.072 (target=0.015)   
step 060: RMS=0.072 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.343332
mris_inflate stimesec    0.115861
mris_inflate ru_maxrss   247120
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   72051
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  8272
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    21
mris_inflate ru_nivcsw   583
@#@FSTIME  2020:09:25:15:06:47 mris_inflate N 3 e 17.89 S 0.12 U 17.34 P 97% M 247320 F 19 R 72053 W 0 c 586 w 22 I 4552 O 8272 L 1.17 1.00 0.65
@#@FSLOADPOST 2020:09:25:15:07:05 mris_inflate N 3 1.13 1.00 0.65
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 15:07:05 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 43.8 mm, total surface area = 61093 mm^2

step 000: RMS=0.137 (target=0.015)   
step 005: RMS=0.111 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.074 (target=0.015)   
step 030: RMS=0.070 (target=0.015)   
step 035: RMS=0.068 (target=0.015)   
step 040: RMS=0.066 (target=0.015)   
step 045: RMS=0.065 (target=0.015)   
step 050: RMS=0.063 (target=0.015)   
step 055: RMS=0.064 (target=0.015)   
step 060: RMS=0.064 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.218239
mris_inflate stimesec    0.076141
mris_inflate ru_maxrss   223428
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   64738
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  7456
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   352
@#@FSTIME  2020:09:25:15:07:05 mris_inflate N 3 e 16.44 S 0.08 U 16.21 P 99% M 223604 F 0 R 64740 W 0 c 355 w 1 I 0 O 7456 L 1.13 1.00 0.65
@#@FSLOADPOST 2020:09:25:15:07:21 mris_inflate N 3 1.10 1.00 0.66

Started at 2020��� 09��� 25��� ��������� 14:55:26 CST 
Ended   at 2020��� 09��� 25��� ��������� 15:07:21 CST
#@#%# recon-all-run-time-hours 0.199
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 15:07:21 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 15:23:44 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        504M        1.0G        6.4M        463M        1.3G
Swap:          2.0G        706M        1.3G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:23:44-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 15:23:44 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 105 control points...
only using 105 control points from file, mean 95.6, scaling by 1.15...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 111
gm peak at 61 (61), valley at 19 (19)
csf peak at 31, setting threshold to 51
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 19 (19)
csf peak at 31, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 53 seconds.
@#@FSTIME  2020:09:25:15:23:44 mri_normalize N 7 e 354.98 S 0.39 U 353.29 P 99% M 583428 F 0 R 312314 W 0 c 4553 w 1 I 0 O 3016 L 0.08 0.16 0.30
@#@FSLOADPOST 2020:09:25:15:29:39 mri_normalize N 7 1.00 0.76 0.54
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 15:29:39 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:15:29:39 mri_mask N 5 e 3.71 S 0.04 U 3.52 P 95% M 74180 F 0 R 17273 W 0 c 55 w 1 I 0 O 2944 L 1.00 0.76 0.54
@#@FSLOADPOST 2020:09:25:15:29:43 mri_mask N 5 1.00 0.76 0.54
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 15:29:43 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:15:29:50 AntsDenoiseImageFs N 4 e 62.72 S 0.08 U 62.56 P 99% M 350824 F 0 R 86515 W 0 c 562 w 1 I 0 O 2984 L 1.00 0.76 0.54
@#@FSLOADPOST 2020:09:25:15:30:53 AntsDenoiseImageFs N 4 1.00 0.81 0.58

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.0 +- 5.7 [79.0 --> 125.0]
CCS GM (71.0) : 69.4 +- 10.4 [30.0 --> 95.0]
 white_mean 104.02
 white_sigma 5.68131
 gray_mean 69.3799
 gray_sigma 10.3871
setting bottom of white matter range wm_low to 79.8
setting top of gray matter range gray_hi to 90.2
 wm_low 79.767
 wm_hi  125
 gray_low 30
 gray_hi  90.1542
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.767
 wm_hi  125
 gray_low 30
 gray_hi  90.1542
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.1542, wm_low = 79.767
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.1542, wmlow=79.767
    111446 voxels processed (0.66%)
     51348 voxels white (0.31%)
     60098 voxels non-white (0.36%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.767, gray_hi=90.1542, wsize=13
    190585 voxels tested (1.14%)
     43565 voxels changed (0.26%)
     39725 multi-scale searches  (0.24%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.767
 wm_hi 125
 slack 5.68131
 pct_thresh 0.33
 intensity_thresh 130.681
 nvox_thresh 8.58
      191 voxels tested (0.00%)
       76 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.767, hithr=90.1542
  smoothing input volume with sigma = 0.250
    75231 voxels tested (0.45%)
    13103 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 5200 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3086 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3899 filled
MRIfindBrightNonWM(): 1510 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.3 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:15:30:53 mri_segment N 6 e 200.09 S 0.07 U 199.68 P 99% M 147400 F 0 R 63188 W 0 c 1904 w 1 I 0 O 616 L 1.00 0.81 0.58
@#@FSLOADPOST 2020:09:25:15:34:13 mri_segment N 6 1.00 0.91 0.67

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  94 found -  94 modified     |    TOTAL:  94
pass   2 (xy+):   0 found -  94 modified     |    TOTAL:  94
pass   1 (xy-):  85 found -  85 modified     |    TOTAL: 179
pass   2 (xy-):   0 found -  85 modified     |    TOTAL: 179
pass   1 (yz+): 159 found - 159 modified     |    TOTAL: 338
pass   2 (yz+):   0 found - 159 modified     |    TOTAL: 338
pass   1 (yz-):  51 found -  51 modified     |    TOTAL: 389
pass   2 (yz-):   0 found -  51 modified     |    TOTAL: 389
pass   1 (xz+): 114 found - 114 modified     |    TOTAL: 503
pass   2 (xz+):   0 found - 114 modified     |    TOTAL: 503
pass   1 (xz-):  85 found -  85 modified     |    TOTAL: 588
pass   2 (xz-):   0 found -  85 modified     |    TOTAL: 588
Iteration Number : 1
pass   1 (+++):  65 found -  65 modified     |    TOTAL:  65
pass   2 (+++):   0 found -  65 modified     |    TOTAL:  65
pass   1 (+++):  22 found -  22 modified     |    TOTAL:  87
pass   2 (+++):   0 found -  22 modified     |    TOTAL:  87
pass   1 (+++):  48 found -  48 modified     |    TOTAL: 135
pass   2 (+++):   0 found -  48 modified     |    TOTAL: 135
pass   1 (+++):  21 found -  21 modified     |    TOTAL: 156
pass   2 (+++):   0 found -  21 modified     |    TOTAL: 156
Iteration Number : 1
pass   1 (++): 136 found - 136 modified     |    TOTAL: 136
pass   2 (++):   0 found - 136 modified     |    TOTAL: 136
pass   1 (+-): 252 found - 252 modified     |    TOTAL: 388
pass   2 (+-):   1 found - 253 modified     |    TOTAL: 389
pass   3 (+-):   0 found - 253 modified     |    TOTAL: 389
pass   1 (--): 168 found - 168 modified     |    TOTAL: 557
pass   2 (--):   0 found - 168 modified     |    TOTAL: 557
pass   1 (-+): 209 found - 209 modified     |    TOTAL: 766
pass   2 (-+):   0 found - 209 modified     |    TOTAL: 766
Iteration Number : 2
pass   1 (xy+):   6 found -   6 modified     |    TOTAL:   6
pass   2 (xy+):   0 found -   6 modified     |    TOTAL:   6
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  11
pass   1 (yz+):  13 found -  13 modified     |    TOTAL:  24
pass   2 (yz+):   0 found -  13 modified     |    TOTAL:  24
pass   1 (yz-):   7 found -   7 modified     |    TOTAL:  31
pass   2 (yz-):   0 found -   7 modified     |    TOTAL:  31
pass   1 (xz+):  17 found -  17 modified     |    TOTAL:  48
pass   2 (xz+):   0 found -  17 modified     |    TOTAL:  48
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  55
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  55
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+-):   7 found -   7 modified     |    TOTAL:  11
pass   2 (+-):   1 found -   8 modified     |    TOTAL:  12
pass   3 (+-):   0 found -   8 modified     |    TOTAL:  12
pass   1 (--):   6 found -   6 modified     |    TOTAL:  18
pass   2 (--):   0 found -   6 modified     |    TOTAL:  18
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  22
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  22
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1596 (out of 304957: 0.523352)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:15:34:13 mri_pretess N 5 e 4.89 S 0.02 U 4.79 P 98% M 57036 F 0 R 17112 W 0 c 359 w 2 I 0 O 608 L 1.00 0.91 0.67
@#@FSLOADPOST 2020:09:25:15:34:18 mri_pretess N 5 1.00 0.91 0.67
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 15:34:18 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 795 (min = 350, max = 1400), aspect = 4.08 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 301599 voxels filled...
filling volume: pass 2 of 3...total of 16408755 voxels filled...
filling volume: pass 3 of 3...total of 301904 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 301599 voxels filled...
filling volume: pass 2 of 3...total of 16408755 voxels filled...
filling volume: pass 3 of 3...total of 301904 voxels filled...done.
filling degenerate left hemisphere surface locations...
362 voxels filled
10 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
362 voxels filled
10 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16408355 voxels filled...
filling volume: pass 3 of 3...total of 302304 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16408355 voxels filled...
filling volume: pass 3 of 3...total of 302304 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  301911 ambiguous voxels remaining
9:  44519 ambiguous voxels remaining
8:  22003 ambiguous voxels remaining
7:  12929 ambiguous voxels remaining
6:  5540 ambiguous voxels remaining
5:  3856 ambiguous voxels remaining
4:  1895 ambiguous voxels remaining
3:  533 ambiguous voxels remaining
2:  127 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.5 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:15:34:18 mri_fill N 12 e 32.23 S 0.06 U 32.10 P 99% M 111352 F 0 R 77596 W 0 c 646 w 1 I 0 O 216 L 1.00 0.91 0.67
@#@FSLOADPOST 2020:09:25:15:34:50 mri_fill N 12 1.00 0.92 0.68
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 15:34:50 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 0 (out of 160565: 0.000000)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:15:34:50 mri_pretess N 4 e 1.30 S 0.00 U 1.29 P 99% M 40432 F 0 R 8847 W 0 c 70 w 1 I 0 O 208 L 1.00 0.92 0.68
@#@FSLOADPOST 2020:09:25:15:34:51 mri_pretess N 4 1.00 0.92 0.68

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3260 vertices, 3425 faces
slice 70: 7318 vertices, 7520 faces
slice 80: 16744 vertices, 17216 faces
slice 90: 37078 vertices, 37848 faces
slice 100: 57068 vertices, 57917 faces
slice 110: 78749 vertices, 79484 faces
slice 120: 96873 vertices, 97610 faces
slice 130: 109215 vertices, 109700 faces
slice 140: 116382 vertices, 116677 faces
slice 150: 118678 vertices, 118836 faces
slice 160: 118678 vertices, 118836 faces
slice 170: 118678 vertices, 118836 faces
slice 180: 118678 vertices, 118836 faces
slice 190: 118678 vertices, 118836 faces
slice 200: 118678 vertices, 118836 faces
slice 210: 118678 vertices, 118836 faces
slice 220: 118678 vertices, 118836 faces
slice 230: 118678 vertices, 118836 faces
slice 240: 118678 vertices, 118836 faces
slice 250: 118678 vertices, 118836 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:15:34:51 mri_tessellate N 3 e 2.27 S 0.01 U 2.24 P 99% M 36540 F 0 R 8154 W 0 c 36 w 1 I 0 O 5576 L 1.00 0.92 0.68
@#@FSLOADPOST 2020:09:25:15:34:54 mri_tessellate N 3 1.00 0.92 0.68

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   118678 voxel in cpt #1: X=-158 [v=118678,e=356508,f=237672] located at (-2.866058, -28.016272, 16.273531)
For the whole surface: X=-158 [v=118678,e=356508,f=237672]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:15:34:54 mris_extract_main_component N 2 e 0.81 S 0.08 U 0.72 P 99% M 238524 F 0 R 65454 W 0 c 51 w 1 I 0 O 8360 L 1.00 0.92 0.68
@#@FSLOADPOST 2020:09:25:15:34:54 mris_extract_main_component N 2 1.00 0.92 0.68
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 15:34:54 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 6 (out of 141746: 0.004233)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:15:34:54 mri_pretess N 4 e 1.73 S 0.01 U 1.70 P 98% M 40492 F 0 R 8848 W 0 c 119 w 1 I 0 O 208 L 1.00 0.92 0.68
@#@FSLOADPOST 2020:09:25:15:34:56 mri_pretess N 4 1.00 0.92 0.68

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 70: 1516 vertices, 1639 faces
slice 80: 8558 vertices, 8922 faces
slice 90: 25638 vertices, 26213 faces
slice 100: 43898 vertices, 44656 faces
slice 110: 65876 vertices, 66620 faces
slice 120: 83837 vertices, 84511 faces
slice 130: 96353 vertices, 96810 faces
slice 140: 104166 vertices, 104439 faces
slice 150: 106344 vertices, 106468 faces
slice 160: 106344 vertices, 106468 faces
slice 170: 106344 vertices, 106468 faces
slice 180: 106344 vertices, 106468 faces
slice 190: 106344 vertices, 106468 faces
slice 200: 106344 vertices, 106468 faces
slice 210: 106344 vertices, 106468 faces
slice 220: 106344 vertices, 106468 faces
slice 230: 106344 vertices, 106468 faces
slice 240: 106344 vertices, 106468 faces
slice 250: 106344 vertices, 106468 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:15:34:56 mri_tessellate N 3 e 2.27 S 0.02 U 2.24 P 99% M 35448 F 0 R 7879 W 0 c 43 w 1 I 0 O 4992 L 1.00 0.92 0.68
@#@FSLOADPOST 2020:09:25:15:34:58 mri_tessellate N 3 1.00 0.93 0.68

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   106344 voxel in cpt #1: X=-124 [v=106344,e=319404,f=212936] located at (57.851200, -24.399477, 16.034962)
For the whole surface: X=-124 [v=106344,e=319404,f=212936]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:15:34:58 mris_extract_main_component N 2 e 0.74 S 0.08 U 0.64 P 98% M 214208 F 0 R 58624 W 0 c 50 w 1 I 0 O 7488 L 1.00 0.93 0.68
@#@FSLOADPOST 2020:09:25:15:34:59 mris_extract_main_component N 2 1.00 0.93 0.68
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 15:34:59 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:15:34:59 mris_smooth N 5 e 4.27 S 0.06 U 4.09 P 97% M 193120 F 0 R 53840 W 0 c 305 w 1 I 0 O 8360 L 1.00 0.93 0.68
@#@FSLOADPOST 2020:09:25:15:35:04 mris_smooth N 5 1.00 0.93 0.69
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 15:35:04 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:15:35:04 mris_smooth N 5 e 3.41 S 0.05 U 3.06 P 91% M 172772 F 0 R 47997 W 0 c 183 w 1 I 0 O 7488 L 1.00 0.93 0.69
@#@FSLOADPOST 2020:09:25:15:35:07 mris_smooth N 5 1.00 0.93 0.69
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 15:35:07 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.8 mm, total surface area = 68338 mm^2

step 000: RMS=0.141 (target=0.015)   
step 005: RMS=0.115 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.089 (target=0.015)   
step 020: RMS=0.085 (target=0.015)   
step 025: RMS=0.082 (target=0.015)   
step 030: RMS=0.078 (target=0.015)   
step 035: RMS=0.076 (target=0.015)   
step 040: RMS=0.075 (target=0.015)   
step 045: RMS=0.075 (target=0.015)   
step 050: RMS=0.074 (target=0.015)   
step 055: RMS=0.074 (target=0.015)   
step 060: RMS=0.075 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.473732
mris_inflate stimesec    0.090823
mris_inflate ru_maxrss   249792
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   72831
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8360
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   939
@#@FSTIME  2020:09:25:15:35:07 mris_inflate N 3 e 19.40 S 0.09 U 17.47 P 90% M 249936 F 0 R 72833 W 0 c 942 w 1 I 0 O 8360 L 1.00 0.93 0.69
@#@FSLOADPOST 2020:09:25:15:35:26 mris_inflate N 3 1.12 0.96 0.70
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 15:35:26 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 43.8 mm, total surface area = 61291 mm^2

step 000: RMS=0.140 (target=0.015)   
step 005: RMS=0.114 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.088 (target=0.015)   
step 020: RMS=0.082 (target=0.015)   
step 025: RMS=0.078 (target=0.015)   
step 030: RMS=0.075 (target=0.015)   
step 035: RMS=0.073 (target=0.015)   
step 040: RMS=0.071 (target=0.015)   
step 045: RMS=0.069 (target=0.015)   
step 050: RMS=0.069 (target=0.015)   
step 055: RMS=0.069 (target=0.015)   
step 060: RMS=0.070 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.465359
mris_inflate stimesec    0.056004
mris_inflate ru_maxrss   224432
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   65017
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  7488
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   356
@#@FSTIME  2020:09:25:15:35:27 mris_inflate N 3 e 16.67 S 0.06 U 16.46 P 99% M 224536 F 0 R 65019 W 0 c 359 w 1 I 0 O 7488 L 1.12 0.96 0.70
@#@FSLOADPOST 2020:09:25:15:35:43 mris_inflate N 3 1.09 0.97 0.71

Started at 2020��� 09��� 25��� ��������� 15:23:44 CST 
Ended   at 2020��� 09��� 25��� ��������� 15:35:43 CST
#@#%# recon-all-run-time-hours 0.200
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 15:35:43 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 15:50:23 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        513M        1.0G        6.4M        476M        1.3G
Swap:          2.0G        702M        1.3G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-07:50:23-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 15:50:23 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 178 control points...
only using 178 control points from file, mean 88.2, scaling by 1.25...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 111
gm peak at 64 (64), valley at 23 (23)
csf peak at 33, setting threshold to 53
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 61 (61), valley at 22 (22)
csf peak at 31, setting threshold to 51
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 45 seconds.
@#@FSTIME  2020:09:25:15:50:23 mri_normalize N 7 e 346.41 S 0.42 U 344.80 P 99% M 583392 F 0 R 312311 W 0 c 3597 w 1 I 0 O 3024 L 0.06 0.15 0.34
@#@FSLOADPOST 2020:09:25:15:56:10 mri_normalize N 7 1.00 0.75 0.56
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 15:56:10 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:15:56:10 mri_mask N 5 e 2.57 S 0.03 U 2.53 P 99% M 74352 F 0 R 17276 W 0 c 38 w 1 I 0 O 2952 L 1.00 0.75 0.56
@#@FSLOADPOST 2020:09:25:15:56:12 mri_mask N 5 1.00 0.75 0.56
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 15:56:12 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:15:56:19 AntsDenoiseImageFs N 4 e 63.18 S 0.07 U 63.02 P 99% M 350832 F 0 R 86515 W 0 c 540 w 1 I 0 O 3008 L 1.00 0.76 0.56
@#@FSLOADPOST 2020:09:25:15:57:22 AntsDenoiseImageFs N 4 1.00 0.80 0.59

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 104.4 +- 6.1 [79.0 --> 125.0]
CCS GM (71.0) : 69.0 +- 10.4 [30.0 --> 95.0]
 white_mean 104.411
 white_sigma 6.10875
 gray_mean 68.9681
 gray_sigma 10.3802
setting bottom of white matter range wm_low to 79.3
setting top of gray matter range gray_hi to 89.7
 wm_low 79.3483
 wm_hi  125
 gray_low 30
 gray_hi  89.7285
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.3483
 wm_hi  125
 gray_low 30
 gray_hi  89.7285
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 89.7285, wm_low = 79.3483
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=89.7285, wmlow=79.3483
    103717 voxels processed (0.62%)
     45462 voxels white (0.27%)
     58255 voxels non-white (0.35%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.3483, gray_hi=89.7285, wsize=13
    189930 voxels tested (1.13%)
     41469 voxels changed (0.25%)
     42814 multi-scale searches  (0.26%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.3483
 wm_hi 125
 slack 6.10875
 pct_thresh 0.33
 intensity_thresh 131.109
 nvox_thresh 8.58
      790 voxels tested (0.00%)
      602 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.3483, hithr=89.7285
  smoothing input volume with sigma = 0.250
    63733 voxels tested (0.38%)
    12733 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 6244 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3087 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3345 filled
MRIfindBrightNonWM(): 2124 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.4 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:15:57:22 mri_segment N 6 e 202.62 S 0.06 U 202.13 P 99% M 147428 F 0 R 60133 W 0 c 1915 w 1 I 0 O 656 L 1.00 0.80 0.59
@#@FSLOADPOST 2020:09:25:16:00:45 mri_segment N 6 1.02 0.92 0.69

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  80 found -  80 modified     |    TOTAL:  80
pass   2 (xy+):   0 found -  80 modified     |    TOTAL:  80
pass   1 (xy-):  83 found -  83 modified     |    TOTAL: 163
pass   2 (xy-):   0 found -  83 modified     |    TOTAL: 163
pass   1 (yz+): 128 found - 128 modified     |    TOTAL: 291
pass   2 (yz+):   0 found - 128 modified     |    TOTAL: 291
pass   1 (yz-):  66 found -  66 modified     |    TOTAL: 357
pass   2 (yz-):   0 found -  66 modified     |    TOTAL: 357
pass   1 (xz+): 107 found - 107 modified     |    TOTAL: 464
pass   2 (xz+):   0 found - 107 modified     |    TOTAL: 464
pass   1 (xz-):  90 found -  90 modified     |    TOTAL: 554
pass   2 (xz-):   0 found -  90 modified     |    TOTAL: 554
Iteration Number : 1
pass   1 (+++):  57 found -  57 modified     |    TOTAL:  57
pass   2 (+++):   0 found -  57 modified     |    TOTAL:  57
pass   1 (+++):  14 found -  14 modified     |    TOTAL:  71
pass   2 (+++):   0 found -  14 modified     |    TOTAL:  71
pass   1 (+++):  42 found -  42 modified     |    TOTAL: 113
pass   2 (+++):   0 found -  42 modified     |    TOTAL: 113
pass   1 (+++):  21 found -  21 modified     |    TOTAL: 134
pass   2 (+++):   0 found -  21 modified     |    TOTAL: 134
Iteration Number : 1
pass   1 (++): 161 found - 161 modified     |    TOTAL: 161
pass   2 (++):   0 found - 161 modified     |    TOTAL: 161
pass   1 (+-): 211 found - 211 modified     |    TOTAL: 372
pass   2 (+-):   0 found - 211 modified     |    TOTAL: 372
pass   1 (--): 177 found - 177 modified     |    TOTAL: 549
pass   2 (--):   1 found - 178 modified     |    TOTAL: 550
pass   3 (--):   0 found - 178 modified     |    TOTAL: 550
pass   1 (-+): 181 found - 181 modified     |    TOTAL: 731
pass   2 (-+):   0 found - 181 modified     |    TOTAL: 731
Iteration Number : 2
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):   9 found -   9 modified     |    TOTAL:  14
pass   2 (xy-):   0 found -   9 modified     |    TOTAL:  14
pass   1 (yz+):  14 found -  14 modified     |    TOTAL:  28
pass   2 (yz+):   0 found -  14 modified     |    TOTAL:  28
pass   1 (yz-):   8 found -   8 modified     |    TOTAL:  36
pass   2 (yz-):   0 found -   8 modified     |    TOTAL:  36
pass   1 (xz+):  15 found -  15 modified     |    TOTAL:  51
pass   2 (xz+):   0 found -  15 modified     |    TOTAL:  51
pass   1 (xz-):   6 found -   6 modified     |    TOTAL:  57
pass   2 (xz-):   0 found -   6 modified     |    TOTAL:  57
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   9 found -   9 modified     |    TOTAL:   9
pass   2 (++):   0 found -   9 modified     |    TOTAL:   9
pass   1 (+-):   8 found -   8 modified     |    TOTAL:  17
pass   2 (+-):   0 found -   8 modified     |    TOTAL:  17
pass   1 (--):   2 found -   2 modified     |    TOTAL:  19
pass   2 (--):   0 found -   2 modified     |    TOTAL:  19
pass   1 (-+):   2 found -   2 modified     |    TOTAL:  21
pass   2 (-+):   0 found -   2 modified     |    TOTAL:  21
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1508 (out of 322266: 0.467936)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:16:00:45 mri_pretess N 5 e 4.46 S 0.03 U 4.37 P 98% M 57084 F 0 R 17113 W 0 c 296 w 2 I 0 O 648 L 1.02 0.92 0.69
@#@FSLOADPOST 2020:09:25:16:00:49 mri_pretess N 5 1.02 0.92 0.69
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 16:00:49 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 811 (min = 350, max = 1400), aspect = 4.08 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 318078 voxels filled...
filling volume: pass 2 of 3...total of 16392278 voxels filled...
filling volume: pass 3 of 3...total of 318381 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 318078 voxels filled...
filling volume: pass 2 of 3...total of 16392278 voxels filled...
filling volume: pass 3 of 3...total of 318381 voxels filled...done.
filling degenerate left hemisphere surface locations...
340 voxels filled
10 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
340 voxels filled
10 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16391928 voxels filled...
filling volume: pass 3 of 3...total of 318731 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16391928 voxels filled...
filling volume: pass 3 of 3...total of 318731 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  318338 ambiguous voxels remaining
9:  47051 ambiguous voxels remaining
8:  22436 ambiguous voxels remaining
7:  12660 ambiguous voxels remaining
6:  5088 ambiguous voxels remaining
5:  3486 ambiguous voxels remaining
4:  1703 ambiguous voxels remaining
3:  699 ambiguous voxels remaining
2:  295 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.5 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:16:00:49 mri_fill N 12 e 31.87 S 0.09 U 31.68 P 99% M 111456 F 0 R 77595 W 0 c 656 w 1 I 0 O 224 L 1.02 0.92 0.69
@#@FSLOADPOST 2020:09:25:16:01:21 mri_fill N 12 1.01 0.93 0.70
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 16:01:21 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 5 (out of 166491: 0.003003)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:16:01:21 mri_pretess N 4 e 2.04 S 0.01 U 2.00 P 98% M 40508 F 0 R 8849 W 0 c 157 w 1 I 0 O 216 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:23 mri_pretess N 4 1.01 0.93 0.70

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 60: 3213 vertices, 3366 faces
slice 70: 7450 vertices, 7647 faces
slice 80: 17380 vertices, 17868 faces
slice 90: 38172 vertices, 38941 faces
slice 100: 58539 vertices, 59363 faces
slice 110: 80414 vertices, 81139 faces
slice 120: 98768 vertices, 99476 faces
slice 130: 111395 vertices, 111859 faces
slice 140: 119118 vertices, 119391 faces
slice 150: 121506 vertices, 121630 faces
slice 160: 121506 vertices, 121630 faces
slice 170: 121506 vertices, 121630 faces
slice 180: 121506 vertices, 121630 faces
slice 190: 121506 vertices, 121630 faces
slice 200: 121506 vertices, 121630 faces
slice 210: 121506 vertices, 121630 faces
slice 220: 121506 vertices, 121630 faces
slice 230: 121506 vertices, 121630 faces
slice 240: 121506 vertices, 121630 faces
slice 250: 121506 vertices, 121630 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:16:01:23 mri_tessellate N 3 e 2.28 S 0.01 U 2.26 P 99% M 36852 F 0 R 8212 W 0 c 41 w 1 I 0 O 5704 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:26 mri_tessellate N 3 1.01 0.93 0.70

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   121506 voxel in cpt #1: X=-124 [v=121506,e=364890,f=243260] located at (-2.621047, -27.957155, 17.235544)
For the whole surface: X=-124 [v=121506,e=364890,f=243260]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:16:01:26 mris_extract_main_component N 2 e 0.81 S 0.10 U 0.70 P 99% M 243908 F 0 R 66985 W 0 c 46 w 1 I 0 O 8552 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:26 mris_extract_main_component N 2 1.01 0.93 0.70
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 16:01:26 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 7 (out of 152253: 0.004598)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:16:01:26 mri_pretess N 4 e 2.03 S 0.02 U 1.98 P 98% M 40392 F 0 R 8844 W 0 c 158 w 1 I 0 O 216 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:28 mri_pretess N 4 1.01 0.93 0.70

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2617 vertices, 2734 faces
slice 70: 6216 vertices, 6397 faces
slice 80: 14235 vertices, 14675 faces
slice 90: 33068 vertices, 33763 faces
slice 100: 52843 vertices, 53668 faces
slice 110: 75285 vertices, 76066 faces
slice 120: 93486 vertices, 94189 faces
slice 130: 106337 vertices, 106822 faces
slice 140: 114477 vertices, 114780 faces
slice 150: 116984 vertices, 117128 faces
slice 160: 116984 vertices, 117128 faces
slice 170: 116984 vertices, 117128 faces
slice 180: 116984 vertices, 117128 faces
slice 190: 116984 vertices, 117128 faces
slice 200: 116984 vertices, 117128 faces
slice 210: 116984 vertices, 117128 faces
slice 220: 116984 vertices, 117128 faces
slice 230: 116984 vertices, 117128 faces
slice 240: 116984 vertices, 117128 faces
slice 250: 116984 vertices, 117128 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:16:01:28 mri_tessellate N 3 e 2.26 S 0.01 U 2.24 P 99% M 36376 F 0 R 8113 W 0 c 42 w 1 I 0 O 5496 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:31 mri_tessellate N 3 1.01 0.93 0.70

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   116984 voxel in cpt #1: X=-144 [v=116984,e=351384,f=234256] located at (58.506290, -26.584909, 18.055914)
For the whole surface: X=-144 [v=116984,e=351384,f=234256]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:16:01:31 mris_extract_main_component N 2 e 0.75 S 0.07 U 0.67 P 99% M 235028 F 0 R 64478 W 0 c 46 w 1 I 0 O 8240 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:32 mris_extract_main_component N 2 1.01 0.93 0.70
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 16:01:32 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:16:01:32 mris_smooth N 5 e 3.45 S 0.05 U 3.40 P 99% M 197536 F 0 R 55090 W 0 c 61 w 1 I 0 O 8552 L 1.01 0.93 0.70
@#@FSLOADPOST 2020:09:25:16:01:35 mris_smooth N 5 1.01 0.94 0.71
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 16:01:35 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:16:01:35 mris_smooth N 5 e 3.21 S 0.05 U 3.15 P 99% M 189256 F 0 R 52780 W 0 c 60 w 1 I 0 O 8240 L 1.01 0.94 0.71
@#@FSLOADPOST 2020:09:25:16:01:38 mris_smooth N 5 1.01 0.94 0.71
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 16:01:38 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.3 mm, total surface area = 70268 mm^2

step 000: RMS=0.137 (target=0.015)   
step 005: RMS=0.111 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.076 (target=0.015)   
step 030: RMS=0.072 (target=0.015)   
step 035: RMS=0.070 (target=0.015)   
step 040: RMS=0.068 (target=0.015)   
step 045: RMS=0.068 (target=0.015)   
step 050: RMS=0.067 (target=0.015)   
step 055: RMS=0.067 (target=0.015)   
step 060: RMS=0.067 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.891547
mris_inflate stimesec    0.067965
mris_inflate ru_maxrss   255440
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   74572
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8552
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   225
@#@FSTIME  2020:09:25:16:01:38 mris_inflate N 3 e 16.98 S 0.07 U 16.89 P 99% M 255544 F 0 R 74574 W 0 c 228 w 1 I 0 O 8552 L 1.01 0.94 0.71
@#@FSLOADPOST 2020:09:25:16:01:55 mris_inflate N 3 1.00 0.94 0.71
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 16:01:55 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.6 mm, total surface area = 67571 mm^2

step 000: RMS=0.137 (target=0.015)   
step 005: RMS=0.110 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.083 (target=0.015)   
step 020: RMS=0.077 (target=0.015)   
step 025: RMS=0.073 (target=0.015)   
step 030: RMS=0.070 (target=0.015)   
step 035: RMS=0.068 (target=0.015)   
step 040: RMS=0.067 (target=0.015)   
step 045: RMS=0.065 (target=0.015)   
step 050: RMS=0.065 (target=0.015)   
step 055: RMS=0.065 (target=0.015)   
step 060: RMS=0.065 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.474654
mris_inflate stimesec    0.064025
mris_inflate ru_maxrss   245096
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   66744
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8240
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   255
@#@FSTIME  2020:09:25:16:01:55 mris_inflate N 3 e 16.60 S 0.07 U 16.47 P 99% M 245344 F 0 R 66747 W 0 c 260 w 1 I 0 O 8240 L 1.00 0.94 0.71
@#@FSLOADPOST 2020:09:25:16:02:12 mris_inflate N 3 1.00 0.94 0.72

Started at 2020��� 09��� 25��� ��������� 15:50:23 CST 
Ended   at 2020��� 09��� 25��� ��������� 16:02:12 CST
#@#%# recon-all-run-time-hours 0.197
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 16:02:12 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 16:43:56 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        527M        934M        6.9M        531M        1.3G
Swap:          2.0G        691M        1.3G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-08:43:56-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 16:43:57 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 268 control points...
only using 268 control points from file, mean 82.5, scaling by 1.33...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 111
gm peak at 65 (65), valley at 22 (22)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 21 (21)
csf peak at 10, setting threshold to 45
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 5 minutes and 40 seconds.
@#@FSTIME  2020:09:25:16:43:57 mri_normalize N 7 e 341.52 S 0.34 U 340.39 P 99% M 583320 F 0 R 312310 W 0 c 3365 w 1 I 0 O 3040 L 0.16 0.12 0.12
@#@FSLOADPOST 2020:09:25:16:49:38 mri_normalize N 7 1.00 0.73 0.40
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 16:49:38 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:16:49:38 mri_mask N 5 e 2.57 S 0.03 U 2.53 P 99% M 74268 F 0 R 17277 W 0 c 52 w 1 I 0 O 2960 L 1.00 0.73 0.40
@#@FSLOADPOST 2020:09:25:16:49:41 mri_mask N 5 1.00 0.73 0.40
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 16:49:41 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:16:49:47 AntsDenoiseImageFs N 4 e 61.32 S 0.10 U 61.15 P 99% M 350688 F 0 R 86511 W 0 c 543 w 1 I 0 O 3024 L 1.00 0.74 0.41
@#@FSLOADPOST 2020:09:25:16:50:49 AntsDenoiseImageFs N 4 1.00 0.79 0.45

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 105.3 +- 6.5 [79.0 --> 125.0]
CCS GM (70.0) : 68.6 +- 10.5 [30.0 --> 95.0]
 white_mean 105.322
 white_sigma 6.51562
 gray_mean 68.6395
 gray_sigma 10.5166
setting bottom of white matter range wm_low to 79.2
setting top of gray matter range gray_hi to 89.7
 wm_low 79.1562
 wm_hi  125
 gray_low 30
 gray_hi  89.6728
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.1562
 wm_hi  125
 gray_low 30
 gray_hi  89.6728
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 89.6728, wm_low = 79.1562
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=89.6728, wmlow=79.1562
    110500 voxels processed (0.66%)
     48248 voxels white (0.29%)
     62252 voxels non-white (0.37%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.1562, gray_hi=89.6728, wsize=13
    193459 voxels tested (1.15%)
     44155 voxels changed (0.26%)
     53643 multi-scale searches  (0.32%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.1562
 wm_hi 125
 slack 6.51562
 pct_thresh 0.33
 intensity_thresh 131.516
 nvox_thresh 8.58
     2039 voxels tested (0.01%)
     1660 voxels changed (0.01%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.1562, hithr=89.6728
  smoothing input volume with sigma = 0.250
    61963 voxels tested (0.37%)
    13249 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 7402 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3757 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 3166 filled
MRIfindBrightNonWM(): 3607 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.4 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:16:50:49 mri_segment N 6 e 206.48 S 0.29 U 205.36 P 99% M 147708 F 0 R 291248 W 0 c 2127 w 1 I 0 O 672 L 1.00 0.79 0.45
@#@FSLOADPOST 2020:09:25:16:54:15 mri_segment N 6 1.00 0.90 0.57

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  76 found -  76 modified     |    TOTAL:  76
pass   2 (xy+):   0 found -  76 modified     |    TOTAL:  76
pass   1 (xy-):  86 found -  86 modified     |    TOTAL: 162
pass   2 (xy-):   0 found -  86 modified     |    TOTAL: 162
pass   1 (yz+):  94 found -  94 modified     |    TOTAL: 256
pass   2 (yz+):   0 found -  94 modified     |    TOTAL: 256
pass   1 (yz-):  51 found -  51 modified     |    TOTAL: 307
pass   2 (yz-):   0 found -  51 modified     |    TOTAL: 307
pass   1 (xz+):  81 found -  81 modified     |    TOTAL: 388
pass   2 (xz+):   0 found -  81 modified     |    TOTAL: 388
pass   1 (xz-):  75 found -  75 modified     |    TOTAL: 463
pass   2 (xz-):   0 found -  75 modified     |    TOTAL: 463
Iteration Number : 1
pass   1 (+++):  70 found -  70 modified     |    TOTAL:  70
pass   2 (+++):   0 found -  70 modified     |    TOTAL:  70
pass   1 (+++):  37 found -  37 modified     |    TOTAL: 107
pass   2 (+++):   0 found -  37 modified     |    TOTAL: 107
pass   1 (+++):  59 found -  59 modified     |    TOTAL: 166
pass   2 (+++):   0 found -  59 modified     |    TOTAL: 166
pass   1 (+++):  40 found -  40 modified     |    TOTAL: 206
pass   2 (+++):   0 found -  40 modified     |    TOTAL: 206
Iteration Number : 1
pass   1 (++): 153 found - 153 modified     |    TOTAL: 153
pass   2 (++):   0 found - 153 modified     |    TOTAL: 153
pass   1 (+-): 237 found - 237 modified     |    TOTAL: 390
pass   2 (+-):   0 found - 237 modified     |    TOTAL: 390
pass   1 (--): 153 found - 153 modified     |    TOTAL: 543
pass   2 (--):   1 found - 154 modified     |    TOTAL: 544
pass   3 (--):   0 found - 154 modified     |    TOTAL: 544
pass   1 (-+): 188 found - 188 modified     |    TOTAL: 732
pass   2 (-+):   0 found - 188 modified     |    TOTAL: 732
Iteration Number : 2
pass   1 (xy+):  12 found -  12 modified     |    TOTAL:  12
pass   2 (xy+):   0 found -  12 modified     |    TOTAL:  12
pass   1 (xy-):  12 found -  12 modified     |    TOTAL:  24
pass   2 (xy-):   0 found -  12 modified     |    TOTAL:  24
pass   1 (yz+):  20 found -  20 modified     |    TOTAL:  44
pass   2 (yz+):   0 found -  20 modified     |    TOTAL:  44
pass   1 (yz-):  13 found -  13 modified     |    TOTAL:  57
pass   2 (yz-):   0 found -  13 modified     |    TOTAL:  57
pass   1 (xz+):  13 found -  13 modified     |    TOTAL:  70
pass   2 (xz+):   0 found -  13 modified     |    TOTAL:  70
pass   1 (xz-):   9 found -   9 modified     |    TOTAL:  79
pass   2 (xz-):   0 found -   9 modified     |    TOTAL:  79
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  10
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  10
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  12
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  12
Iteration Number : 2
pass   1 (++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+-):  13 found -  13 modified     |    TOTAL:  21
pass   2 (+-):   0 found -  13 modified     |    TOTAL:  21
pass   1 (--):   6 found -   6 modified     |    TOTAL:  27
pass   2 (--):   0 found -   6 modified     |    TOTAL:  27
pass   1 (-+):   9 found -   9 modified     |    TOTAL:  36
pass   2 (-+):   0 found -   9 modified     |    TOTAL:  36
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   4
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   5
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   4
pass   1 (--):   0 found -   0 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 4
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1547 (out of 332362: 0.465456)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:16:54:15 mri_pretess N 5 e 5.22 S 0.02 U 5.12 P 98% M 57172 F 0 R 17114 W 0 c 351 w 1 I 0 O 672 L 1.00 0.90 0.57
@#@FSLOADPOST 2020:09:25:16:54:21 mri_pretess N 5 1.00 0.90 0.57
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 16:54:21 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 822 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 324979 voxels filled...
filling volume: pass 2 of 3...total of 16385428 voxels filled...
filling volume: pass 3 of 3...total of 325231 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 324979 voxels filled...
filling volume: pass 2 of 3...total of 16385428 voxels filled...
filling volume: pass 3 of 3...total of 325231 voxels filled...done.
filling degenerate left hemisphere surface locations...
424 voxels filled
9 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
424 voxels filled
9 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16384985 voxels filled...
filling volume: pass 3 of 3...total of 325674 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16384985 voxels filled...
filling volume: pass 3 of 3...total of 325674 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  325281 ambiguous voxels remaining
9:  50963 ambiguous voxels remaining
8:  23445 ambiguous voxels remaining
7:  12179 ambiguous voxels remaining
6:  5567 ambiguous voxels remaining
5:  3843 ambiguous voxels remaining
4:  1776 ambiguous voxels remaining
3:  681 ambiguous voxels remaining
2:  272 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.5 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:16:54:21 mri_fill N 12 e 31.32 S 0.07 U 31.16 P 99% M 111696 F 0 R 77595 W 0 c 647 w 1 I 0 O 224 L 1.00 0.90 0.57
@#@FSLOADPOST 2020:09:25:16:54:52 mri_fill N 12 1.00 0.91 0.59
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 16:54:52 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 5 (out of 168806: 0.002962)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:16:54:52 mri_pretess N 4 e 2.08 S 0.02 U 2.02 P 98% M 40408 F 0 R 8845 W 0 c 156 w 1 I 0 O 216 L 1.00 0.91 0.59
@#@FSLOADPOST 2020:09:25:16:54:54 mri_pretess N 4 1.00 0.91 0.59

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 58 vertices, 74 faces
slice 60: 3466 vertices, 3602 faces
slice 70: 7860 vertices, 8040 faces
slice 80: 18001 vertices, 18480 faces
slice 90: 39289 vertices, 40040 faces
slice 100: 59768 vertices, 60590 faces
slice 110: 81672 vertices, 82402 faces
slice 120: 100057 vertices, 100762 faces
slice 130: 112688 vertices, 113149 faces
slice 140: 120397 vertices, 120669 faces
slice 150: 122788 vertices, 122910 faces
slice 160: 122788 vertices, 122910 faces
slice 170: 122788 vertices, 122910 faces
slice 180: 122788 vertices, 122910 faces
slice 190: 122788 vertices, 122910 faces
slice 200: 122788 vertices, 122910 faces
slice 210: 122788 vertices, 122910 faces
slice 220: 122788 vertices, 122910 faces
slice 230: 122788 vertices, 122910 faces
slice 240: 122788 vertices, 122910 faces
slice 250: 122788 vertices, 122910 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:16:54:54 mri_tessellate N 3 e 2.31 S 0.01 U 2.29 P 99% M 36896 F 0 R 8240 W 0 c 39 w 1 I 0 O 5768 L 1.00 0.91 0.59
@#@FSLOADPOST 2020:09:25:16:54:56 mri_tessellate N 3 1.00 0.91 0.59

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   122788 voxel in cpt #1: X=-122 [v=122788,e=368730,f=245820] located at (-2.592851, -28.223499, 18.074381)
For the whole surface: X=-122 [v=122788,e=368730,f=245820]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:16:54:56 mris_extract_main_component N 2 e 0.81 S 0.08 U 0.72 P 99% M 246616 F 0 R 67670 W 0 c 51 w 1 I 0 O 8648 L 1.00 0.91 0.59
@#@FSLOADPOST 2020:09:25:16:54:57 mris_extract_main_component N 2 1.00 0.92 0.59
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 16:54:57 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 4 (out of 156878: 0.002550)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:16:54:57 mri_pretess N 4 e 1.71 S 0.02 U 1.67 P 98% M 40444 F 0 R 8846 W 0 c 113 w 1 I 0 O 216 L 1.00 0.92 0.59
@#@FSLOADPOST 2020:09:25:16:54:59 mri_pretess N 4 1.00 0.92 0.59

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2671 vertices, 2788 faces
slice 70: 6596 vertices, 6776 faces
slice 80: 15927 vertices, 16393 faces
slice 90: 36330 vertices, 37094 faces
slice 100: 57800 vertices, 58677 faces
slice 110: 80113 vertices, 80922 faces
slice 120: 98322 vertices, 99055 faces
slice 130: 111226 vertices, 111735 faces
slice 140: 119371 vertices, 119699 faces
slice 150: 121868 vertices, 122038 faces
slice 160: 121868 vertices, 122038 faces
slice 170: 121868 vertices, 122038 faces
slice 180: 121868 vertices, 122038 faces
slice 190: 121868 vertices, 122038 faces
slice 200: 121868 vertices, 122038 faces
slice 210: 121868 vertices, 122038 faces
slice 220: 121868 vertices, 122038 faces
slice 230: 121868 vertices, 122038 faces
slice 240: 121868 vertices, 122038 faces
slice 250: 121868 vertices, 122038 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:16:54:59 mri_tessellate N 3 e 2.33 S 0.00 U 2.31 P 99% M 36888 F 0 R 8221 W 0 c 44 w 2 I 0 O 5720 L 1.00 0.92 0.59
@#@FSLOADPOST 2020:09:25:16:55:01 mri_tessellate N 3 1.00 0.92 0.59

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   121868 voxel in cpt #1: X=-170 [v=121868,e=366114,f=244076] located at (58.462173, -27.333878, 19.559048)
For the whole surface: X=-170 [v=121868,e=366114,f=244076]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:16:55:01 mris_extract_main_component N 2 e 0.80 S 0.09 U 0.71 P 99% M 244832 F 0 R 67172 W 0 c 49 w 1 I 0 O 8584 L 1.00 0.92 0.59
@#@FSLOADPOST 2020:09:25:16:55:02 mris_extract_main_component N 2 1.00 0.92 0.59
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 16:55:02 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:16:55:02 mris_smooth N 5 e 3.62 S 0.07 U 3.53 P 99% M 198880 F 0 R 55514 W 0 c 59 w 1 I 0 O 8648 L 1.00 0.92 0.59
@#@FSLOADPOST 2020:09:25:16:55:06 mris_smooth N 5 1.00 0.92 0.59
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 16:55:06 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:16:55:06 mris_smooth N 5 e 3.58 S 0.06 U 3.51 P 99% M 197612 F 0 R 55181 W 0 c 61 w 1 I 0 O 8584 L 1.00 0.92 0.59
@#@FSLOADPOST 2020:09:25:16:55:09 mris_smooth N 5 1.00 0.92 0.60
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 16:55:09 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.2 mm, total surface area = 71266 mm^2

step 000: RMS=0.137 (target=0.015)   
step 005: RMS=0.110 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.075 (target=0.015)   
step 030: RMS=0.073 (target=0.015)   
step 035: RMS=0.071 (target=0.015)   
step 040: RMS=0.069 (target=0.015)   
step 045: RMS=0.067 (target=0.015)   
step 050: RMS=0.066 (target=0.015)   
step 055: RMS=0.065 (target=0.015)   
step 060: RMS=0.066 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.691295
mris_inflate stimesec    0.092351
mris_inflate ru_maxrss   257956
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   75354
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8648
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   239
@#@FSTIME  2020:09:25:16:55:09 mris_inflate N 3 e 17.84 S 0.10 U 17.69 P 99% M 258136 F 0 R 75356 W 0 c 242 w 1 I 0 O 8648 L 1.00 0.92 0.60
@#@FSLOADPOST 2020:09:25:16:55:27 mris_inflate N 3 1.00 0.93 0.61
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 16:55:27 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.2 mm, total surface area = 69939 mm^2

step 000: RMS=0.140 (target=0.015)   
step 005: RMS=0.112 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.086 (target=0.015)   
step 020: RMS=0.081 (target=0.015)   
step 025: RMS=0.077 (target=0.015)   
step 030: RMS=0.074 (target=0.015)   
step 035: RMS=0.073 (target=0.015)   
step 040: RMS=0.071 (target=0.015)   
step 045: RMS=0.070 (target=0.015)   
step 050: RMS=0.070 (target=0.015)   
step 055: RMS=0.071 (target=0.015)   
step 060: RMS=0.071 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.705038
mris_inflate stimesec    0.092276
mris_inflate ru_maxrss   255980
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   74778
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8584
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   249
@#@FSTIME  2020:09:25:16:55:27 mris_inflate N 3 e 17.82 S 0.10 U 17.70 P 99% M 256240 F 0 R 74781 W 0 c 252 w 1 I 0 O 8584 L 1.00 0.93 0.61
@#@FSLOADPOST 2020:09:25:16:55:45 mris_inflate N 3 1.00 0.93 0.61

Started at 2020��� 09��� 25��� ��������� 16:43:56 CST 
Ended   at 2020��� 09��� 25��� ��������� 16:55:45 CST
#@#%# recon-all-run-time-hours 0.197
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 16:55:45 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 20:08:26 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        530M        915M        6.9M        547M        1.3G
Swap:          2.0G        690M        1.3G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:26-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-12:08:27-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Intensity Normalization2 2020��� 09��� 25��� ��������� 20:08:27 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_normalize -seed 1234 -f /usr/local/freesurfer/subjects/monkey2/tmp/control.dat -mprage brainmask.mgz brain.mgz 

setting seed for random number genererator to 1234
using control points from file /usr/local/freesurfer/subjects/monkey2/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from brainmask.mgz...
normalizing image...
Reading 310 control points...
only using 310 control points from file, mean 81.4, scaling by 1.35...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 112
gm peak at 65 (65), valley at 22 (22)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 22 (22)
csf peak at 10, setting threshold to 45
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 6 minutes and 55 seconds.
@#@FSTIME  2020:09:25:20:08:27 mri_normalize N 7 e 416.53 S 0.93 U 365.88 P 88% M 583388 F 0 R 316391 W 0 c 34901 w 1 I 0 O 3032 L 0.19 0.21 0.11
@#@FSLOADPOST 2020:09:25:20:15:23 mri_normalize N 7 1.21 1.02 0.56
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 20:15:23 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:20:15:23 mri_mask N 5 e 2.61 S 0.02 U 2.55 P 98% M 74480 F 7 R 17275 W 0 c 107 w 8 I 512 O 2960 L 1.21 1.02 0.56
@#@FSLOADPOST 2020:09:25:20:15:26 mri_mask N 5 1.21 1.02 0.56
#--------------------------------------------
#@# WM Segmentation 2020��� 09��� 25��� ��������� 20:15:26 CST

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm255.mgz
Binarizing based on threshold
min        255
max        255
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 3365 values in range
Counting number of voxels in first frame
Found 3364 voxels in final mask
Count: 3364 3364.000000 16777216 0.020051
mri_binarize done

 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 


7.1.0
cwd /usr/local/freesurfer/subjects/monkey2/mri
cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 
sysname  Linux
hostname zhao-VirtualBox
machine  x86_64
user     zhao

input      wm.mgz
frame      0
nErode3d   0
nErode2d   0
output     wm1.mgz
Binarizing based on threshold
min        1
max        1
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 174478 values in range
Counting number of voxels in first frame
Found 174477 voxels in final mask
Count: 174477 174477.000000 16777216 1.039964
mri_binarize done

 rm wm1.mgz wm255.mgz 

Found wm edits: 174477 deletes, 3364 fills

 cp wm.mgz wm.seg.mgz 


 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2020:09:25:20:15:33 AntsDenoiseImageFs N 4 e 64.18 S 0.07 U 61.84 P 96% M 350768 F 0 R 86518 W 0 c 3146 w 1 I 0 O 3016 L 1.17 1.02 0.56
@#@FSLOADPOST 2020:09:25:20:16:37 AntsDenoiseImageFs N 4 1.06 1.02 0.59

 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
wsizemm = 13, voxres = 1, wsize = 13
 WHITE_MATTER_MEAN  110
 wsize  13
assuming input volume is MGH (Van der Kouwe) MP-RAGE
 wm_low 79
 wm_hi  125
 gray_low 30
 gray_hi  99
Doing initial trinary intensity segmentation 
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (105.0): 105.2 +- 6.4 [79.0 --> 125.0]
CCS GM (71.0) : 68.9 +- 10.7 [30.0 --> 95.0]
 white_mean 105.185
 white_sigma 6.40216
 gray_mean 68.9259
 gray_sigma 10.7143
setting bottom of white matter range wm_low to 79.6
setting top of gray matter range gray_hi to 90.4
 wm_low 79.6403
 wm_hi  125
 gray_low 30
 gray_hi  90.3546
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
 wm_low 79.6403
 wm_hi  125
 gray_low 30
 gray_hi  90.3546
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 90.3546, wm_low = 79.6403
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.3546, wmlow=79.6403
    122612 voxels processed (0.73%)
     52613 voxels white (0.31%)
     69999 voxels non-white (0.42%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=74.6403, gray_hi=90.3546, wsize=13
    209552 voxels tested (1.25%)
     45955 voxels changed (0.27%)
     56668 multi-scale searches  (0.34%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 79.6403
 wm_hi 125
 slack 6.40216
 pct_thresh 0.33
 intensity_thresh 131.402
 nvox_thresh 8.58
     1300 voxels tested (0.01%)
     1021 voxels changed (0.01%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=74.6403, hithr=90.3546
  smoothing input volume with sigma = 0.250
    67955 voxels tested (0.41%)
    14547 voxels changed (0.09%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 7466 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
3544 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 2888 filled
MRIfindBrightNonWM(): 3307 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 3.5 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2020:09:25:20:16:37 mri_segment N 6 e 211.44 S 0.28 U 209.92 P 99% M 147636 F 2 R 291170 W 0 c 6293 w 3 I 320 O 672 L 1.06 1.02 0.59
@#@FSLOADPOST 2020:09:25:20:20:08 mri_segment N 6 1.00 1.00 0.69

 mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  78 found -  78 modified     |    TOTAL:  78
pass   2 (xy+):   0 found -  78 modified     |    TOTAL:  78
pass   1 (xy-):  86 found -  86 modified     |    TOTAL: 164
pass   2 (xy-):   0 found -  86 modified     |    TOTAL: 164
pass   1 (yz+):  97 found -  97 modified     |    TOTAL: 261
pass   2 (yz+):   0 found -  97 modified     |    TOTAL: 261
pass   1 (yz-):  63 found -  63 modified     |    TOTAL: 324
pass   2 (yz-):   0 found -  63 modified     |    TOTAL: 324
pass   1 (xz+): 108 found - 108 modified     |    TOTAL: 432
pass   2 (xz+):   0 found - 108 modified     |    TOTAL: 432
pass   1 (xz-):  82 found -  82 modified     |    TOTAL: 514
pass   2 (xz-):   0 found -  82 modified     |    TOTAL: 514
Iteration Number : 1
pass   1 (+++):  64 found -  64 modified     |    TOTAL:  64
pass   2 (+++):   0 found -  64 modified     |    TOTAL:  64
pass   1 (+++):  34 found -  34 modified     |    TOTAL:  98
pass   2 (+++):   0 found -  34 modified     |    TOTAL:  98
pass   1 (+++):  49 found -  49 modified     |    TOTAL: 147
pass   2 (+++):   0 found -  49 modified     |    TOTAL: 147
pass   1 (+++):  28 found -  28 modified     |    TOTAL: 175
pass   2 (+++):   0 found -  28 modified     |    TOTAL: 175
Iteration Number : 1
pass   1 (++): 163 found - 163 modified     |    TOTAL: 163
pass   2 (++):   0 found - 163 modified     |    TOTAL: 163
pass   1 (+-): 232 found - 232 modified     |    TOTAL: 395
pass   2 (+-):   0 found - 232 modified     |    TOTAL: 395
pass   1 (--): 181 found - 181 modified     |    TOTAL: 576
pass   2 (--):   0 found - 181 modified     |    TOTAL: 576
pass   1 (-+): 168 found - 168 modified     |    TOTAL: 744
pass   2 (-+):   0 found - 168 modified     |    TOTAL: 744
Iteration Number : 2
pass   1 (xy+):   6 found -   6 modified     |    TOTAL:   6
pass   2 (xy+):   0 found -   6 modified     |    TOTAL:   6
pass   1 (xy-):  12 found -  12 modified     |    TOTAL:  18
pass   2 (xy-):   0 found -  12 modified     |    TOTAL:  18
pass   1 (yz+):  18 found -  18 modified     |    TOTAL:  36
pass   2 (yz+):   0 found -  18 modified     |    TOTAL:  36
pass   1 (yz-):  19 found -  19 modified     |    TOTAL:  55
pass   2 (yz-):   0 found -  19 modified     |    TOTAL:  55
pass   1 (xz+):  12 found -  12 modified     |    TOTAL:  67
pass   2 (xz+):   0 found -  12 modified     |    TOTAL:  67
pass   1 (xz-):  11 found -  11 modified     |    TOTAL:  78
pass   2 (xz-):   0 found -  11 modified     |    TOTAL:  78
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  12
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  12
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  14
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  14
Iteration Number : 2
pass   1 (++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+-):  10 found -  10 modified     |    TOTAL:  18
pass   2 (+-):   0 found -  10 modified     |    TOTAL:  18
pass   1 (--):   6 found -   6 modified     |    TOTAL:  24
pass   2 (--):   0 found -   6 modified     |    TOTAL:  24
pass   1 (-+):   6 found -   6 modified     |    TOTAL:  30
pass   2 (-+):   0 found -   6 modified     |    TOTAL:  30
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   3
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1562 (out of 332884: 0.469233)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  kept 3365 WM ON voxels
  kept 174478 WM OFF voxels

mri_pretess done

@#@FSTIME  2020:09:25:20:20:08 mri_pretess N 5 e 7.43 S 0.02 U 5.46 P 73% M 57200 F 0 R 17119 W 0 c 1013 w 1 I 0 O 664 L 1.00 1.00 0.69
@#@FSLOADPOST 2020:09:25:20:20:16 mri_pretess N 5 1.00 1.00 0.69
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 20:20:16 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 821 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 325410 voxels filled...
filling volume: pass 2 of 3...total of 16384957 voxels filled...
filling volume: pass 3 of 3...total of 325702 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 325410 voxels filled...
filling volume: pass 2 of 3...total of 16384957 voxels filled...
filling volume: pass 3 of 3...total of 325702 voxels filled...done.
filling degenerate left hemisphere surface locations...
418 voxels filled
10 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
418 voxels filled
10 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16384511 voxels filled...
filling volume: pass 3 of 3...total of 326148 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16384511 voxels filled...
filling volume: pass 3 of 3...total of 326148 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  325755 ambiguous voxels remaining
9:  48748 ambiguous voxels remaining
8:  22067 ambiguous voxels remaining
7:  12458 ambiguous voxels remaining
6:  5747 ambiguous voxels remaining
5:  3690 ambiguous voxels remaining
4:  1936 ambiguous voxels remaining
3:  849 ambiguous voxels remaining
2:  195 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:20:20:16 mri_fill N 12 e 35.82 S 0.07 U 34.88 P 97% M 111600 F 2 R 77595 W 0 c 1684 w 3 I 272 O 232 L 1.00 1.00 0.69
@#@FSLOADPOST 2020:09:25:20:20:52 mri_fill N 12 1.00 1.00 0.70
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 20:20:52 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   3
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   5
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 6 (out of 169309: 0.003544)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:20:20:52 mri_pretess N 4 e 2.90 S 0.00 U 2.10 P 72% M 40456 F 0 R 8846 W 0 c 403 w 1 I 0 O 224 L 1.00 1.00 0.70
@#@FSLOADPOST 2020:09:25:20:20:55 mri_pretess N 4 1.00 1.00 0.70

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 51 vertices, 68 faces
slice 60: 3498 vertices, 3640 faces
slice 70: 8011 vertices, 8192 faces
slice 80: 18133 vertices, 18619 faces
slice 90: 39961 vertices, 40761 faces
slice 100: 60546 vertices, 61400 faces
slice 110: 82687 vertices, 83451 faces
slice 120: 101106 vertices, 101849 faces
slice 130: 113988 vertices, 114509 faces
slice 140: 121930 vertices, 122238 faces
slice 150: 124296 vertices, 124456 faces
slice 160: 124296 vertices, 124456 faces
slice 170: 124296 vertices, 124456 faces
slice 180: 124296 vertices, 124456 faces
slice 190: 124296 vertices, 124456 faces
slice 200: 124296 vertices, 124456 faces
slice 210: 124296 vertices, 124456 faces
slice 220: 124296 vertices, 124456 faces
slice 230: 124296 vertices, 124456 faces
slice 240: 124296 vertices, 124456 faces
slice 250: 124296 vertices, 124456 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:20:20:55 mri_tessellate N 3 e 2.47 S 0.02 U 2.37 P 97% M 37036 F 0 R 8272 W 0 c 106 w 1 I 0 O 5832 L 1.00 1.00 0.70
@#@FSLOADPOST 2020:09:25:20:20:57 mri_tessellate N 3 1.00 1.00 0.70

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   124296 voxel in cpt #1: X=-160 [v=124296,e=373368,f=248912] located at (-2.608113, -28.222750, 18.229420)
For the whole surface: X=-160 [v=124296,e=373368,f=248912]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:20:20:57 mris_extract_main_component N 2 e 0.90 S 0.09 U 0.77 P 95% M 249308 F 0 R 68525 W 0 c 90 w 1 I 0 O 8752 L 1.00 1.00 0.70
@#@FSLOADPOST 2020:09:25:20:20:58 mris_extract_main_component N 2 1.00 1.00 0.70
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 20:20:58 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 4 (out of 156850: 0.002550)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:20:20:58 mri_pretess N 4 e 2.32 S 0.01 U 1.77 P 77% M 40424 F 0 R 8843 W 0 c 295 w 1 I 0 O 224 L 1.00 1.00 0.70
@#@FSLOADPOST 2020:09:25:20:21:01 mri_pretess N 4 1.00 1.00 0.70

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2681 vertices, 2807 faces
slice 70: 6481 vertices, 6650 faces
slice 80: 14653 vertices, 15087 faces
slice 90: 34192 vertices, 34897 faces
slice 100: 54939 vertices, 55763 faces
slice 110: 77490 vertices, 78276 faces
slice 120: 96164 vertices, 96909 faces
slice 130: 109720 vertices, 110232 faces
slice 140: 118026 vertices, 118342 faces
slice 150: 120496 vertices, 120654 faces
slice 160: 120496 vertices, 120654 faces
slice 170: 120496 vertices, 120654 faces
slice 180: 120496 vertices, 120654 faces
slice 190: 120496 vertices, 120654 faces
slice 200: 120496 vertices, 120654 faces
slice 210: 120496 vertices, 120654 faces
slice 220: 120496 vertices, 120654 faces
slice 230: 120496 vertices, 120654 faces
slice 240: 120496 vertices, 120654 faces
slice 250: 120496 vertices, 120654 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:20:21:01 mri_tessellate N 3 e 2.38 S 0.01 U 2.30 P 97% M 36708 F 0 R 8190 W 0 c 110 w 1 I 0 O 5656 L 1.00 1.00 0.70
@#@FSLOADPOST 2020:09:25:20:21:03 mri_tessellate N 3 1.16 1.03 0.72

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   120496 voxel in cpt #1: X=-158 [v=120496,e=361962,f=241308] located at (58.261578, -26.651516, 18.300816)
For the whole surface: X=-158 [v=120496,e=361962,f=241308]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:20:21:03 mris_extract_main_component N 2 e 0.86 S 0.09 U 0.72 P 95% M 242104 F 0 R 66408 W 0 c 78 w 1 I 0 O 8488 L 1.16 1.03 0.72
@#@FSLOADPOST 2020:09:25:20:21:04 mris_extract_main_component N 2 1.16 1.03 0.72
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 20:21:04 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:20:21:04 mris_smooth N 5 e 3.61 S 0.09 U 3.43 P 97% M 201732 F 2 R 56298 W 0 c 158 w 3 I 312 O 8752 L 1.16 1.03 0.72
@#@FSLOADPOST 2020:09:25:20:21:08 mris_smooth N 5 1.15 1.03 0.72
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 20:21:08 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:20:21:08 mris_smooth N 5 e 3.36 S 0.05 U 3.23 P 97% M 194836 F 0 R 54347 W 0 c 151 w 1 I 0 O 8488 L 1.15 1.03 0.72
@#@FSLOADPOST 2020:09:25:20:21:11 mris_smooth N 5 1.15 1.03 0.72
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 20:21:11 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.9 mm, total surface area = 71868 mm^2

step 000: RMS=0.139 (target=0.015)   
step 005: RMS=0.112 (target=0.015)   
step 010: RMS=0.095 (target=0.015)   
step 015: RMS=0.088 (target=0.015)   
step 020: RMS=0.082 (target=0.015)   
step 025: RMS=0.077 (target=0.015)   
step 030: RMS=0.075 (target=0.015)   
step 035: RMS=0.073 (target=0.015)   
step 040: RMS=0.070 (target=0.015)   
step 045: RMS=0.069 (target=0.015)   
step 050: RMS=0.068 (target=0.015)   
step 055: RMS=0.069 (target=0.015)   
step 060: RMS=0.070 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.857887
mris_inflate stimesec    0.079421
mris_inflate ru_maxrss   261128
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   76344
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  8
mris_inflate ru_oublock  8752
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1
mris_inflate ru_nivcsw   749
@#@FSTIME  2020:09:25:20:21:11 mris_inflate N 3 e 18.57 S 0.08 U 17.85 P 96% M 261272 F 0 R 76346 W 0 c 753 w 2 I 8 O 8752 L 1.15 1.03 0.72
@#@FSLOADPOST 2020:09:25:20:21:30 mris_inflate N 3 1.10 1.03 0.73
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 20:21:30 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.9 mm, total surface area = 69558 mm^2

step 000: RMS=0.138 (target=0.015)   
step 005: RMS=0.111 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.085 (target=0.015)   
step 020: RMS=0.080 (target=0.015)   
step 025: RMS=0.076 (target=0.015)   
step 030: RMS=0.074 (target=0.015)   
step 035: RMS=0.072 (target=0.015)   
step 040: RMS=0.069 (target=0.015)   
step 045: RMS=0.069 (target=0.015)   
step 050: RMS=0.068 (target=0.015)   
step 055: RMS=0.068 (target=0.015)   
step 060: RMS=0.068 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.970125
mris_inflate stimesec    0.063797
mris_inflate ru_maxrss   252336
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   68735
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8488
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   567
@#@FSTIME  2020:09:25:20:21:30 mris_inflate N 3 e 17.12 S 0.07 U 16.97 P 99% M 252428 F 0 R 68737 W 0 c 570 w 1 I 0 O 8488 L 1.10 1.03 0.73
@#@FSLOADPOST 2020:09:25:20:21:47 mris_inflate N 3 1.07 1.03 0.73

Started at 2020��� 09��� 25��� ��������� 20:08:26 CST 
Ended   at 2020��� 09��� 25��� ��������� 20:21:47 CST
#@#%# recon-all-run-time-hours 0.222
recon-all -s monkey2 finished without error at 2020��� 09��� 25��� ��������� 20:21:47 CST



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 21:25:35 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-wm -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        763M        591M         16M        638M        1.0G
Swap:          2.0G        655M        1.4G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:35-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:25:36-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 21:25:36 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:21:25:36 mri_mask N 5 e 2.70 S 0.02 U 2.62 P 98% M 74340 F 0 R 17274 W 0 c 120 w 1 I 0 O 2960 L 0.01 0.08 0.08
@#@FSLOADPOST 2020:09:25:21:25:39 mri_mask N 5 0.01 0.08 0.08
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 21:25:39 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 -segmentation aseg.presurf.mgz wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
using segmentation aseg.presurf.mgz...
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.presurf.mgz
error: mghRead(/usr/local/freesurfer/subjects/monkey2/mri/aseg.presurf.mgz, -1): could not open file
error: mri_fill: could not read segmentation from aseg.presurf.mgz
Command exited with non-zero status 255
@#@FSTIME  2020:09:25:21:25:39 mri_fill N 14 e 3.08 S 0.01 U 3.00 P 97% M 60808 F 0 R 17246 W 0 c 217 w 1 I 0 O 8 L 0.01 0.08 0.08
@#@FSLOADPOST 2020:09:25:21:25:42 mri_fill N 14 0.09 0.10 0.08
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s monkey2 exited with ERRORS at 2020��� 09��� 25��� ��������� 21:25:42 CST

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



#New# invocation of recon-all 



2020��� 09��� 25��� ��������� 21:46:10 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        788M        517M         16M        687M        1.0G
Swap:          2.0G        647M        1.4G

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/09/25-13:46:11-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# Mask BFS 2020��� 09��� 25��� ��������� 21:46:11 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:09:25:21:46:11 mri_mask N 5 e 2.65 S 0.02 U 2.57 P 97% M 74296 F 0 R 17276 W 0 c 117 w 1 I 0 O 2960 L 0.09 0.05 0.01
@#@FSLOADPOST 2020:09:25:21:46:14 mri_mask N 5 0.09 0.05 0.01
#--------------------------------------------
#@# Fill 2020��� 09��� 25��� ��������� 21:46:14 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 821 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 325683 voxels filled...
filling volume: pass 2 of 3...total of 16384681 voxels filled...
filling volume: pass 3 of 3...total of 325978 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 325683 voxels filled...
filling volume: pass 2 of 3...total of 16384681 voxels filled...
filling volume: pass 3 of 3...total of 325978 voxels filled...done.
filling degenerate left hemisphere surface locations...
404 voxels filled
9 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
404 voxels filled
9 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16384250 voxels filled...
filling volume: pass 3 of 3...total of 326409 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16384250 voxels filled...
filling volume: pass 3 of 3...total of 326409 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  326016 ambiguous voxels remaining
9:  44743 ambiguous voxels remaining
8:  22019 ambiguous voxels remaining
7:  12418 ambiguous voxels remaining
6:  5740 ambiguous voxels remaining
5:  3689 ambiguous voxels remaining
4:  1936 ambiguous voxels remaining
3:  849 ambiguous voxels remaining
2:  195 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.6 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:09:25:21:46:14 mri_fill N 12 e 35.28 S 0.09 U 33.80 P 96% M 111672 F 0 R 77595 W 0 c 2028 w 1 I 0 O 232 L 0.09 0.05 0.01
@#@FSLOADPOST 2020:09:25:21:46:49 mri_fill N 12 0.49 0.16 0.05
#--------------------------------------------
#@# Tessellate lh 2020��� 09��� 25��� ��������� 21:46:49 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   3
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   5
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 6 (out of 169309: 0.003544)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:21:46:49 mri_pretess N 4 e 3.30 S 0.01 U 2.16 P 65% M 40408 F 0 R 8845 W 0 c 430 w 1 I 0 O 224 L 0.49 0.16 0.05
@#@FSLOADPOST 2020:09:25:21:46:52 mri_pretess N 4 0.61 0.19 0.06

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 51 vertices, 68 faces
slice 60: 3498 vertices, 3640 faces
slice 70: 8011 vertices, 8192 faces
slice 80: 18133 vertices, 18619 faces
slice 90: 39961 vertices, 40761 faces
slice 100: 60546 vertices, 61400 faces
slice 110: 82687 vertices, 83451 faces
slice 120: 101106 vertices, 101849 faces
slice 130: 113988 vertices, 114509 faces
slice 140: 121930 vertices, 122238 faces
slice 150: 124296 vertices, 124456 faces
slice 160: 124296 vertices, 124456 faces
slice 170: 124296 vertices, 124456 faces
slice 180: 124296 vertices, 124456 faces
slice 190: 124296 vertices, 124456 faces
slice 200: 124296 vertices, 124456 faces
slice 210: 124296 vertices, 124456 faces
slice 220: 124296 vertices, 124456 faces
slice 230: 124296 vertices, 124456 faces
slice 240: 124296 vertices, 124456 faces
slice 250: 124296 vertices, 124456 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:21:46:52 mri_tessellate N 3 e 2.87 S 0.02 U 2.71 P 95% M 37080 F 0 R 8274 W 0 c 145 w 1 I 0 O 5832 L 0.61 0.19 0.06
@#@FSLOADPOST 2020:09:25:21:46:55 mri_tessellate N 3 0.61 0.19 0.06

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   124296 voxel in cpt #1: X=-160 [v=124296,e=373368,f=248912] located at (-2.608113, -28.222750, 18.229420)
For the whole surface: X=-160 [v=124296,e=373368,f=248912]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:21:46:55 mris_extract_main_component N 2 e 0.95 S 0.08 U 0.79 P 92% M 249444 F 0 R 68532 W 0 c 92 w 1 I 0 O 8752 L 0.61 0.19 0.06
@#@FSLOADPOST 2020:09:25:21:46:56 mris_extract_main_component N 2 0.64 0.20 0.06
#--------------------------------------------
#@# Tessellate rh 2020��� 09��� 25��� ��������� 21:46:56 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 4 (out of 157111: 0.002546)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:09:25:21:46:56 mri_pretess N 4 e 2.47 S 0.01 U 1.74 P 71% M 40400 F 0 R 8845 W 0 c 304 w 1 I 0 O 224 L 0.64 0.20 0.06
@#@FSLOADPOST 2020:09:25:21:46:59 mri_pretess N 4 0.64 0.20 0.06

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2681 vertices, 2807 faces
slice 70: 6481 vertices, 6650 faces
slice 80: 14653 vertices, 15087 faces
slice 90: 34192 vertices, 34897 faces
slice 100: 54939 vertices, 55763 faces
slice 110: 77490 vertices, 78276 faces
slice 120: 96030 vertices, 96754 faces
slice 130: 109362 vertices, 109856 faces
slice 140: 117668 vertices, 117966 faces
slice 150: 120138 vertices, 120278 faces
slice 160: 120138 vertices, 120278 faces
slice 170: 120138 vertices, 120278 faces
slice 180: 120138 vertices, 120278 faces
slice 190: 120138 vertices, 120278 faces
slice 200: 120138 vertices, 120278 faces
slice 210: 120138 vertices, 120278 faces
slice 220: 120138 vertices, 120278 faces
slice 230: 120138 vertices, 120278 faces
slice 240: 120138 vertices, 120278 faces
slice 250: 120138 vertices, 120278 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:09:25:21:46:59 mri_tessellate N 3 e 2.40 S 0.01 U 2.29 P 96% M 36724 F 0 R 8185 W 0 c 134 w 1 I 0 O 5640 L 0.64 0.20 0.06
@#@FSLOADPOST 2020:09:25:21:47:01 mri_tessellate N 3 0.67 0.22 0.07

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   120138 voxel in cpt #1: X=-140 [v=120138,e=360834,f=240556] located at (58.308079, -26.707903, 18.489620)
For the whole surface: X=-140 [v=120138,e=360834,f=240556]
One single component has been found
nothing to do
done

@#@FSTIME  2020:09:25:21:47:01 mris_extract_main_component N 2 e 0.85 S 0.09 U 0.69 P 92% M 241200 F 0 R 66199 W 0 c 82 w 1 I 0 O 8456 L 0.67 0.22 0.07
@#@FSLOADPOST 2020:09:25:21:47:02 mris_extract_main_component N 2 0.67 0.22 0.07
#--------------------------------------------
#@# Smooth1 lh 2020��� 09��� 25��� ��������� 21:47:02 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:21:47:02 mris_smooth N 5 e 3.67 S 0.07 U 3.49 P 97% M 201608 F 0 R 56300 W 0 c 167 w 1 I 0 O 8752 L 0.67 0.22 0.07
@#@FSLOADPOST 2020:09:25:21:47:06 mris_smooth N 5 0.70 0.23 0.07
#--------------------------------------------
#@# Smooth1 rh 2020��� 09��� 25��� ��������� 21:47:06 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:09:25:21:47:06 mris_smooth N 5 e 3.56 S 0.07 U 3.37 P 96% M 195040 F 0 R 54382 W 0 c 185 w 1 I 0 O 8456 L 0.70 0.23 0.07
@#@FSLOADPOST 2020:09:25:21:47:10 mris_smooth N 5 0.70 0.23 0.07
#--------------------------------------------
#@# Inflation1 lh 2020��� 09��� 25��� ��������� 21:47:10 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.9 mm, total surface area = 71868 mm^2

step 000: RMS=0.139 (target=0.015)   
step 005: RMS=0.112 (target=0.015)   
step 010: RMS=0.095 (target=0.015)   
step 015: RMS=0.088 (target=0.015)   
step 020: RMS=0.082 (target=0.015)   
step 025: RMS=0.077 (target=0.015)   
step 030: RMS=0.075 (target=0.015)   
step 035: RMS=0.073 (target=0.015)   
step 040: RMS=0.070 (target=0.015)   
step 045: RMS=0.069 (target=0.015)   
step 050: RMS=0.068 (target=0.015)   
step 055: RMS=0.069 (target=0.015)   
step 060: RMS=0.070 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.691959
mris_inflate stimesec    0.095653
mris_inflate ru_maxrss   261140
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   76343
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8752
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   695
@#@FSTIME  2020:09:25:21:47:10 mris_inflate N 3 e 18.00 S 0.10 U 17.69 P 98% M 261304 F 0 R 76345 W 0 c 699 w 1 I 0 O 8752 L 0.70 0.23 0.07
@#@FSLOADPOST 2020:09:25:21:47:28 mris_inflate N 3 0.78 0.28 0.10
#--------------------------------------------
#@# Inflation1 rh 2020��� 09��� 25��� ��������� 21:47:28 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.8 mm, total surface area = 69373 mm^2

step 000: RMS=0.136 (target=0.015)   
step 005: RMS=0.109 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.078 (target=0.015)   
step 025: RMS=0.073 (target=0.015)   
step 030: RMS=0.072 (target=0.015)   
step 035: RMS=0.069 (target=0.015)   
step 040: RMS=0.067 (target=0.015)   
step 045: RMS=0.067 (target=0.015)   
step 050: RMS=0.065 (target=0.015)   
step 055: RMS=0.066 (target=0.015)   
step 060: RMS=0.066 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    16.861200
mris_inflate stimesec    0.103589
mris_inflate ru_maxrss   252480
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   73669
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8464
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    0
mris_inflate ru_nivcsw   706
@#@FSTIME  2020:09:25:21:47:28 mris_inflate N 3 e 17.19 S 0.11 U 16.86 P 98% M 252588 F 0 R 73671 W 0 c 709 w 1 I 0 O 8464 L 0.78 0.28 0.10
@#@FSLOADPOST 2020:09:25:21:47:45 mris_inflate N 3 0.83 0.32 0.11
#--------------------------------------------
#@# QSphere lh 2020��� 09��� 25��� ��������� 21:47:45 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.271...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=180.666, avgs=0
005/300: dt: 0.9000, rms radial error=180.407, avgs=0
010/300: dt: 0.9000, rms radial error=179.852, avgs=0
015/300: dt: 0.9000, rms radial error=179.122, avgs=0
020/300: dt: 0.9000, rms radial error=178.290, avgs=0
025/300: dt: 0.9000, rms radial error=177.400, avgs=0
030/300: dt: 0.9000, rms radial error=176.477, avgs=0
035/300: dt: 0.9000, rms radial error=175.536, avgs=0
040/300: dt: 0.9000, rms radial error=174.587, avgs=0
045/300: dt: 0.9000, rms radial error=173.634, avgs=0
050/300: dt: 0.9000, rms radial error=172.681, avgs=0
055/300: dt: 0.9000, rms radial error=171.730, avgs=0
060/300: dt: 0.9000, rms radial error=170.782, avgs=0
065/300: dt: 0.9000, rms radial error=169.837, avgs=0
070/300: dt: 0.9000, rms radial error=168.897, avgs=0
075/300: dt: 0.9000, rms radial error=167.960, avgs=0
080/300: dt: 0.9000, rms radial error=167.029, avgs=0
085/300: dt: 0.9000, rms radial error=166.106, avgs=0
090/300: dt: 0.9000, rms radial error=165.187, avgs=0
095/300: dt: 0.9000, rms radial error=164.273, avgs=0
100/300: dt: 0.9000, rms radial error=163.364, avgs=0
105/300: dt: 0.9000, rms radial error=162.459, avgs=0
110/300: dt: 0.9000, rms radial error=161.559, avgs=0
115/300: dt: 0.9000, rms radial error=160.664, avgs=0
120/300: dt: 0.9000, rms radial error=159.773, avgs=0
125/300: dt: 0.9000, rms radial error=158.887, avgs=0
130/300: dt: 0.9000, rms radial error=158.006, avgs=0
135/300: dt: 0.9000, rms radial error=157.129, avgs=0
140/300: dt: 0.9000, rms radial error=156.256, avgs=0
145/300: dt: 0.9000, rms radial error=155.389, avgs=0
150/300: dt: 0.9000, rms radial error=154.526, avgs=0
155/300: dt: 0.9000, rms radial error=153.667, avgs=0
160/300: dt: 0.9000, rms radial error=152.813, avgs=0
165/300: dt: 0.9000, rms radial error=151.964, avgs=0
170/300: dt: 0.9000, rms radial error=151.119, avgs=0
175/300: dt: 0.9000, rms radial error=150.279, avgs=0
180/300: dt: 0.9000, rms radial error=149.443, avgs=0
185/300: dt: 0.9000, rms radial error=148.611, avgs=0
190/300: dt: 0.9000, rms radial error=147.785, avgs=0
195/300: dt: 0.9000, rms radial error=146.962, avgs=0
200/300: dt: 0.9000, rms radial error=146.144, avgs=0
205/300: dt: 0.9000, rms radial error=145.331, avgs=0
210/300: dt: 0.9000, rms radial error=144.522, avgs=0
215/300: dt: 0.9000, rms radial error=143.717, avgs=0
220/300: dt: 0.9000, rms radial error=142.917, avgs=0
225/300: dt: 0.9000, rms radial error=142.121, avgs=0
230/300: dt: 0.9000, rms radial error=141.329, avgs=0
235/300: dt: 0.9000, rms radial error=140.542, avgs=0
240/300: dt: 0.9000, rms radial error=139.759, avgs=0
245/300: dt: 0.9000, rms radial error=138.980, avgs=0
250/300: dt: 0.9000, rms radial error=138.206, avgs=0
255/300: dt: 0.9000, rms radial error=137.436, avgs=0
260/300: dt: 0.9000, rms radial error=136.670, avgs=0
265/300: dt: 0.9000, rms radial error=135.908, avgs=0
270/300: dt: 0.9000, rms radial error=135.151, avgs=0
275/300: dt: 0.9000, rms radial error=134.397, avgs=0
280/300: dt: 0.9000, rms radial error=133.648, avgs=0
285/300: dt: 0.9000, rms radial error=132.903, avgs=0
290/300: dt: 0.9000, rms radial error=132.162, avgs=0
295/300: dt: 0.9000, rms radial error=131.425, avgs=0
300/300: dt: 0.9000, rms radial error=130.693, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.09 +- 0.79 (0.00-->15.03) (max @ vno 36176 --> 36185)
face area 0.02 +- 0.04 (-0.29-->1.80)
epoch 1 (K=10.0), pass 1, starting sse = 15077.29
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00016
epoch 2 (K=40.0), pass 1, starting sse = 2738.89
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00019
epoch 3 (K=160.0), pass 1, starting sse = 359.18
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/13 = 0.00256
epoch 4 (K=640.0), pass 1, starting sse = 44.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/15 = 0.00430
final distance error %100000.00
writing spherical brain to ../surf/lh.qsphere.nofix
mris_sphere utimesec    116.584266
mris_sphere stimesec    0.374612
mris_sphere ru_maxrss   899456
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   314777
mris_sphere ru_majflt   11
mris_sphere ru_nswap    0
mris_sphere ru_inblock  3072
mris_sphere ru_oublock  8752
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    16
mris_sphere ru_nivcsw   3694
spherical transformation took 0.0328 hours
FSRUNTIME@ mris_sphere  0.0328 hours 1 threads
@#@FSTIME  2020:09:25:21:47:45 mris_sphere N 9 e 118.07 S 0.40 U 116.58 P 99% M 899456 F 14 R 314778 W 0 c 3707 w 20 I 3400 O 8752 L 0.83 0.32 0.11
@#@FSLOADPOST 2020:09:25:21:49:43 mris_sphere N 9 0.98 0.55 0.22
#--------------------------------------------
#@# QSphere rh 2020��� 09��� 25��� ��������� 21:49:43 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.276...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=180.437, avgs=0
005/300: dt: 0.9000, rms radial error=180.182, avgs=0
010/300: dt: 0.9000, rms radial error=179.633, avgs=0
015/300: dt: 0.9000, rms radial error=178.913, avgs=0
020/300: dt: 0.9000, rms radial error=178.092, avgs=0
025/300: dt: 0.9000, rms radial error=177.211, avgs=0
030/300: dt: 0.9000, rms radial error=176.296, avgs=0
035/300: dt: 0.9000, rms radial error=175.364, avgs=0
040/300: dt: 0.9000, rms radial error=174.423, avgs=0
045/300: dt: 0.9000, rms radial error=173.480, avgs=0
050/300: dt: 0.9000, rms radial error=172.537, avgs=0
055/300: dt: 0.9000, rms radial error=171.595, avgs=0
060/300: dt: 0.9000, rms radial error=170.657, avgs=0
065/300: dt: 0.9000, rms radial error=169.723, avgs=0
070/300: dt: 0.9000, rms radial error=168.797, avgs=0
075/300: dt: 0.9000, rms radial error=167.874, avgs=0
080/300: dt: 0.9000, rms radial error=166.956, avgs=0
085/300: dt: 0.9000, rms radial error=166.042, avgs=0
090/300: dt: 0.9000, rms radial error=165.133, avgs=0
095/300: dt: 0.9000, rms radial error=164.228, avgs=0
100/300: dt: 0.9000, rms radial error=163.327, avgs=0
105/300: dt: 0.9000, rms radial error=162.431, avgs=0
110/300: dt: 0.9000, rms radial error=161.539, avgs=0
115/300: dt: 0.9000, rms radial error=160.652, avgs=0
120/300: dt: 0.9000, rms radial error=159.769, avgs=0
125/300: dt: 0.9000, rms radial error=158.891, avgs=0
130/300: dt: 0.9000, rms radial error=158.017, avgs=0
135/300: dt: 0.9000, rms radial error=157.148, avgs=0
140/300: dt: 0.9000, rms radial error=156.283, avgs=0
145/300: dt: 0.9000, rms radial error=155.422, avgs=0
150/300: dt: 0.9000, rms radial error=154.566, avgs=0
155/300: dt: 0.9000, rms radial error=153.714, avgs=0
160/300: dt: 0.9000, rms radial error=152.866, avgs=0
165/300: dt: 0.9000, rms radial error=152.023, avgs=0
170/300: dt: 0.9000, rms radial error=151.184, avgs=0
175/300: dt: 0.9000, rms radial error=150.349, avgs=0
180/300: dt: 0.9000, rms radial error=149.519, avgs=0
185/300: dt: 0.9000, rms radial error=148.693, avgs=0
190/300: dt: 0.9000, rms radial error=147.871, avgs=0
195/300: dt: 0.9000, rms radial error=147.054, avgs=0
200/300: dt: 0.9000, rms radial error=146.241, avgs=0
205/300: dt: 0.9000, rms radial error=145.432, avgs=0
210/300: dt: 0.9000, rms radial error=144.628, avgs=0
215/300: dt: 0.9000, rms radial error=143.828, avgs=0
220/300: dt: 0.9000, rms radial error=143.032, avgs=0
225/300: dt: 0.9000, rms radial error=142.240, avgs=0
230/300: dt: 0.9000, rms radial error=141.452, avgs=0
235/300: dt: 0.9000, rms radial error=140.669, avgs=0
240/300: dt: 0.9000, rms radial error=139.890, avgs=0
245/300: dt: 0.9000, rms radial error=139.115, avgs=0
250/300: dt: 0.9000, rms radial error=138.344, avgs=0
255/300: dt: 0.9000, rms radial error=137.577, avgs=0
260/300: dt: 0.9000, rms radial error=136.814, avgs=0
265/300: dt: 0.9000, rms radial error=136.055, avgs=0
270/300: dt: 0.9000, rms radial error=135.301, avgs=0
275/300: dt: 0.9000, rms radial error=134.551, avgs=0
280/300: dt: 0.9000, rms radial error=133.804, avgs=0
285/300: dt: 0.9000, rms radial error=133.062, avgs=0
290/300: dt: 0.9000, rms radial error=132.323, avgs=0
295/300: dt: 0.9000, rms radial error=131.589, avgs=0
300/300: dt: 0.9000, rms radial error=130.858, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.11 +- 0.82 (0.00-->11.63) (max @ vno 29057 --> 29068)
face area 0.02 +- 0.04 (-0.21-->1.12)
epoch 1 (K=10.0), pass 1, starting sse = 14517.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00026
epoch 2 (K=40.0), pass 1, starting sse = 2629.72
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00022
epoch 3 (K=160.0), pass 1, starting sse = 350.99
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/13 = 0.00340
epoch 4 (K=640.0), pass 1, starting sse = 45.14
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/17 = 0.00420
final distance error %100000.00
writing spherical brain to ../surf/rh.qsphere.nofix
mris_sphere utimesec    115.961036
mris_sphere stimesec    0.311144
mris_sphere ru_maxrss   887724
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   312015
mris_sphere ru_majflt   12
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10536
mris_sphere ru_oublock  8464
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    32
mris_sphere ru_nivcsw   3655
spherical transformation took 0.0325 hours
FSRUNTIME@ mris_sphere  0.0325 hours 1 threads
@#@FSTIME  2020:09:25:21:49:43 mris_sphere N 9 e 117.19 S 0.33 U 115.96 P 99% M 887796 F 12 R 312017 W 0 c 3667 w 33 I 10536 O 8464 L 0.98 0.55 0.22
@#@FSLOADPOST 2020:09:25:21:51:40 mris_sphere N 9 1.00 0.70 0.32
#@# Fix Topology lh 2020��� 09��� 25��� ��������� 21:51:40 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 lh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-160 (nv=124296, nf=248912, ne=373368, g=81)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
24273 ambiguous faces found in tessellation
segmenting defects...
50 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 21 into 8
      -merging segment 26 into 8
      -merging segment 31 into 8
      -merging segment 18 into 8
      -merging segment 19 into 15
      -merging segment 23 into 25
      -merging segment 35 into 25
      -merging segment 37 into 30
42 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7469  (-4.8735)
      -vertex     loglikelihood: -6.8070  (-3.4035)
      -normal dot loglikelihood: -3.5346  (-3.5346)
      -quad curv  loglikelihood: -5.3756  (-2.6878)
      Total Loglikelihood : -25.4642
CORRECTING DEFECT 0 (vertices=96, convex hull=75, v0=10)
After retessellation of defect 0 (v0=10), euler #=-37 (110709,329168,218422) : difference with theory (-39) = -2 
CORRECTING DEFECT 1 (vertices=589, convex hull=320, v0=170)
After retessellation of defect 1 (v0=170), euler #=-37 (110874,329827,218916) : difference with theory (-38) = -1 
CORRECTING DEFECT 2 (vertices=35, convex hull=30, v0=1755)
After retessellation of defect 2 (v0=1755), euler #=-36 (110874,329835,218925) : difference with theory (-37) = -1 
CORRECTING DEFECT 3 (vertices=30, convex hull=50, v0=2198)
After retessellation of defect 3 (v0=2198), euler #=-35 (110891,329904,218978) : difference with theory (-36) = -1 
CORRECTING DEFECT 4 (vertices=8, convex hull=11, v0=2581)
After retessellation of defect 4 (v0=2581), euler #=-34 (110892,329908,218982) : difference with theory (-35) = -1 
CORRECTING DEFECT 5 (vertices=176, convex hull=58, v0=3487)
After retessellation of defect 5 (v0=3487), euler #=-33 (110911,329989,219045) : difference with theory (-34) = -1 
CORRECTING DEFECT 6 (vertices=11, convex hull=13, v0=4373)
After retessellation of defect 6 (v0=4373), euler #=-32 (110912,329995,219051) : difference with theory (-33) = -1 
CORRECTING DEFECT 7 (vertices=13, convex hull=18, v0=4453)
After retessellation of defect 7 (v0=4453), euler #=-31 (110913,330003,219059) : difference with theory (-32) = -1 
CORRECTING DEFECT 8 (vertices=5488, convex hull=1641, v0=8027)
normal vector of length zero at vertex 116858 with 6 faces
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 116254 with 6 faces
normal vector of length zero at vertex 116257 with 8 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
first tangent vector of length zero at vertex 26457
second tangent vector of length zero at vertex 26457
normal vector of length zero at vertex 116589 with 7 faces
normal vector of length zero at vertex 116784 with 6 faces
normal vector of length zero at vertex 116784 with 6 faces
normal vector of length zero at vertex 115429 with 6 faces
normal vector of length zero at vertex 115489 with 4 faces
normal vector of length zero at vertex 116096 with 4 faces
normal vector of length zero at vertex 116784 with 6 faces
normal vector of length zero at vertex 116106 with 4 faces
normal vector of length zero at vertex 116253 with 4 faces
normal vector of length zero at vertex 116321 with 4 faces
normal vector of length zero at vertex 116321 with 4 faces
normal vector of length zero at vertex 115886 with 6 faces
normal vector of length zero at vertex 115981 with 4 faces
normal vector of length zero at vertex 115886 with 6 faces
normal vector of length zero at vertex 115974 with 4 faces
normal vector of length zero at vertex 115428 with 4 faces
normal vector of length zero at vertex 116323 with 4 faces
normal vector of length zero at vertex 115432 with 4 faces
normal vector of length zero at vertex 116027 with 4 faces
normal vector of length zero at vertex 116177 with 4 faces
normal vector of length zero at vertex 116319 with 4 faces
normal vector of length zero at vertex 115432 with 4 faces
normal vector of length zero at vertex 115372 with 4 faces
normal vector of length zero at vertex 115432 with 4 faces
normal vector of length zero at vertex 115318 with 4 faces
normal vector of length zero at vertex 115372 with 4 faces
normal vector of length zero at vertex 115372 with 4 faces
normal vector of length zero at vertex 115642 with 4 faces
normal vector of length zero at vertex 115279 with 6 faces
normal vector of length zero at vertex 115372 with 4 faces
normal vector of length zero at vertex 115431 with 4 faces
normal vector of length zero at vertex 115862 with 4 faces
normal vector of length zero at vertex 116027 with 4 faces
normal vector of length zero at vertex 116097 with 14 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 115862 with 4 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 115862 with 4 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
normal vector of length zero at vertex 26473 with 6 faces
first tangent vector of length zero at vertex 26473
second tangent vector of length zero at vertex 26473
normal vector of length zero at vertex 115372 with 4 faces
normal vector of length zero at vertex 115642 with 4 faces
normal vector of length zero at vertex 115605 with 4 faces
normal vector of length zero at vertex 116455 with 4 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
first tangent vector of length zero at vertex 26457
second tangent vector of length zero at vertex 26457
normal vector of length zero at vertex 116455 with 3 faces
normal vector of length zero at vertex 116455 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116904 with 3 faces
normal vector of length zero at vertex 116784 with 6 faces
normal vector of length zero at vertex 116784 with 6 faces
normal vector of length zero at vertex 115938 with 4 faces
normal vector of length zero at vertex 115938 with 4 faces
normal vector of length zero at vertex 114974 with 4 faces
normal vector of length zero at vertex 116350 with 4 faces
normal vector of length zero at vertex 115938 with 4 faces
normal vector of length zero at vertex 115938 with 3 faces
normal vector of length zero at vertex 115938 with 4 faces
normal vector of length zero at vertex 115731 with 4 faces
normal vector of length zero at vertex 115938 with 4 faces
normal vector of length zero at vertex 115938 with 3 faces
normal vector of length zero at vertex 116497 with 4 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
normal vector of length zero at vertex 26457 with 6 faces
first tangent vector of length zero at vertex 26457
second tangent vector of length zero at vertex 26457
normal vector of length zero at vertex 115372 with 4 faces
normal vector of length zero at vertex 115372 with 4 faces
After retessellation of defect 8 (v0=8027), euler #=-33 (112485,335683,223165) : difference with theory (-31) = 2 
CORRECTING DEFECT 9 (vertices=1186, convex hull=340, v0=8211)
A large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 117756 with 4 faces
normal vector of length zero at vertex 117997 with 4 faces
normal vector of length zero at vertex 117721 with 6 faces
normal vector of length zero at vertex 117395 with 4 faces
normal vector of length zero at vertex 117721 with 6 faces
normal vector of length zero at vertex 117510 with 4 faces
normal vector of length zero at vertex 117721 with 6 faces
normal vector of length zero at vertex 117395 with 4 faces
normal vector of length zero at vertex 117395 with 4 faces
normal vector of length zero at vertex 117428 with 4 faces
normal vector of length zero at vertex 117721 with 6 faces
normal vector of length zero at vertex 118131 with 4 faces
normal vector of length zero at vertex 117429 with 5 faces
normal vector of length zero at vertex 117429 with 4 faces
normal vector of length zero at vertex 117394 with 4 faces
normal vector of length zero at vertex 117395 with 4 faces
normal vector of length zero at vertex 117395 with 4 faces
normal vector of length zero at vertex 117429 with 4 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117460 with 4 faces
normal vector of length zero at vertex 117401 with 3 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 117510 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117446 with 4 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117510 with 3 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117484 with 4 faces
normal vector of length zero at vertex 117429 with 6 faces
normal vector of length zero at vertex 117510 with 4 faces
normal vector of length zero at vertex 117429 with 4 faces
normal vector of length zero at vertex 117429 with 4 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117429 with 3 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117541 with 3 faces
normal vector of length zero at vertex 117484 with 4 faces
normal vector of length zero at vertex 117484 with 4 faces
normal vector of length zero at vertex 117541 with 5 faces
normal vector of length zero at vertex 117484 with 4 faces
normal vector of length zero at vertex 117484 with 4 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 117571 with 3 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
normal vector of length zero at vertex 13309 with 4 faces
first tangent vector of length zero at vertex 13309
second tangent vector of length zero at vertex 13309
normal vector of length zero at vertex 117429 with 4 faces
normal vector of length zero at vertex 117429 with 4 faces
After retessellation of defect 9 (v0=8211), euler #=-34 (112743,336641,223864) : difference with theory (-30) = 4 
CORRECTING DEFECT 10 (vertices=62, convex hull=36, v0=9461)
After retessellation of defect 10 (v0=9461), euler #=-33 (112751,336678,223894) : difference with theory (-29) = 4 
CORRECTING DEFECT 11 (vertices=174, convex hull=131, v0=10368)
After retessellation of defect 11 (v0=10368), euler #=-32 (112798,336881,224051) : difference with theory (-28) = 4 
CORRECTING DEFECT 12 (vertices=33, convex hull=56, v0=12209)
After retessellation of defect 12 (v0=12209), euler #=-31 (112808,336934,224095) : difference with theory (-27) = 4 
CORRECTING DEFECT 13 (vertices=6, convex hull=25, v0=13792)
After retessellation of defect 13 (v0=13792), euler #=-30 (112810,336947,224107) : difference with theory (-26) = 4 
CORRECTING DEFECT 14 (vertices=41, convex hull=40, v0=16483)
After retessellation of defect 14 (v0=16483), euler #=-29 (112815,336979,224135) : difference with theory (-25) = 4 
CORRECTING DEFECT 15 (vertices=1005, convex hull=215, v0=19928)
normal vector of length zero at vertex 118870 with 3 faces
normal vector of length zero at vertex 118740 with 6 faces
normal vector of length zero at vertex 118804 with 4 faces
normal vector of length zero at vertex 118974 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118804 with 4 faces
normal vector of length zero at vertex 118946 with 6 faces
normal vector of length zero at vertex 118974 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118946 with 6 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118804 with 4 faces
normal vector of length zero at vertex 118946 with 6 faces
normal vector of length zero at vertex 118974 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118946 with 6 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 16819 with 6 faces
normal vector of length zero at vertex 118804 with 4 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119379 with 6 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 118689 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119630 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119495 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119495 with 4 faces
normal vector of length zero at vertex 119495 with 4 faces
normal vector of length zero at vertex 119495 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119495 with 4 faces
normal vector of length zero at vertex 119059 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119630 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 118840 with 6 faces
normal vector of length zero at vertex 119251 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119058 with 4 faces
normal vector of length zero at vertex 118839 with 4 faces
normal vector of length zero at vertex 118839 with 4 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119494 with 4 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 119252 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 118840 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 119059 with 6 faces
normal vector of length zero at vertex 119100 with 4 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 119059 with 6 faces
normal vector of length zero at vertex 119469 with 6 faces
normal vector of length zero at vertex 118839 with 4 faces
normal vector of length zero at vertex 118840 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 118839 with 4 faces
normal vector of length zero at vertex 118936 with 12 faces
normal vector of length zero at vertex 119100 with 4 faces
normal vector of length zero at vertex 119252 with 4 faces
normal vector of length zero at vertex 118839 with 4 faces
normal vector of length zero at vertex 118936 with 12 faces
normal vector of length zero at vertex 119100 with 4 faces
normal vector of length zero at vertex 119252 with 4 faces
normal vector of length zero at vertex 119100 with 4 faces
normal vector of length zero at vertex 118840 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 119630 with 4 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 118840 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 119059 with 4 faces
normal vector of length zero at vertex 119059 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 118839 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 118839 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 119015 with 7 faces
normal vector of length zero at vertex 118839 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 118839 with 4 faces
normal vector of length zero at vertex 118899 with 4 faces
normal vector of length zero at vertex 118804 with 4 faces
normal vector of length zero at vertex 118974 with 4 faces
normal vector of length zero at vertex 119252 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119099 with 4 faces
normal vector of length zero at vertex 119252 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 118862 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 118860 with 6 faces
normal vector of length zero at vertex 118862 with 4 faces
normal vector of length zero at vertex 119521 with 4 faces
normal vector of length zero at vertex 119099 with 4 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 119059 with 8 faces
normal vector of length zero at vertex 119545 with 4 faces
normal vector of length zero at vertex 118870 with 4 faces
normal vector of length zero at vertex 119059 with 4 faces
normal vector of length zero at vertex 119059 with 4 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 119015 with 4 faces
normal vector of length zero at vertex 119252 with 4 faces
normal vector of length zero at vertex 118805 with 4 faces
normal vector of length zero at vertex 118968 with 4 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 118975 with 4 faces
normal vector of length zero at vertex 119015 with 6 faces
normal vector of length zero at vertex 119015 with 6 faces
After retessellation of defect 15 (v0=19928), euler #=-27 (113056,337804,224721) : difference with theory (-24) = 3 
CORRECTING DEFECT 16 (vertices=1196, convex hull=756, v0=22919)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 16 (v0=22919), euler #=-26 (113548,339677,226103) : difference with theory (-23) = 3 
CORRECTING DEFECT 17 (vertices=204, convex hull=124, v0=23584)
After retessellation of defect 17 (v0=23584), euler #=-25 (113582,339841,226234) : difference with theory (-22) = 3 
CORRECTING DEFECT 18 (vertices=6, convex hull=28, v0=28801)
After retessellation of defect 18 (v0=28801), euler #=-24 (113584,339856,226248) : difference with theory (-21) = 3 
CORRECTING DEFECT 19 (vertices=720, convex hull=192, v0=35395)
After retessellation of defect 19 (v0=35395), euler #=-23 (113623,340075,226429) : difference with theory (-20) = 3 
CORRECTING DEFECT 20 (vertices=340, convex hull=191, v0=37572)
After retessellation of defect 20 (v0=37572), euler #=-22 (113782,340642,226838) : difference with theory (-19) = 3 
CORRECTING DEFECT 21 (vertices=370, convex hull=193, v0=41552)
After retessellation of defect 21 (v0=41552), euler #=-19 (113874,341020,227127) : difference with theory (-18) = 1 
CORRECTING DEFECT 22 (vertices=22, convex hull=29, v0=44565)
After retessellation of defect 22 (v0=44565), euler #=-18 (113879,341043,227146) : difference with theory (-17) = 1 
CORRECTING DEFECT 23 (vertices=28, convex hull=48, v0=44671)
After retessellation of defect 23 (v0=44671), euler #=-17 (113891,341103,227195) : difference with theory (-16) = 1 
CORRECTING DEFECT 24 (vertices=28, convex hull=58, v0=48721)
After retessellation of defect 24 (v0=48721), euler #=-16 (113905,341169,227248) : difference with theory (-15) = 1 
CORRECTING DEFECT 25 (vertices=265, convex hull=147, v0=48838)
After retessellation of defect 25 (v0=48838), euler #=-14 (114000,341522,227508) : difference with theory (-14) = 0 
CORRECTING DEFECT 26 (vertices=607, convex hull=226, v0=50966)
After retessellation of defect 26 (v0=50966), euler #=-13 (114017,341678,227648) : difference with theory (-13) = 0 
CORRECTING DEFECT 27 (vertices=48, convex hull=33, v0=51873)
After retessellation of defect 27 (v0=51873), euler #=-12 (114026,341715,227677) : difference with theory (-12) = 0 
CORRECTING DEFECT 28 (vertices=16, convex hull=19, v0=53079)
After retessellation of defect 28 (v0=53079), euler #=-11 (114032,341740,227697) : difference with theory (-11) = 0 
CORRECTING DEFECT 29 (vertices=26, convex hull=35, v0=53795)
After retessellation of defect 29 (v0=53795), euler #=-10 (114035,341764,227719) : difference with theory (-10) = 0 
CORRECTING DEFECT 30 (vertices=19, convex hull=48, v0=59275)
After retessellation of defect 30 (v0=59275), euler #=-9 (114043,341803,227751) : difference with theory (-9) = 0 
CORRECTING DEFECT 31 (vertices=24, convex hull=46, v0=60194)
After retessellation of defect 31 (v0=60194), euler #=-8 (114054,341854,227792) : difference with theory (-8) = 0 
CORRECTING DEFECT 32 (vertices=232, convex hull=240, v0=63956)
After retessellation of defect 32 (v0=63956), euler #=-7 (114145,342250,228098) : difference with theory (-7) = 0 
CORRECTING DEFECT 33 (vertices=6, convex hull=20, v0=67188)
After retessellation of defect 33 (v0=67188), euler #=-6 (114146,342258,228106) : difference with theory (-6) = 0 
CORRECTING DEFECT 34 (vertices=47, convex hull=46, v0=70205)
After retessellation of defect 34 (v0=70205), euler #=-5 (114155,342302,228142) : difference with theory (-5) = 0 
CORRECTING DEFECT 35 (vertices=75, convex hull=37, v0=77423)
After retessellation of defect 35 (v0=77423), euler #=-4 (114168,342354,228182) : difference with theory (-4) = 0 
CORRECTING DEFECT 36 (vertices=139, convex hull=84, v0=84486)
After retessellation of defect 36 (v0=84486), euler #=-3 (114189,342456,228264) : difference with theory (-3) = 0 
CORRECTING DEFECT 37 (vertices=24, convex hull=26, v0=88433)
After retessellation of defect 37 (v0=88433), euler #=-2 (114189,342465,228274) : difference with theory (-2) = 0 
CORRECTING DEFECT 38 (vertices=23, convex hull=25, v0=89624)
After retessellation of defect 38 (v0=89624), euler #=-1 (114192,342480,228287) : difference with theory (-1) = 0 
CORRECTING DEFECT 39 (vertices=127, convex hull=129, v0=93362)
After retessellation of defect 39 (v0=93362), euler #=0 (114248,342711,228463) : difference with theory (0) = 0 
CORRECTING DEFECT 40 (vertices=20, convex hull=19, v0=110401)
After retessellation of defect 40 (v0=110401), euler #=1 (114249,342719,228471) : difference with theory (1) = 0 
CORRECTING DEFECT 41 (vertices=36, convex hull=60, v0=112604)
After retessellation of defect 41 (v0=112604), euler #=2 (114258,342768,228512) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.92 +- 0.39 (0.02-->23.99) (max @ vno 9427 --> 14308)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.92 +- 0.39 (0.02-->23.99) (max @ vno 9427 --> 14308)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
116 mutations (36.9%), 198 crossovers (63.1%), 822 vertices were eliminated
building final representation...
10038 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=114258, nf=228512, ne=342768, g=0)
writing corrected surface to /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.premesh...

0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 2539 intersecting
001: 502 intersecting
002: 231 intersecting
003: 125 intersecting
004: 99 intersecting
005: 95 intersecting
step 1 with no progress (num=95, old_num=95)
006: 95 intersecting
step 2 with no progress (num=95, old_num=95)
007: 95 intersecting
step 3 with no progress (num=95, old_num=95)
008: 95 intersecting
step 4 with no progress (num=95, old_num=95)
009: 95 intersecting
step 5 with no progress (num=95, old_num=95)
010: 95 intersecting
step 6 with no progress (num=95, old_num=95)
011: 95 intersecting
step 7 with no progress (num=95, old_num=95)
012: 95 intersecting
step 8 with no progress (num=95, old_num=95)
013: 95 intersecting
step 9 with no progress (num=95, old_num=95)
014: 95 intersecting
step 10 with no progress (num=95, old_num=95)
015: 95 intersecting
step 11 with no progress (num=95, old_num=95)
016: 95 intersecting
step 12 with no progress (num=95, old_num=95)
017: 95 intersecting
step 13 with no progress (num=95, old_num=95)
018: 95 intersecting
step 14 with no progress (num=95, old_num=95)
019: 95 intersecting
step 15 with no progress (num=95, old_num=95)
020: 95 intersecting
step 16 with no progress (num=95, old_num=95)
terminating search with 95 intersecting
topology fixing took 54.0 minutes
FSRUNTIME@ mris_fix_topology lh  0.8999 hours 1 threads
#VMPC# mris_fix_topology VmPeak  837752
@#@FSTIME  2020:09:25:21:51:40 mris_fix_topology N 14 e 3239.72 S 0.41 U 3219.73 P 99% M 789844 F 19 R 232207 W 0 c 95710 w 29 I 15216 O 10968 L 1.00 0.70 0.32
@#@FSLOADPOST 2020:09:25:22:45:40 mris_fix_topology N 14 1.00 1.00 1.00
#@# Fix Topology rh 2020��� 09��� 25��� ��������� 22:45:40 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 rh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-140 (nv=120138, nf=240556, ne=360834, g=71)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 14 iterations
marking ambiguous vertices...
26405 ambiguous faces found in tessellation
segmenting defects...
45 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 17 into 9
      -merging segment 21 into 9
      -merging segment 30 into 9
      -merging segment 35 into 16
      -merging segment 39 into 27
      -merging segment 26 into 28
39 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -9.9534  (-4.9767)
      -vertex     loglikelihood: -6.9756  (-3.4878)
      -normal dot loglikelihood: -3.4949  (-3.4949)
      -quad curv  loglikelihood: -5.4002  (-2.7001)
      Total Loglikelihood : -25.8241
CORRECTING DEFECT 0 (vertices=27, convex hull=29, v0=0)
After retessellation of defect 0 (v0=0), euler #=-28 (105379,313077,207670) : difference with theory (-36) = -8 
CORRECTING DEFECT 1 (vertices=128, convex hull=134, v0=36)
After retessellation of defect 1 (v0=36), euler #=-27 (105440,313317,207850) : difference with theory (-35) = -8 
CORRECTING DEFECT 2 (vertices=26, convex hull=23, v0=39)
After retessellation of defect 2 (v0=39), euler #=-26 (105445,313338,207867) : difference with theory (-34) = -8 
CORRECTING DEFECT 3 (vertices=166, convex hull=59, v0=306)
After retessellation of defect 3 (v0=306), euler #=-25 (105455,313392,207912) : difference with theory (-33) = -8 
CORRECTING DEFECT 4 (vertices=1041, convex hull=344, v0=460)
After retessellation of defect 4 (v0=460), euler #=-24 (105576,313925,208325) : difference with theory (-32) = -8 
CORRECTING DEFECT 5 (vertices=47, convex hull=35, v0=1219)
After retessellation of defect 5 (v0=1219), euler #=-23 (105585,313963,208355) : difference with theory (-31) = -8 
CORRECTING DEFECT 6 (vertices=24, convex hull=27, v0=2239)
After retessellation of defect 6 (v0=2239), euler #=-22 (105589,313987,208376) : difference with theory (-30) = -8 
CORRECTING DEFECT 7 (vertices=24, convex hull=27, v0=2685)
After retessellation of defect 7 (v0=2685), euler #=-21 (105593,314005,208391) : difference with theory (-29) = -8 
CORRECTING DEFECT 8 (vertices=42, convex hull=61, v0=5566)
After retessellation of defect 8 (v0=5566), euler #=-20 (105607,314068,208441) : difference with theory (-28) = -8 
CORRECTING DEFECT 9 (vertices=2426, convex hull=1243, v0=6028)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 9 (v0=6028), euler #=-19 (106509,317435,210907) : difference with theory (-27) = -8 
CORRECTING DEFECT 10 (vertices=954, convex hull=268, v0=8563)
normal vector of length zero at vertex 110213 with 3 faces
After retessellation of defect 10 (v0=8563), euler #=-18 (106657,318026,211351) : difference with theory (-26) = -8 
CORRECTING DEFECT 11 (vertices=23, convex hull=27, v0=9753)
After retessellation of defect 11 (v0=9753), euler #=-17 (106659,318041,211365) : difference with theory (-25) = -8 
CORRECTING DEFECT 12 (vertices=105, convex hull=65, v0=12995)
After retessellation of defect 12 (v0=12995), euler #=-16 (106670,318101,211415) : difference with theory (-24) = -8 
CORRECTING DEFECT 13 (vertices=20, convex hull=39, v0=13900)
After retessellation of defect 13 (v0=13900), euler #=-15 (106684,318158,211459) : difference with theory (-23) = -8 
CORRECTING DEFECT 14 (vertices=96, convex hull=47, v0=16188)
After retessellation of defect 14 (v0=16188), euler #=-14 (106693,318206,211499) : difference with theory (-22) = -8 
CORRECTING DEFECT 15 (vertices=3815, convex hull=351, v0=16291)
normal vector of length zero at vertex 112991 with 6 faces
normal vector of length zero at vertex 113445 with 5 faces
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 113612 with 6 faces
normal vector of length zero at vertex 21183 with 7 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 21183 with 7 faces
normal vector of length zero at vertex 110892 with 6 faces
normal vector of length zero at vertex 110937 with 4 faces
normal vector of length zero at vertex 110992 with 6 faces
normal vector of length zero at vertex 112731 with 4 faces
normal vector of length zero at vertex 113613 with 4 faces
normal vector of length zero at vertex 113613 with 4 faces
normal vector of length zero at vertex 113612 with 6 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 110888 with 4 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 113612 with 6 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 113705 with 9 faces
normal vector of length zero at vertex 110704 with 4 faces
normal vector of length zero at vertex 111044 with 8 faces
normal vector of length zero at vertex 111466 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 113705 with 8 faces
normal vector of length zero at vertex 114189 with 6 faces
normal vector of length zero at vertex 112161 with 3 faces
normal vector of length zero at vertex 113307 with 4 faces
normal vector of length zero at vertex 113522 with 4 faces
normal vector of length zero at vertex 114189 with 6 faces
normal vector of length zero at vertex 110704 with 4 faces
normal vector of length zero at vertex 111044 with 8 faces
normal vector of length zero at vertex 111466 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 113705 with 8 faces
normal vector of length zero at vertex 114189 with 6 faces
normal vector of length zero at vertex 112104 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 113307 with 6 faces
normal vector of length zero at vertex 111041 with 5 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 111741 with 6 faces
normal vector of length zero at vertex 15681 with 4 faces
normal vector of length zero at vertex 15681 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 111259 with 4 faces
normal vector of length zero at vertex 112316 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 111259 with 4 faces
normal vector of length zero at vertex 112316 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 111259 with 4 faces
normal vector of length zero at vertex 112316 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 111258 with 4 faces
normal vector of length zero at vertex 112732 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112808 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112808 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 112751 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 111259 with 4 faces
normal vector of length zero at vertex 112316 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 114189 with 6 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 110967 with 4 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 111141 with 6 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 111080 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 111081 with 4 faces
normal vector of length zero at vertex 111139 with 4 faces
normal vector of length zero at vertex 111230 with 6 faces
normal vector of length zero at vertex 112996 with 5 faces
normal vector of length zero at vertex 113206 with 4 faces
normal vector of length zero at vertex 111141 with 7 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 113410 with 6 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 110868 with 4 faces
normal vector of length zero at vertex 111081 with 4 faces
normal vector of length zero at vertex 111103 with 4 faces
normal vector of length zero at vertex 112154 with 6 faces
normal vector of length zero at vertex 112676 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 113307 with 6 faces
normal vector of length zero at vertex 111103 with 4 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 111103 with 4 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 111103 with 4 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 112751 with 6 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 21156 with 5 faces
normal vector of length zero at vertex 111141 with 7 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 113410 with 6 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 111141 with 7 faces
normal vector of length zero at vertex 111203 with 4 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 112104 with 6 faces
normal vector of length zero at vertex 112808 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 111203 with 4 faces
normal vector of length zero at vertex 111325 with 6 faces
normal vector of length zero at vertex 112808 with 4 faces
normal vector of length zero at vertex 111203 with 4 faces
normal vector of length zero at vertex 111325 with 6 faces
normal vector of length zero at vertex 111203 with 4 faces
normal vector of length zero at vertex 111203 with 4 faces
normal vector of length zero at vertex 111141 with 7 faces
normal vector of length zero at vertex 111203 with 3 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 112841 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 111325 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 111325 with 6 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 111887 with 4 faces
normal vector of length zero at vertex 112838 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 114189 with 6 faces
normal vector of length zero at vertex 111887 with 4 faces
normal vector of length zero at vertex 114189 with 6 faces
normal vector of length zero at vertex 111141 with 7 faces
normal vector of length zero at vertex 111203 with 3 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 112841 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 111325 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 111325 with 6 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 111260 with 4 faces
normal vector of length zero at vertex 111524 with 4 faces
normal vector of length zero at vertex 112104 with 4 faces
normal vector of length zero at vertex 111261 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 111161 with 6 faces
normal vector of length zero at vertex 111383 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 112907 with 3 faces
normal vector of length zero at vertex 113306 with 4 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 111165 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
normal vector of length zero at vertex 16975 with 6 faces
first tangent vector of length zero at vertex 16975
second tangent vector of length zero at vertex 16975
normal vector of length zero at vertex 111161 with 6 faces
normal vector of length zero at vertex 111383 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 111024 with 3 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 112705 with 3 faces
normal vector of length zero at vertex 112838 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 111139 with 6 faces
normal vector of length zero at vertex 111325 with 4 faces
normal vector of length zero at vertex 111024 with 3 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 111024 with 3 faces
normal vector of length zero at vertex 112705 with 3 faces
normal vector of length zero at vertex 112838 with 4 faces
normal vector of length zero at vertex 114189 with 4 faces
normal vector of length zero at vertex 112838 with 4 faces
normal vector of length zero at vertex 111024 with 3 faces
normal vector of length zero at vertex 111222 with 3 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 24714 with 6 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 112827 with 4 faces
normal vector of length zero at vertex 21156 with 4 faces
normal vector of length zero at vertex 111103 with 4 faces
normal vector of length zero at vertex 111103 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 111259 with 4 faces
normal vector of length zero at vertex 112316 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
normal vector of length zero at vertex 110848 with 4 faces
normal vector of length zero at vertex 111259 with 4 faces
normal vector of length zero at vertex 112316 with 4 faces
normal vector of length zero at vertex 112991 with 4 faces
After retessellation of defect 15 (v0=16291), euler #=-15 (107549,320965,213401) : difference with theory (-21) = -6 
CORRECTING DEFECT 16 (vertices=1473, convex hull=673, v0=20996)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 16 (v0=20996), euler #=-18 (108064,322884,214802) : difference with theory (-20) = -2 
CORRECTING DEFECT 17 (vertices=37, convex hull=44, v0=23107)
After retessellation of defect 17 (v0=23107), euler #=-17 (108080,322949,214852) : difference with theory (-19) = -2 
CORRECTING DEFECT 18 (vertices=23, convex hull=55, v0=23731)
After retessellation of defect 18 (v0=23731), euler #=-16 (108092,323007,214899) : difference with theory (-18) = -2 
CORRECTING DEFECT 19 (vertices=28, convex hull=37, v0=24178)
After retessellation of defect 19 (v0=24178), euler #=-15 (108095,323031,214921) : difference with theory (-17) = -2 
CORRECTING DEFECT 20 (vertices=58, convex hull=54, v0=25747)
After retessellation of defect 20 (v0=25747), euler #=-14 (108106,323086,214966) : difference with theory (-16) = -2 
CORRECTING DEFECT 21 (vertices=881, convex hull=142, v0=29978)
After retessellation of defect 21 (v0=29978), euler #=-14 (108134,323246,215098) : difference with theory (-15) = -1 
CORRECTING DEFECT 22 (vertices=115, convex hull=95, v0=30571)
After retessellation of defect 22 (v0=30571), euler #=-13 (108179,323420,215228) : difference with theory (-14) = -1 
CORRECTING DEFECT 23 (vertices=126, convex hull=86, v0=31351)
After retessellation of defect 23 (v0=31351), euler #=-12 (108191,323492,215289) : difference with theory (-13) = -1 
CORRECTING DEFECT 24 (vertices=2079, convex hull=1194, v0=32028)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 24 (v0=32028), euler #=-12 (108609,325379,216758) : difference with theory (-12) = 0 
CORRECTING DEFECT 25 (vertices=145, convex hull=214, v0=34472)
After retessellation of defect 25 (v0=34472), euler #=-10 (108680,325693,217003) : difference with theory (-11) = -1 
CORRECTING DEFECT 26 (vertices=63, convex hull=64, v0=34910)
After retessellation of defect 26 (v0=34910), euler #=-9 (108689,325746,217048) : difference with theory (-10) = -1 
CORRECTING DEFECT 27 (vertices=85, convex hull=90, v0=41310)
After retessellation of defect 27 (v0=41310), euler #=-8 (108702,325824,217114) : difference with theory (-9) = -1 
CORRECTING DEFECT 28 (vertices=147, convex hull=122, v0=41472)
After retessellation of defect 28 (v0=41472), euler #=-8 (108752,326036,217276) : difference with theory (-8) = 0 
CORRECTING DEFECT 29 (vertices=65, convex hull=54, v0=50339)
After retessellation of defect 29 (v0=50339), euler #=-7 (108761,326084,217316) : difference with theory (-7) = 0 
CORRECTING DEFECT 30 (vertices=24, convex hull=57, v0=55243)
After retessellation of defect 30 (v0=55243), euler #=-6 (108764,326119,217349) : difference with theory (-6) = 0 
CORRECTING DEFECT 31 (vertices=28, convex hull=57, v0=58195)
After retessellation of defect 31 (v0=58195), euler #=-5 (108774,326173,217394) : difference with theory (-5) = 0 
CORRECTING DEFECT 32 (vertices=48, convex hull=76, v0=64937)
After retessellation of defect 32 (v0=64937), euler #=-4 (108783,326231,217444) : difference with theory (-4) = 0 
CORRECTING DEFECT 33 (vertices=207, convex hull=118, v0=67106)
After retessellation of defect 33 (v0=67106), euler #=-3 (108801,326342,217538) : difference with theory (-3) = 0 
CORRECTING DEFECT 34 (vertices=66, convex hull=32, v0=71651)
After retessellation of defect 34 (v0=71651), euler #=-2 (108810,326379,217567) : difference with theory (-2) = 0 
CORRECTING DEFECT 35 (vertices=33, convex hull=35, v0=81539)
After retessellation of defect 35 (v0=81539), euler #=-1 (108811,326394,217582) : difference with theory (-1) = 0 
CORRECTING DEFECT 36 (vertices=23, convex hull=41, v0=88837)
After retessellation of defect 36 (v0=88837), euler #=0 (108816,326426,217610) : difference with theory (0) = 0 
CORRECTING DEFECT 37 (vertices=29, convex hull=36, v0=94156)
After retessellation of defect 37 (v0=94156), euler #=1 (108822,326453,217632) : difference with theory (1) = 0 
CORRECTING DEFECT 38 (vertices=7, convex hull=23, v0=112222)
After retessellation of defect 38 (v0=112222), euler #=2 (108822,326460,217640) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.92 +- 0.36 (0.01-->17.85) (max @ vno 24786 --> 114084)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.92 +- 0.36 (0.01-->17.85) (max @ vno 24786 --> 114084)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
128 mutations (35.8%), 230 crossovers (64.2%), 894 vertices were eliminated
building final representation...
11316 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=108822, nf=217640, ne=326460, g=0)
writing corrected surface to /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.premesh...

0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 1828 intersecting
001: 567 intersecting
002: 256 intersecting
003: 216 intersecting
004: 212 intersecting
005: 211 intersecting
step 1 with no progress (num=211, old_num=211)
006: 211 intersecting
step 2 with no progress (num=211, old_num=211)
007: 211 intersecting
step 3 with no progress (num=211, old_num=211)
008: 211 intersecting
step 4 with no progress (num=211, old_num=211)
009: 211 intersecting
step 5 with no progress (num=211, old_num=211)
010: 211 intersecting
step 6 with no progress (num=211, old_num=211)
011: 211 intersecting
step 7 with no progress (num=211, old_num=211)
012: 211 intersecting
step 8 with no progress (num=211, old_num=211)
013: 211 intersecting
step 9 with no progress (num=211, old_num=211)
014: 211 intersecting
step 10 with no progress (num=211, old_num=211)
015: 211 intersecting
step 11 with no progress (num=211, old_num=211)
016: 211 intersecting
step 12 with no progress (num=211, old_num=211)
017: 211 intersecting
step 13 with no progress (num=211, old_num=211)
018: 211 intersecting
step 14 with no progress (num=211, old_num=211)
019: 211 intersecting
step 15 with no progress (num=211, old_num=211)
020: 211 intersecting
step 16 with no progress (num=211, old_num=211)
terminating search with 211 intersecting
topology fixing took 7.0 minutes
FSRUNTIME@ mris_fix_topology rh  0.1175 hours 1 threads
#VMPC# mris_fix_topology VmPeak  772788
@#@FSTIME  2020:09:25:22:45:40 mris_fix_topology N 14 e 422.89 S 0.31 U 420.22 P 99% M 724816 F 0 R 200470 W 0 c 13299 w 5 I 3512 O 10488 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:52:43 mris_fix_topology N 14 1.00 1.00 1.00

 mris_euler_number ../surf/lh.orig.premesh 

euler # = v-e+f = 2g-2: 114258 - 342768 + 228512 = 2 --> 0 holes
      F =2V-4:          228512 = 228516-4 (0)
      2E=3F:            685536 = 685536 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig.premesh 

euler # = v-e+f = 2g-2: 108822 - 326460 + 217640 = 2 --> 0 holes
      F =2V-4:          217640 = 217644-4 (0)
      2E=3F:            652920 = 652920 (0)

total defect index = 0
2020��� 09��� 25��� ��������� 22:52:44 CST

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer/subjects/monkey2/scripts
/usr/local/freesurfer/bin/defect2seg --s monkey2

freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
defect2seg 7.1.0
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
pid 15212
mri_label2vol --defects /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz 1000 0 /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mri_label2vol supposed to be reproducible but seed not set
Changing input type 0 to MRI_INT
Converting defects to volume: offset=1000, merge=0
Writing to /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mris_defects_pointset -s /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix -d /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels -o /usr/local/freesurfer/subjects/monkey2/surf/lh.defects.pointset
Reading in surface /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix
Reading in defect segmentation /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels
#VMPC# mris_defects_pointset 180516
mris_defects_pointset done
mri_label2vol --defects /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz 2000 1 /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mri_label2vol supposed to be reproducible but seed not set
Converting defects to volume: offset=2000, merge=1
Writing to /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mris_defects_pointset -s /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix -d /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels -o /usr/local/freesurfer/subjects/monkey2/surf/rh.defects.pointset
Reading in surface /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix
Reading in defect segmentation /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels
#VMPC# mris_defects_pointset 175588
mris_defects_pointset done
 
Started at 2020��� 09��� 25��� ��������� 22:52:44 CST 
Ended   at 2020��� 09��� 25��� ��������� 22:52:51 CST
Defect2seg-Run-Time-Sec 7
Defect2seg-Run-Time-Min 0.14
Defect2seg-Run-Time-Hours 0.00
 
tkmeditfv monkey2 orig.mgz -defect -c /usr/local/freesurfer/subjects/monkey2/surf/?h.defects.pointset
defect2seg Done
@#@FSTIME  2020:09:25:22:52:44 defect2seg N 2 e 7.19 S 0.25 U 6.84 P 98% M 232844 F 48 R 217820 W 0 c 533 w 296 I 30168 O 456 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:52:51 defect2seg N 2 1.00 1.00 1.00

 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.premesh --output /usr/local/freesurfer/subjects/monkey2/surf/lh.orig 

iters = 3
standard remeshing without target
   adjusted l: 0.737868
remeshing to edge length 0.737868 with 3 iterations

avg qual before   : 0.876579  after: 0.970771

Removing intersections
removing intersecting faces
000: 281 intersecting
001: 72 intersecting
002: 45 intersecting
step 1 with no progress (num=46, old_num=45)
003: 46 intersecting
step 2 with no progress (num=46, old_num=46)
004: 46 intersecting
005: 45 intersecting
step 1 with no progress (num=45, old_num=45)
006: 45 intersecting
step 2 with no progress (num=45, old_num=45)
007: 45 intersecting
step 3 with no progress (num=45, old_num=45)
008: 45 intersecting
step 4 with no progress (num=45, old_num=45)
009: 45 intersecting
step 5 with no progress (num=45, old_num=45)
010: 45 intersecting
step 6 with no progress (num=45, old_num=45)
011: 45 intersecting
step 7 with no progress (num=45, old_num=45)
012: 45 intersecting
step 8 with no progress (num=45, old_num=45)
013: 45 intersecting
step 9 with no progress (num=45, old_num=45)
014: 45 intersecting
step 10 with no progress (num=45, old_num=45)
015: 45 intersecting
step 11 with no progress (num=45, old_num=45)
016: 45 intersecting
step 12 with no progress (num=45, old_num=45)
017: 45 intersecting
step 13 with no progress (num=45, old_num=45)
018: 45 intersecting
step 14 with no progress (num=45, old_num=45)
019: 45 intersecting
step 15 with no progress (num=45, old_num=45)
020: 45 intersecting
step 16 with no progress (num=45, old_num=45)
terminating search with 45 intersecting
Remeshed surface quality stats nv0 = 114258  nv = 116088  1.01602
Area    232172  0.32365  0.03763 0.000770   0.7396
Corner  696516 60.00000  8.98606 1.270003 177.3998
Edge    348258  0.87290  0.08766 0.060612   1.4618
Hinge   348258  8.05034 11.02494 0.000000 178.1097
mris_remesh done
@#@FSTIME  2020:09:25:22:52:51 mris_remesh N 7 e 70.39 S 0.31 U 69.73 P 99% M 813888 F 19 R 265174 W 0 c 2124 w 22 I 4248 O 8168 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:54:02 mris_remesh N 7 1.00 1.00 1.00

 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.premesh --output /usr/local/freesurfer/subjects/monkey2/surf/rh.orig 

iters = 3
standard remeshing without target
   adjusted l: 0.734175
remeshing to edge length 0.734175 with 3 iterations

avg qual before   : 0.879263  after: 0.970942

Removing intersections
removing intersecting faces
000: 312 intersecting
001: 158 intersecting
002: 127 intersecting
003: 116 intersecting
004: 115 intersecting
step 1 with no progress (num=115, old_num=115)
005: 115 intersecting
step 2 with no progress (num=115, old_num=115)
006: 115 intersecting
step 3 with no progress (num=115, old_num=115)
007: 115 intersecting
step 4 with no progress (num=115, old_num=115)
008: 115 intersecting
step 5 with no progress (num=115, old_num=115)
009: 115 intersecting
step 6 with no progress (num=115, old_num=115)
010: 115 intersecting
step 7 with no progress (num=115, old_num=115)
011: 115 intersecting
step 8 with no progress (num=115, old_num=115)
012: 115 intersecting
step 9 with no progress (num=115, old_num=115)
013: 115 intersecting
step 10 with no progress (num=115, old_num=115)
014: 115 intersecting
step 11 with no progress (num=115, old_num=115)
015: 115 intersecting
step 12 with no progress (num=115, old_num=115)
016: 115 intersecting
step 13 with no progress (num=115, old_num=115)
017: 115 intersecting
step 14 with no progress (num=115, old_num=115)
018: 115 intersecting
step 15 with no progress (num=115, old_num=115)
019: 115 intersecting
step 16 with no progress (num=115, old_num=115)
terminating search with 115 intersecting
Remeshed surface quality stats nv0 = 108822  nv = 111246  1.02227
Area    222488  0.32096  0.03701 0.000917   0.5909
Corner  667464 60.00000  8.96307 0.592801 176.3733
Edge    333732  0.86923  0.08691 0.035738   1.5290
Hinge   333732  7.94753 10.79722 0.000000 179.9500
mris_remesh done
@#@FSTIME  2020:09:25:22:54:02 mris_remesh N 7 e 64.26 S 0.29 U 63.59 P 99% M 779380 F 0 R 255674 W 0 c 2004 w 1 I 0 O 7824 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:55:06 mris_remesh N 7 1.00 1.00 1.00
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.01 hours
removing intersecting faces
000: 45 intersecting
step 1 with no progress (num=45, old_num=45)
001: 45 intersecting
step 2 with no progress (num=45, old_num=45)
002: 45 intersecting
step 3 with no progress (num=45, old_num=45)
003: 45 intersecting
step 4 with no progress (num=45, old_num=45)
004: 45 intersecting
step 5 with no progress (num=45, old_num=45)
005: 45 intersecting
step 6 with no progress (num=45, old_num=45)
006: 45 intersecting
step 7 with no progress (num=45, old_num=45)
007: 45 intersecting
step 8 with no progress (num=45, old_num=45)
008: 45 intersecting
step 9 with no progress (num=45, old_num=45)
009: 45 intersecting
step 10 with no progress (num=45, old_num=45)
010: 45 intersecting
step 11 with no progress (num=45, old_num=45)
011: 45 intersecting
step 12 with no progress (num=45, old_num=45)
012: 45 intersecting
step 13 with no progress (num=45, old_num=45)
013: 45 intersecting
step 14 with no progress (num=45, old_num=45)
014: 45 intersecting
step 15 with no progress (num=45, old_num=45)
015: 45 intersecting
step 16 with no progress (num=45, old_num=45)
terminating search with 45 intersecting
writing corrected surface to ../surf/lh.orig
@#@FSTIME  2020:09:25:22:55:06 mris_remove_intersection N 2 e 32.93 S 0.12 U 32.61 P 99% M 304740 F 18 R 91881 W 0 c 1022 w 21 I 3952 O 8168 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:55:39 mris_remove_intersection N 2 1.00 1.00 1.00

 rm ../surf/lh.inflated 

rm: cannot remove '../surf/lh.inflated': No such file or directory
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.01 hours
removing intersecting faces
000: 115 intersecting
step 1 with no progress (num=115, old_num=115)
001: 115 intersecting
step 2 with no progress (num=115, old_num=115)
002: 115 intersecting
step 3 with no progress (num=115, old_num=115)
003: 115 intersecting
step 4 with no progress (num=115, old_num=115)
004: 115 intersecting
step 5 with no progress (num=115, old_num=115)
005: 115 intersecting
step 6 with no progress (num=115, old_num=115)
006: 115 intersecting
step 7 with no progress (num=115, old_num=115)
007: 115 intersecting
step 8 with no progress (num=115, old_num=115)
008: 115 intersecting
step 9 with no progress (num=115, old_num=115)
009: 115 intersecting
step 10 with no progress (num=115, old_num=115)
010: 115 intersecting
step 11 with no progress (num=115, old_num=115)
011: 115 intersecting
step 12 with no progress (num=115, old_num=115)
012: 115 intersecting
step 13 with no progress (num=115, old_num=115)
013: 115 intersecting
step 14 with no progress (num=115, old_num=115)
014: 115 intersecting
step 15 with no progress (num=115, old_num=115)
015: 115 intersecting
step 16 with no progress (num=115, old_num=115)
terminating search with 115 intersecting
writing corrected surface to ../surf/rh.orig
@#@FSTIME  2020:09:25:22:55:39 mris_remove_intersection N 2 e 31.68 S 0.13 U 31.36 P 99% M 294432 F 0 R 89120 W 0 c 945 w 1 I 0 O 7824 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:56:11 mris_remove_intersection N 2 1.00 1.00 1.00

 rm ../surf/rh.inflated 

rm: cannot remove '../surf/rh.inflated': No such file or directory
#--------------------------------------------
#@# AutoDetGWStats lh 2020��� 09��� 25��� ��������� 22:56:11 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 

border white:    217011 voxels (1.29%)
border gray      272756 voxels (1.63%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/lh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=31706, wmmin=5, clip=110 
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (101.0): 99.9 +- 9.3 [70.0 --> 110.0]
CCS GM (71.0) : 71.9 +- 13.5 [30.0 --> 110.0]
white_mean = 99.8906 +/- 9.28913, gray_mean = 71.9085 +/- 13.4997
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=255 nbins=256
intensity peaks found at WM=107+-5.2,    GM=70+-7.0
white_mode = 107, gray_mode = 70
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 56.5 (was 70.000000)
setting MAX_BORDER_WHITE to 116.3 (was 105.000000)
setting MIN_BORDER_WHITE to 70.0 (was 85.000000)
setting MAX_CSF to 43.0 (was 40.000000)
setting MAX_GRAY to 97.7 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 56.5 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 29.5 (was 40.000000)
When placing the white surface
  white_border_hi   = 116.289;
  white_border_low  = 70;
  white_outside_low = 56.5003;
  white_inside_hi   = 120;
  white_outside_hi  = 116.289;
When placing the pial surface
  pial_border_hi   = 56.5003;
  pial_border_low  = 29.5008;
  pial_outside_low = 10;
  pial_inside_hi   = 97.7109;
  pial_outside_hi  = 49.7504;
#VMPC# mris_autodet_gwstats VmPeak  251228
mris_autodet_gwstats done
@#@FSTIME  2020:09:25:22:56:11 mris_autodet_gwstats N 8 e 11.80 S 0.08 U 11.65 P 99% M 215632 F 17 R 63420 W 0 c 400 w 21 I 7248 O 8 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:56:23 mris_autodet_gwstats N 8 1.00 1.00 1.00
#--------------------------------------------
#@# AutoDetGWStats rh 2020��� 09��� 25��� ��������� 22:56:23 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 

border white:    217011 voxels (1.29%)
border gray      272756 voxels (1.63%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/rh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=31706, wmmin=5, clip=110 
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (101.0): 99.9 +- 9.3 [70.0 --> 110.0]
CCS GM (71.0) : 71.9 +- 13.5 [30.0 --> 110.0]
white_mean = 99.8906 +/- 9.28913, gray_mean = 71.9085 +/- 13.4997
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=255 nbins=256
intensity peaks found at WM=107+-7.0,    GM=65+-7.8
white_mode = 107, gray_mode = 65
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 51.5 (was 70.000000)
setting MAX_BORDER_WHITE to 116.3 (was 105.000000)
setting MIN_BORDER_WHITE to 65.0 (was 85.000000)
setting MAX_CSF to 38.0 (was 40.000000)
setting MAX_GRAY to 97.7 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 24.5 (was 40.000000)
When placing the white surface
  white_border_hi   = 116.289;
  white_border_low  = 65;
  white_outside_low = 51.5003;
  white_inside_hi   = 120;
  white_outside_hi  = 116.289;
When placing the pial surface
  pial_border_hi   = 51.5003;
  pial_border_low  = 24.5008;
  pial_outside_low = 10;
  pial_inside_hi   = 97.7109;
  pial_outside_hi  = 44.7504;
#VMPC# mris_autodet_gwstats VmPeak  243580
mris_autodet_gwstats done
@#@FSTIME  2020:09:25:22:56:23 mris_autodet_gwstats N 8 e 11.74 S 0.08 U 11.60 P 99% M 207980 F 0 R 61186 W 0 c 374 w 1 I 0 O 8 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:56:34 mris_autodet_gwstats N 8 1.00 1.00 1.00
#--------------------------------------------
#@# WhitePreAparc lh 2020��� 09��� 25��� ��������� 22:56:34 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5
7.1.0
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 

Reading in input surface ../surf/lh.orig
Smoothing surface with 5 iterations
removing intersecting faces
000: 40 intersecting
step 1 with no progress (num=40, old_num=40)
001: 40 intersecting
002: 32 intersecting
003: 27 intersecting
step 1 with no progress (num=31, old_num=27)
004: 31 intersecting
005: 29 intersecting
step 1 with no progress (num=29, old_num=29)
006: 29 intersecting
step 2 with no progress (num=29, old_num=29)
007: 29 intersecting
step 3 with no progress (num=29, old_num=29)
008: 29 intersecting
step 4 with no progress (num=29, old_num=29)
009: 29 intersecting
step 5 with no progress (num=29, old_num=29)
010: 29 intersecting
step 6 with no progress (num=29, old_num=29)
011: 29 intersecting
step 7 with no progress (num=29, old_num=29)
012: 29 intersecting
step 8 with no progress (num=29, old_num=29)
013: 29 intersecting
step 9 with no progress (num=29, old_num=29)
014: 29 intersecting
step 10 with no progress (num=29, old_num=29)
015: 29 intersecting
step 11 with no progress (num=29, old_num=29)
016: 29 intersecting
step 12 with no progress (num=29, old_num=29)
017: 29 intersecting
step 13 with no progress (num=29, old_num=29)
018: 29 intersecting
step 14 with no progress (num=29, old_num=29)
019: 29 intersecting
step 15 with no progress (num=29, old_num=29)
020: 29 intersecting
step 16 with no progress (num=29, old_num=29)
terminating search with 27 intersecting
Area    232172  0.29594  0.07123 0.000000   0.7715
Corner  696516 60.00000  9.87204 0.000743 179.9961
Edge    348258  0.83011  0.12329 0.001018   1.6158
Hinge   348258  4.98630  6.97771 0.000000 176.3595
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=31706, wmmin=5, clip=110 
MRIfindBrightNonWM(): 6721 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
ERROR: need seg for ripping
Command exited with non-zero status 1
@#@FSTIME  2020:09:25:22:56:35 mris_place_surface N 14 e 49.63 S 0.14 U 49.15 P 99% M 490280 F 25 R 136431 W 0 c 1478 w 27 I 5168 O 0 L 1.00 1.00 1.00
@#@FSLOADPOST 2020:09:25:22:57:24 mris_place_surface N 14 1.00 1.00 1.00
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s monkey2 exited with ERRORS at 2020��� 09��� 25��� ��������� 22:57:24 CST

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



#New# invocation of recon-all 



2020��� 10��� 05��� ��������� 00:10:16 CST
/usr/local/freesurfer/subjects/monkey2
/usr/local/freesurfer/bin/recon-all
-s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
subjid monkey2
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 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      7796 
maxlocks     unlimited
maxsignal    7796 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           1.9G        463M        1.0G         13M        462M        1.3G
Swap:          2.0G        1.2G        867M

########################################
program versions used
7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b)
7.1.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:16-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.0

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.0
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.0  TimeStamp: 2020/10/04-16:10:17-GMT  BuildTime: May 11 2020 12:09:35  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b  User: zhao  Machine: zhao-VirtualBox  Platform: Linux  PlatformVersion: 4.15.0-118-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
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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
#######################################
#--------------------------------------------
#@# Mask BFS 2020��� 10��� 05��� ��������� 00:10:17 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1729527 voxels in mask (pct= 10.31)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2020:10:05:00:10:17 mri_mask N 5 e 3.10 S 0.05 U 2.64 P 86% M 74136 F 5 R 17274 W 0 c 829 w 10 I 7152 O 2960 L 0.72 0.81 0.75
@#@FSLOADPOST 2020:10:05:00:10:20 mri_mask N 5 1.06 0.88 0.77
#--------------------------------------------
#@# Fill 2020��� 10��� 05��� ��������� 00:10:20 CST
/usr/local/freesurfer/subjects/monkey2/mri

 mri_fill -a ../scripts/ponscc.cut.log -Pv 99 105 80 -Cv 100 85 112 wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using voxel position (99, 105, 80) as pons seed point
using voxel position (100, 85, 112) as corpus callosum seed point
reading input volume...done.
searching for cutting planes...talairach transform
 1.21719  -0.10560   0.00398  -90.19860;
 0.09776   1.12808   0.03437  -123.53568;
-0.00740  -0.03780   1.26141  -60.18553;
 0.00000   0.00000   0.00000   1.00000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
voxel to talairach voxel transform
 1.21719   0.00398   0.10560  -7.51974;
-0.00740   1.26141   0.03780   11.85634;
-0.09776  -0.03437   1.12808   67.44872;
 0.00000   0.00000   0.00000   1.00000;
Looking for area (min, max) = (350, 1400)
area[0] = 761 (min = 350, max = 1400), aspect = 4.25 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 123, 181), TAL = (1.5, 36.6, 15.2)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
Calculated talairach cc position (1.54, 36.59, 15.18)
Using the seed to calculate the cutting plane
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (122, 147, 144), TAL = (6.1, -0.1, -8.8)
talairach voxel to voxel transform
 0.81542  -0.00465  -0.07618   11.32478;
 0.00267   0.79203  -0.02679  -7.56380;
 0.07074   0.02373   0.87904  -59.03981;
 0.00000   0.00000   0.00000   1.00000;
talairach cc position changed to (1.90, 36.49, 14.75)
Using voxel pons seed point, calculated talairach pons position (6.06, -0.10, -8.84)
find_cutting_plane:seed point not in structure! Searching neighborhood...
done.
filling left hemisphere...
filling volume: pass 1 of 3...total of 303417 voxels filled...
filling volume: pass 2 of 3...total of 16407043 voxels filled...
filling volume: pass 3 of 3...total of 303616 voxels filled...done.
filling right hemisphere...
filling volume: pass 1 of 3...total of 303417 voxels filled...
filling volume: pass 2 of 3...total of 16407043 voxels filled...
filling volume: pass 3 of 3...total of 303616 voxels filled...done.
filling degenerate left hemisphere surface locations...
525 voxels filled
12 voxels filled
0 voxels filled
filling degenerate right hemisphere surface locations...
525 voxels filled
12 voxels filled
0 voxels filled
refilling left hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16406502 voxels filled...
filling volume: pass 3 of 3...total of 304157 voxels filled...done.
refilling right hemisphere...
filling volume: pass 1 of 3...total of 0 voxels filled...
filling volume: pass 2 of 3...total of 16406502 voxels filled...
filling volume: pass 3 of 3...total of 304157 voxels filled...done.
combining hemispheres...
using variable coefficient diffusion to correct hemispheric overlap...
26:  303764 ambiguous voxels remaining
9:  37701 ambiguous voxels remaining
8:  16149 ambiguous voxels remaining
7:  6460 ambiguous voxels remaining
6:  2840 ambiguous voxels remaining
5:  1359 ambiguous voxels remaining
4:  726 ambiguous voxels remaining
3:  341 ambiguous voxels remaining
2:  98 ambiguous voxels remaining
1:  0 ambiguous voxels remaining
writing output to filled.mgz...
filling took 0.7 minutes
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.90, 36.49, 14.75) SRC: (85.03, 85.30, 110.63)
search lh wm seed point around talairach space (-16.10, 36.49, 14.75), SRC: (114.38, 85.39, 113.17)
@#@FSTIME  2020:10:05:00:10:20 mri_fill N 12 e 45.08 S 0.16 U 34.84 P 77% M 111184 F 6 R 77594 W 0 c 13198 w 8 I 2224 O 224 L 1.06 0.88 0.77
@#@FSLOADPOST 2020:10:05:00:11:06 mri_fill N 12 1.49 1.02 0.82
#--------------------------------------------
#@# Tessellate lh 2020��� 10��� 05��� ��������� 00:11:06 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 5 (out of 158289: 0.003159)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:10:05:00:11:06 mri_pretess N 4 e 2.82 S 0.00 U 2.39 P 85% M 40344 F 16 R 8835 W 0 c 836 w 18 I 3472 O 216 L 1.49 1.02 0.82
@#@FSLOADPOST 2020:10:05:00:11:08 mri_pretess N 4 1.61 1.06 0.84

 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

7.1.0
  7.1.0
slice 50: 51 vertices, 67 faces
slice 60: 3431 vertices, 3570 faces
slice 70: 7785 vertices, 7964 faces
slice 80: 17154 vertices, 17635 faces
slice 90: 34916 vertices, 35702 faces
slice 100: 55179 vertices, 55987 faces
slice 110: 75859 vertices, 76585 faces
slice 120: 94091 vertices, 94804 faces
slice 130: 106956 vertices, 107449 faces
slice 140: 114898 vertices, 115178 faces
slice 150: 117264 vertices, 117396 faces
slice 160: 117264 vertices, 117396 faces
slice 170: 117264 vertices, 117396 faces
slice 180: 117264 vertices, 117396 faces
slice 190: 117264 vertices, 117396 faces
slice 200: 117264 vertices, 117396 faces
slice 210: 117264 vertices, 117396 faces
slice 220: 117264 vertices, 117396 faces
slice 230: 117264 vertices, 117396 faces
slice 240: 117264 vertices, 117396 faces
slice 250: 117264 vertices, 117396 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:10:05:00:11:08 mri_tessellate N 3 e 3.07 S 0.03 U 2.61 P 86% M 36288 F 5 R 8116 W 0 c 785 w 7 I 1216 O 5504 L 1.61 1.06 0.84
@#@FSLOADPOST 2020:10:05:00:11:12 mri_tessellate N 3 1.61 1.06 0.84

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   117264 voxel in cpt #1: X=-132 [v=117264,e=352188,f=234792] located at (-3.558364, -27.523043, 18.236612)
For the whole surface: X=-132 [v=117264,e=352188,f=234792]
One single component has been found
nothing to do
done

@#@FSTIME  2020:10:05:00:11:12 mris_extract_main_component N 2 e 1.07 S 0.10 U 0.82 P 86% M 235528 F 17 R 64688 W 0 c 298 w 24 I 4304 O 8256 L 1.61 1.06 0.84
@#@FSLOADPOST 2020:10:05:00:11:13 mris_extract_main_component N 2 1.61 1.06 0.84
#--------------------------------------------
#@# Tessellate rh 2020��� 10��� 05��� ��������� 00:11:13 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1 (out of 145875: 0.000686)
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2020:10:05:00:11:13 mri_pretess N 4 e 2.26 S 0.01 U 1.93 P 86% M 40436 F 0 R 8848 W 0 c 647 w 1 I 0 O 216 L 1.61 1.06 0.84
@#@FSLOADPOST 2020:10:05:00:11:15 mri_pretess N 4 1.56 1.06 0.84

 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

7.1.0
  7.1.0
slice 60: 2255 vertices, 2367 faces
slice 70: 5983 vertices, 6139 faces
slice 80: 13505 vertices, 13909 faces
slice 90: 29301 vertices, 30003 faces
slice 100: 49801 vertices, 50580 faces
slice 110: 70881 vertices, 71595 faces
slice 120: 89202 vertices, 89874 faces
slice 130: 102503 vertices, 102948 faces
slice 140: 110790 vertices, 111038 faces
slice 150: 113260 vertices, 113350 faces
slice 160: 113260 vertices, 113350 faces
slice 170: 113260 vertices, 113350 faces
slice 180: 113260 vertices, 113350 faces
slice 190: 113260 vertices, 113350 faces
slice 200: 113260 vertices, 113350 faces
slice 210: 113260 vertices, 113350 faces
slice 220: 113260 vertices, 113350 faces
slice 230: 113260 vertices, 113350 faces
slice 240: 113260 vertices, 113350 faces
slice 250: 113260 vertices, 113350 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
@#@FSTIME  2020:10:05:00:11:15 mri_tessellate N 3 e 3.83 S 0.02 U 3.22 P 84% M 35972 F 0 R 8034 W 0 c 978 w 3 I 8 O 5320 L 1.56 1.06 0.84
@#@FSLOADPOST 2020:10:05:00:11:19 mri_tessellate N 3 1.51 1.05 0.84

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   113260 voxel in cpt #1: X=-90 [v=113260,e=340050,f=226700] located at (59.163925, -25.847811, 17.698702)
For the whole surface: X=-90 [v=113260,e=340050,f=226700]
One single component has been found
nothing to do
done

@#@FSTIME  2020:10:05:00:11:19 mris_extract_main_component N 2 e 1.32 S 0.12 U 0.98 P 83% M 227932 F 0 R 62456 W 0 c 350 w 3 I 0 O 7976 L 1.51 1.05 0.84
@#@FSLOADPOST 2020:10:05:00:11:20 mris_extract_main_component N 2 1.51 1.05 0.84
#--------------------------------------------
#@# Smooth1 lh 2020��� 10��� 05��� ��������� 00:11:20 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:10:05:00:11:20 mris_smooth N 5 e 6.07 S 0.12 U 4.94 P 83% M 190044 F 5 R 52988 W 0 c 1474 w 11 I 1296 O 8256 L 1.51 1.05 0.84
@#@FSLOADPOST 2020:10:05:00:11:26 mris_smooth N 5 1.63 1.09 0.85
#--------------------------------------------
#@# Smooth1 rh 2020��� 10��� 05��� ��������� 00:11:26 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2020:10:05:00:11:26 mris_smooth N 5 e 4.87 S 0.10 U 4.10 P 86% M 184460 F 0 R 51371 W 0 c 1227 w 4 I 0 O 7976 L 1.63 1.09 0.85
@#@FSLOADPOST 2020:10:05:00:11:31 mris_smooth N 5 1.58 1.09 0.85
#--------------------------------------------
#@# Inflation1 lh 2020��� 10��� 05��� ��������� 00:11:31 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 45.4 mm, total surface area = 67200 mm^2

step 000: RMS=0.135 (target=0.015)   
step 005: RMS=0.109 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.078 (target=0.015)   
step 025: RMS=0.074 (target=0.015)   
step 030: RMS=0.071 (target=0.015)   
step 035: RMS=0.069 (target=0.015)   
step 040: RMS=0.067 (target=0.015)   
step 045: RMS=0.065 (target=0.015)   
step 050: RMS=0.064 (target=0.015)   
step 055: RMS=0.063 (target=0.015)   
step 060: RMS=0.063 (target=0.015)   writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.4 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    21.196069
mris_inflate stimesec    0.110099
mris_inflate ru_maxrss   247012
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   71962
mris_inflate ru_majflt   19
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4552
mris_inflate ru_oublock  8256
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    25
mris_inflate ru_nivcsw   6167
@#@FSTIME  2020:10:05:00:11:31 mris_inflate N 3 e 24.65 S 0.11 U 21.19 P 86% M 247112 F 19 R 71964 W 0 c 6170 w 26 I 4552 O 8256 L 1.58 1.09 0.85
@#@FSLOADPOST 2020:10:05:00:11:56 mris_inflate N 3 1.83 1.19 0.89
#--------------------------------------------
#@# Inflation1 rh 2020��� 10��� 05��� ��������� 00:11:56 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 45.4 mm, total surface area = 64737 mm^2

step 000: RMS=0.132 (target=0.015)   
step 005: RMS=0.105 (target=0.015)   
step 010: RMS=0.086 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.073 (target=0.015)   
step 025: RMS=0.068 (target=0.015)   
step 030: RMS=0.065 (target=0.015)   
step 035: RMS=0.064 (target=0.015)   
step 040: RMS=0.061 (target=0.015)   
step 045: RMS=0.059 (target=0.015)   
step 050: RMS=0.058 (target=0.015)   
step 055: RMS=0.057 (target=0.015)   
step 060: RMS=0.057 (target=0.015)   writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.3 minutes

inflation complete.
Not saving sulc
mris_inflate utimesec    17.598468
mris_inflate stimesec    0.084221
mris_inflate ru_maxrss   237656
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   64654
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  7976
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1
mris_inflate ru_nivcsw   5049
@#@FSTIME  2020:10:05:00:11:56 mris_inflate N 3 e 20.18 S 0.09 U 17.59 P 87% M 237728 F 0 R 64656 W 0 c 5051 w 2 I 0 O 7976 L 1.83 1.19 0.89
@#@FSLOADPOST 2020:10:05:00:12:16 mris_inflate N 3 1.72 1.21 0.91
#--------------------------------------------
#@# QSphere lh 2020��� 10��� 05��� ��������� 00:12:16 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.292...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=179.416, avgs=0
005/300: dt: 0.9000, rms radial error=179.160, avgs=0
010/300: dt: 0.9000, rms radial error=178.613, avgs=0
015/300: dt: 0.9000, rms radial error=177.894, avgs=0
020/300: dt: 0.9000, rms radial error=177.076, avgs=0
025/300: dt: 0.9000, rms radial error=176.201, avgs=0
030/300: dt: 0.9000, rms radial error=175.295, avgs=0
035/300: dt: 0.9000, rms radial error=174.371, avgs=0
040/300: dt: 0.9000, rms radial error=173.439, avgs=0
045/300: dt: 0.9000, rms radial error=172.504, avgs=0
050/300: dt: 0.9000, rms radial error=171.568, avgs=0
055/300: dt: 0.9000, rms radial error=170.635, avgs=0
060/300: dt: 0.9000, rms radial error=169.704, avgs=0
065/300: dt: 0.9000, rms radial error=168.777, avgs=0
070/300: dt: 0.9000, rms radial error=167.854, avgs=0
075/300: dt: 0.9000, rms radial error=166.935, avgs=0
080/300: dt: 0.9000, rms radial error=166.020, avgs=0
085/300: dt: 0.9000, rms radial error=165.110, avgs=0
090/300: dt: 0.9000, rms radial error=164.203, avgs=0
095/300: dt: 0.9000, rms radial error=163.301, avgs=0
100/300: dt: 0.9000, rms radial error=162.403, avgs=0
105/300: dt: 0.9000, rms radial error=161.509, avgs=0
110/300: dt: 0.9000, rms radial error=160.620, avgs=0
115/300: dt: 0.9000, rms radial error=159.735, avgs=0
120/300: dt: 0.9000, rms radial error=158.854, avgs=0
125/300: dt: 0.9000, rms radial error=157.978, avgs=0
130/300: dt: 0.9000, rms radial error=157.105, avgs=0
135/300: dt: 0.9000, rms radial error=156.238, avgs=0
140/300: dt: 0.9000, rms radial error=155.374, avgs=0
145/300: dt: 0.9000, rms radial error=154.515, avgs=0
150/300: dt: 0.9000, rms radial error=153.660, avgs=0
155/300: dt: 0.9000, rms radial error=152.810, avgs=0
160/300: dt: 0.9000, rms radial error=151.963, avgs=0
165/300: dt: 0.9000, rms radial error=151.121, avgs=0
170/300: dt: 0.9000, rms radial error=150.284, avgs=0
175/300: dt: 0.9000, rms radial error=149.451, avgs=0
180/300: dt: 0.9000, rms radial error=148.622, avgs=0
185/300: dt: 0.9000, rms radial error=147.797, avgs=0
190/300: dt: 0.9000, rms radial error=146.977, avgs=0
195/300: dt: 0.9000, rms radial error=146.161, avgs=0
200/300: dt: 0.9000, rms radial error=145.350, avgs=0
205/300: dt: 0.9000, rms radial error=144.542, avgs=0
210/300: dt: 0.9000, rms radial error=143.739, avgs=0
215/300: dt: 0.9000, rms radial error=142.940, avgs=0
220/300: dt: 0.9000, rms radial error=142.146, avgs=0
225/300: dt: 0.9000, rms radial error=141.355, avgs=0
230/300: dt: 0.9000, rms radial error=140.569, avgs=0
235/300: dt: 0.9000, rms radial error=139.787, avgs=0
240/300: dt: 0.9000, rms radial error=139.009, avgs=0
245/300: dt: 0.9000, rms radial error=138.235, avgs=0
250/300: dt: 0.9000, rms radial error=137.466, avgs=0
255/300: dt: 0.9000, rms radial error=136.701, avgs=0
260/300: dt: 0.9000, rms radial error=135.940, avgs=0
265/300: dt: 0.9000, rms radial error=135.183, avgs=0
270/300: dt: 0.9000, rms radial error=134.430, avgs=0
275/300: dt: 0.9000, rms radial error=133.681, avgs=0
280/300: dt: 0.9000, rms radial error=132.937, avgs=0
285/300: dt: 0.9000, rms radial error=132.197, avgs=0
290/300: dt: 0.9000, rms radial error=131.460, avgs=0
295/300: dt: 0.9000, rms radial error=130.728, avgs=0
300/300: dt: 0.9000, rms radial error=130.000, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.14 +- 0.79 (0.00-->16.76) (max @ vno 41915 --> 43896)
face area 0.02 +- 0.04 (-0.29-->1.09)
epoch 1 (K=10.0), pass 1, starting sse = 13897.65
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00019
epoch 2 (K=40.0), pass 1, starting sse = 2423.85
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00017
epoch 3 (K=160.0), pass 1, starting sse = 296.42
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/13 = 0.00236
epoch 4 (K=640.0), pass 1, starting sse = 34.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/17 = 0.00581
final distance error %100000.00
writing spherical brain to ../surf/lh.qsphere.nofix
mris_sphere utimesec    119.270528
mris_sphere stimesec    0.480758
mris_sphere ru_maxrss   866008
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   328697
mris_sphere ru_majflt   9
mris_sphere ru_nswap    0
mris_sphere ru_inblock  2680
mris_sphere ru_oublock  8256
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    17
mris_sphere ru_nivcsw   34164
spherical transformation took 0.0377 hours
FSRUNTIME@ mris_sphere  0.0377 hours 1 threads
@#@FSTIME  2020:10:05:00:12:16 mris_sphere N 9 e 135.86 S 0.50 U 119.27 P 88% M 866192 F 9 R 328699 W 0 c 34173 w 18 I 2680 O 8256 L 1.72 1.21 0.91
@#@FSLOADPOST 2020:10:05:00:14:32 mris_sphere N 9 1.73 1.32 0.99
#--------------------------------------------
#@# QSphere rh 2020��� 10��� 05��� ��������� 00:14:32 CST
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.282...
inflating...
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=180.236, avgs=0
005/300: dt: 0.9000, rms radial error=179.980, avgs=0
010/300: dt: 0.9000, rms radial error=179.430, avgs=0
015/300: dt: 0.9000, rms radial error=178.708, avgs=0
020/300: dt: 0.9000, rms radial error=177.886, avgs=0
025/300: dt: 0.9000, rms radial error=177.006, avgs=0
030/300: dt: 0.9000, rms radial error=176.094, avgs=0
035/300: dt: 0.9000, rms radial error=175.164, avgs=0
040/300: dt: 0.9000, rms radial error=174.227, avgs=0
045/300: dt: 0.9000, rms radial error=173.287, avgs=0
050/300: dt: 0.9000, rms radial error=172.347, avgs=0
055/300: dt: 0.9000, rms radial error=171.409, avgs=0
060/300: dt: 0.9000, rms radial error=170.475, avgs=0
065/300: dt: 0.9000, rms radial error=169.544, avgs=0
070/300: dt: 0.9000, rms radial error=168.618, avgs=0
075/300: dt: 0.9000, rms radial error=167.696, avgs=0
080/300: dt: 0.9000, rms radial error=166.778, avgs=0
085/300: dt: 0.9000, rms radial error=165.864, avgs=0
090/300: dt: 0.9000, rms radial error=164.954, avgs=0
095/300: dt: 0.9000, rms radial error=164.049, avgs=0
100/300: dt: 0.9000, rms radial error=163.148, avgs=0
105/300: dt: 0.9000, rms radial error=162.251, avgs=0
110/300: dt: 0.9000, rms radial error=161.359, avgs=0
115/300: dt: 0.9000, rms radial error=160.471, avgs=0
120/300: dt: 0.9000, rms radial error=159.588, avgs=0
125/300: dt: 0.9000, rms radial error=158.709, avgs=0
130/300: dt: 0.9000, rms radial error=157.834, avgs=0
135/300: dt: 0.9000, rms radial error=156.963, avgs=0
140/300: dt: 0.9000, rms radial error=156.097, avgs=0
145/300: dt: 0.9000, rms radial error=155.235, avgs=0
150/300: dt: 0.9000, rms radial error=154.378, avgs=0
155/300: dt: 0.9000, rms radial error=153.525, avgs=0
160/300: dt: 0.9000, rms radial error=152.676, avgs=0
165/300: dt: 0.9000, rms radial error=151.832, avgs=0
170/300: dt: 0.9000, rms radial error=150.992, avgs=0
175/300: dt: 0.9000, rms radial error=150.156, avgs=0
180/300: dt: 0.9000, rms radial error=149.325, avgs=0
185/300: dt: 0.9000, rms radial error=148.498, avgs=0
190/300: dt: 0.9000, rms radial error=147.675, avgs=0
195/300: dt: 0.9000, rms radial error=146.857, avgs=0
200/300: dt: 0.9000, rms radial error=146.043, avgs=0
205/300: dt: 0.9000, rms radial error=145.234, avgs=0
210/300: dt: 0.9000, rms radial error=144.428, avgs=0
215/300: dt: 0.9000, rms radial error=143.627, avgs=0
220/300: dt: 0.9000, rms radial error=142.830, avgs=0
225/300: dt: 0.9000, rms radial error=142.038, avgs=0
230/300: dt: 0.9000, rms radial error=141.249, avgs=0
235/300: dt: 0.9000, rms radial error=140.465, avgs=0
240/300: dt: 0.9000, rms radial error=139.685, avgs=0
245/300: dt: 0.9000, rms radial error=138.909, avgs=0
250/300: dt: 0.9000, rms radial error=138.137, avgs=0
255/300: dt: 0.9000, rms radial error=137.370, avgs=0
260/300: dt: 0.9000, rms radial error=136.607, avgs=0
265/300: dt: 0.9000, rms radial error=135.847, avgs=0
270/300: dt: 0.9000, rms radial error=135.092, avgs=0
275/300: dt: 0.9000, rms radial error=134.341, avgs=0
280/300: dt: 0.9000, rms radial error=133.594, avgs=0
285/300: dt: 0.9000, rms radial error=132.851, avgs=0
290/300: dt: 0.9000, rms radial error=132.113, avgs=0
295/300: dt: 0.9000, rms radial error=131.378, avgs=0
300/300: dt: 0.9000, rms radial error=130.647, avgs=0

spherical inflation complete.
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.14 +- 0.82 (0.00-->15.33) (max @ vno 28103 --> 28122)
face area 0.02 +- 0.04 (-0.31-->0.97)
epoch 1 (K=10.0), pass 1, starting sse = 13579.35
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00017
epoch 2 (K=40.0), pass 1, starting sse = 2428.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/13 = 0.00019
epoch 3 (K=160.0), pass 1, starting sse = 308.88
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/13 = 0.00260
epoch 4 (K=640.0), pass 1, starting sse = 34.69
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/16 = 0.00428
final distance error %100000.00
writing spherical brain to ../surf/rh.qsphere.nofix
mris_sphere utimesec    108.667574
mris_sphere stimesec    0.377665
mris_sphere ru_maxrss   825452
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   288171
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  7976
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    4
mris_sphere ru_nivcsw   30964
spherical transformation took 0.0341 hours
FSRUNTIME@ mris_sphere  0.0341 hours 1 threads
@#@FSTIME  2020:10:05:00:14:32 mris_sphere N 9 e 122.88 S 0.40 U 108.66 P 88% M 825640 F 0 R 288174 W 0 c 30973 w 5 I 0 O 7976 L 1.73 1.32 0.99
@#@FSLOADPOST 2020:10:05:00:16:35 mris_sphere N 9 1.28 1.27 1.02
#@# Fix Topology lh 2020��� 10��� 05��� ��������� 00:16:35 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 lh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-132 (nv=117264, nf=234792, ne=352188, g=67)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
14537 ambiguous faces found in tessellation
segmenting defects...
51 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 11 into 6
      -merging segment 28 into 6
      -merging segment 26 into 24
      -merging segment 31 into 32
      -merging segment 35 into 34
46 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7279  (-4.8640)
      -vertex     loglikelihood: -6.8204  (-3.4102)
      -normal dot loglikelihood: -3.4621  (-3.4621)
      -quad curv  loglikelihood: -5.5451  (-2.7725)
      Total Loglikelihood : -25.5555
CORRECTING DEFECT 0 (vertices=60, convex hull=31, v0=10)
After retessellation of defect 0 (v0=10), euler #=-40 (108809,323946,215097) : difference with theory (-43) = -3 
CORRECTING DEFECT 1 (vertices=619, convex hull=326, v0=169)
After retessellation of defect 1 (v0=169), euler #=-39 (108881,324336,215416) : difference with theory (-42) = -3 
CORRECTING DEFECT 2 (vertices=50, convex hull=22, v0=1725)
After retessellation of defect 2 (v0=1725), euler #=-38 (108884,324354,215432) : difference with theory (-41) = -3 
CORRECTING DEFECT 3 (vertices=29, convex hull=52, v0=2159)
After retessellation of defect 3 (v0=2159), euler #=-37 (108902,324426,215487) : difference with theory (-40) = -3 
CORRECTING DEFECT 4 (vertices=11, convex hull=16, v0=4295)
After retessellation of defect 4 (v0=4295), euler #=-36 (108905,324440,215499) : difference with theory (-39) = -3 
CORRECTING DEFECT 5 (vertices=13, convex hull=19, v0=4375)
After retessellation of defect 5 (v0=4375), euler #=-35 (108906,324447,215506) : difference with theory (-38) = -3 
CORRECTING DEFECT 6 (vertices=4263, convex hull=1918, v0=7801)
normal vector of length zero at vertex 32382 with 10 faces
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 113507 with 4 faces
normal vector of length zero at vertex 113507 with 4 faces
normal vector of length zero at vertex 32382 with 6 faces
normal vector of length zero at vertex 32382 with 6 faces
normal vector of length zero at vertex 32382 with 6 faces
normal vector of length zero at vertex 33993 with 6 faces
normal vector of length zero at vertex 33993 with 6 faces
normal vector of length zero at vertex 33993 with 6 faces
normal vector of length zero at vertex 113507 with 4 faces
After retessellation of defect 6 (v0=7801), euler #=-36 (110103,329106,218967) : difference with theory (-37) = -1 
CORRECTING DEFECT 7 (vertices=38, convex hull=39, v0=8541)
After retessellation of defect 7 (v0=8541), euler #=-35 (110109,329133,218989) : difference with theory (-36) = -1 
CORRECTING DEFECT 8 (vertices=27, convex hull=54, v0=11850)
After retessellation of defect 8 (v0=11850), euler #=-34 (110124,329199,219041) : difference with theory (-35) = -1 
CORRECTING DEFECT 9 (vertices=22, convex hull=25, v0=12083)
After retessellation of defect 9 (v0=12083), euler #=-33 (110128,329218,219057) : difference with theory (-34) = -1 
CORRECTING DEFECT 10 (vertices=16, convex hull=22, v0=12499)
After retessellation of defect 10 (v0=12499), euler #=-32 (110132,329233,219069) : difference with theory (-33) = -1 
CORRECTING DEFECT 11 (vertices=41, convex hull=39, v0=15729)
After retessellation of defect 11 (v0=15729), euler #=-31 (110136,329260,219093) : difference with theory (-32) = -1 
CORRECTING DEFECT 12 (vertices=1356, convex hull=689, v0=19471)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 12 (v0=19471), euler #=-31 (110595,330981,220355) : difference with theory (-31) = 0 
CORRECTING DEFECT 13 (vertices=10, convex hull=27, v0=20310)
After retessellation of defect 13 (v0=20310), euler #=-30 (110595,330988,220363) : difference with theory (-30) = 0 
CORRECTING DEFECT 14 (vertices=155, convex hull=105, v0=21661)
After retessellation of defect 14 (v0=21661), euler #=-30 (110612,331094,220452) : difference with theory (-29) = 1 
CORRECTING DEFECT 15 (vertices=354, convex hull=210, v0=25432)
After retessellation of defect 15 (v0=25432), euler #=-30 (110798,331757,220929) : difference with theory (-28) = 2 
CORRECTING DEFECT 16 (vertices=5, convex hull=13, v0=25578)
After retessellation of defect 16 (v0=25578), euler #=-29 (110798,331759,220932) : difference with theory (-27) = 2 
CORRECTING DEFECT 17 (vertices=43, convex hull=71, v0=27862)
After retessellation of defect 17 (v0=27862), euler #=-28 (110821,331855,221006) : difference with theory (-26) = 2 
CORRECTING DEFECT 18 (vertices=319, convex hull=152, v0=32602)
After retessellation of defect 18 (v0=32602), euler #=-28 (110913,332214,221273) : difference with theory (-25) = 3 
CORRECTING DEFECT 19 (vertices=33, convex hull=43, v0=32755)
After retessellation of defect 19 (v0=32755), euler #=-27 (110917,332244,221300) : difference with theory (-24) = 3 
CORRECTING DEFECT 20 (vertices=21, convex hull=37, v0=33463)
After retessellation of defect 20 (v0=33463), euler #=-26 (110917,332258,221315) : difference with theory (-23) = 3 
CORRECTING DEFECT 21 (vertices=31, convex hull=89, v0=33621)
After retessellation of defect 21 (v0=33621), euler #=-25 (110934,332342,221383) : difference with theory (-22) = 3 
CORRECTING DEFECT 22 (vertices=24, convex hull=37, v0=36596)
After retessellation of defect 22 (v0=36596), euler #=-24 (110936,332359,221399) : difference with theory (-21) = 3 
CORRECTING DEFECT 23 (vertices=26, convex hull=64, v0=39650)
After retessellation of defect 23 (v0=39650), euler #=-22 (110945,332409,221442) : difference with theory (-20) = 2 
CORRECTING DEFECT 24 (vertices=6, convex hull=22, v0=39682)
After retessellation of defect 24 (v0=39682), euler #=-21 (110946,332417,221450) : difference with theory (-19) = 2 
CORRECTING DEFECT 25 (vertices=10, convex hull=16, v0=43233)
After retessellation of defect 25 (v0=43233), euler #=-20 (110947,332422,221455) : difference with theory (-18) = 2 
CORRECTING DEFECT 26 (vertices=17, convex hull=42, v0=45895)
After retessellation of defect 26 (v0=45895), euler #=-19 (110958,332471,221494) : difference with theory (-17) = 2 
CORRECTING DEFECT 27 (vertices=20, convex hull=38, v0=46529)
After retessellation of defect 27 (v0=46529), euler #=-18 (110961,332492,221513) : difference with theory (-16) = 2 
CORRECTING DEFECT 28 (vertices=25, convex hull=47, v0=47756)
After retessellation of defect 28 (v0=47756), euler #=-16 (110966,332522,221540) : difference with theory (-15) = 1 
CORRECTING DEFECT 29 (vertices=26, convex hull=46, v0=51864)
After retessellation of defect 29 (v0=51864), euler #=-15 (110981,332584,221588) : difference with theory (-14) = 1 
CORRECTING DEFECT 30 (vertices=94, convex hull=117, v0=52801)
After retessellation of defect 30 (v0=52801), euler #=-13 (111017,332745,221715) : difference with theory (-13) = 0 
CORRECTING DEFECT 31 (vertices=30, convex hull=34, v0=58025)
After retessellation of defect 31 (v0=58025), euler #=-12 (111023,332775,221740) : difference with theory (-12) = 0 
CORRECTING DEFECT 32 (vertices=26, convex hull=31, v0=58418)
After retessellation of defect 32 (v0=58418), euler #=-11 (111027,332796,221758) : difference with theory (-11) = 0 
CORRECTING DEFECT 33 (vertices=22, convex hull=59, v0=60252)
After retessellation of defect 33 (v0=60252), euler #=-10 (111037,332851,221804) : difference with theory (-10) = 0 
CORRECTING DEFECT 34 (vertices=56, convex hull=38, v0=60539)
After retessellation of defect 34 (v0=60539), euler #=-9 (111044,332883,221830) : difference with theory (-9) = 0 
CORRECTING DEFECT 35 (vertices=20, convex hull=71, v0=64640)
After retessellation of defect 35 (v0=64640), euler #=-8 (111055,332940,221877) : difference with theory (-8) = 0 
CORRECTING DEFECT 36 (vertices=36, convex hull=34, v0=70899)
After retessellation of defect 36 (v0=70899), euler #=-7 (111063,332973,221903) : difference with theory (-7) = 0 
CORRECTING DEFECT 37 (vertices=38, convex hull=60, v0=72833)
After retessellation of defect 37 (v0=72833), euler #=-6 (111072,333024,221946) : difference with theory (-6) = 0 
CORRECTING DEFECT 38 (vertices=12, convex hull=14, v0=72913)
After retessellation of defect 38 (v0=72913), euler #=-5 (111073,333029,221951) : difference with theory (-5) = 0 
CORRECTING DEFECT 39 (vertices=150, convex hull=85, v0=77573)
After retessellation of defect 39 (v0=77573), euler #=-4 (111089,333115,222022) : difference with theory (-4) = 0 
CORRECTING DEFECT 40 (vertices=37, convex hull=27, v0=81479)
After retessellation of defect 40 (v0=81479), euler #=-3 (111091,333131,222037) : difference with theory (-3) = 0 
CORRECTING DEFECT 41 (vertices=23, convex hull=31, v0=82670)
After retessellation of defect 41 (v0=82670), euler #=-2 (111095,333154,222057) : difference with theory (-2) = 0 
CORRECTING DEFECT 42 (vertices=46, convex hull=82, v0=84542)
After retessellation of defect 42 (v0=84542), euler #=-1 (111121,333265,222143) : difference with theory (-1) = 0 
CORRECTING DEFECT 43 (vertices=134, convex hull=131, v0=86388)
After retessellation of defect 43 (v0=86388), euler #=0 (111135,333372,222237) : difference with theory (0) = 0 
CORRECTING DEFECT 44 (vertices=23, convex hull=24, v0=103369)
After retessellation of defect 44 (v0=103369), euler #=1 (111138,333387,222250) : difference with theory (1) = 0 
CORRECTING DEFECT 45 (vertices=38, convex hull=54, v0=105572)
After retessellation of defect 45 (v0=105572), euler #=2 (111155,333459,222306) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.90 +- 0.28 (0.01-->16.08) (max @ vno 143 --> 2167)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.90 +- 0.28 (0.01-->16.08) (max @ vno 143 --> 2167)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
166 mutations (36.2%), 292 crossovers (63.8%), 498 vertices were eliminated
building final representation...
6109 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=111155, nf=222306, ne=333459, g=0)
writing corrected surface to /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.premesh...

0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 1042 intersecting
001: 120 intersecting
002: 9 intersecting
003: 6 intersecting
004: 5 intersecting
terminating search with 0 intersecting
topology fixing took 10.9 minutes
FSRUNTIME@ mris_fix_topology lh  0.1814 hours 1 threads
#VMPC# mris_fix_topology VmPeak  769124
@#@FSTIME  2020:10:05:00:16:35 mris_fix_topology N 14 e 653.09 S 0.77 U 576.99 P 88% M 721040 F 8 R 199439 W 0 c 165601 w 14 I 2000 O 10584 L 1.28 1.27 1.02
@#@FSLOADPOST 2020:10:05:00:27:28 mris_fix_topology N 14 1.38 1.43 1.21
#@# Fix Topology rh 2020��� 10��� 05��� ��������� 00:27:28 CST

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 monkey2 rh 

reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.1.0
  7.1.0
before topology correction, eno=-90 (nv=113260, nf=226700, ne=340050, g=46)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
13905 ambiguous faces found in tessellation
segmenting defects...
40 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 26 into 9
      -merging segment 25 into 22
38 defects to be corrected 
0 vertices coincident
reading input surface /usr/local/freesurfer/subjects/monkey2/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8959  (-4.9479)
      -vertex     loglikelihood: -6.9687  (-3.4843)
      -normal dot loglikelihood: -3.5961  (-3.5961)
      -quad curv  loglikelihood: -5.5224  (-2.7612)
      Total Loglikelihood : -25.9830
CORRECTING DEFECT 0 (vertices=1094, convex hull=347, v0=73)
A large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 0 (v0=73), euler #=-30 (105456,314485,208999) : difference with theory (-35) = -5 
CORRECTING DEFECT 1 (vertices=12, convex hull=19, v0=115)
After retessellation of defect 1 (v0=115), euler #=-29 (105460,314503,209014) : difference with theory (-34) = -5 
CORRECTING DEFECT 2 (vertices=18, convex hull=31, v0=207)
After retessellation of defect 2 (v0=207), euler #=-28 (105464,314526,209034) : difference with theory (-33) = -5 
CORRECTING DEFECT 3 (vertices=7, convex hull=27, v0=517)
After retessellation of defect 3 (v0=517), euler #=-27 (105465,314537,209045) : difference with theory (-32) = -5 
CORRECTING DEFECT 4 (vertices=55, convex hull=41, v0=658)
After retessellation of defect 4 (v0=658), euler #=-26 (105474,314583,209083) : difference with theory (-31) = -5 
CORRECTING DEFECT 5 (vertices=9, convex hull=15, v0=1283)
After retessellation of defect 5 (v0=1283), euler #=-25 (105475,314589,209089) : difference with theory (-30) = -5 
CORRECTING DEFECT 6 (vertices=3006, convex hull=1513, v0=5146)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109189 with 4 faces
normal vector of length zero at vertex 109202 with 6 faces
After retessellation of defect 6 (v0=5146), euler #=-28 (106102,317283,211153) : difference with theory (-29) = -1 
CORRECTING DEFECT 7 (vertices=51, convex hull=64, v0=12158)
After retessellation of defect 7 (v0=12158), euler #=-27 (106113,317342,211202) : difference with theory (-28) = -1 
CORRECTING DEFECT 8 (vertices=23, convex hull=38, v0=12373)
After retessellation of defect 8 (v0=12373), euler #=-26 (106124,317387,211237) : difference with theory (-27) = -1 
CORRECTING DEFECT 9 (vertices=458, convex hull=348, v0=16124)
After retessellation of defect 9 (v0=16124), euler #=-25 (106269,317999,211705) : difference with theory (-26) = -1 
CORRECTING DEFECT 10 (vertices=17, convex hull=28, v0=16458)
After retessellation of defect 10 (v0=16458), euler #=-24 (106276,318028,211728) : difference with theory (-25) = -1 
CORRECTING DEFECT 11 (vertices=43, convex hull=47, v0=18348)
After retessellation of defect 11 (v0=18348), euler #=-23 (106294,318098,211781) : difference with theory (-24) = -1 
CORRECTING DEFECT 12 (vertices=14, convex hull=24, v0=19319)
After retessellation of defect 12 (v0=19319), euler #=-22 (106296,318109,211791) : difference with theory (-23) = -1 
CORRECTING DEFECT 13 (vertices=1513, convex hull=568, v0=19817)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
After retessellation of defect 13 (v0=19817), euler #=-21 (106723,319683,212939) : difference with theory (-22) = -1 
CORRECTING DEFECT 14 (vertices=18, convex hull=68, v0=20406)
After retessellation of defect 14 (v0=20406), euler #=-20 (106733,319741,212988) : difference with theory (-21) = -1 
CORRECTING DEFECT 15 (vertices=5, convex hull=23, v0=24595)
After retessellation of defect 15 (v0=24595), euler #=-19 (106735,319753,212999) : difference with theory (-20) = -1 
CORRECTING DEFECT 16 (vertices=680, convex hull=192, v0=25560)
After retessellation of defect 16 (v0=25560), euler #=-19 (106771,319977,213187) : difference with theory (-19) = 0 
CORRECTING DEFECT 17 (vertices=276, convex hull=99, v0=27616)
After retessellation of defect 17 (v0=27616), euler #=-19 (106869,320320,213432) : difference with theory (-18) = 1 
CORRECTING DEFECT 18 (vertices=10, convex hull=34, v0=29800)
After retessellation of defect 18 (v0=29800), euler #=-18 (106870,320335,213447) : difference with theory (-17) = 1 
CORRECTING DEFECT 19 (vertices=9, convex hull=20, v0=30021)
After retessellation of defect 19 (v0=30021), euler #=-17 (106871,320344,213456) : difference with theory (-16) = 1 
CORRECTING DEFECT 20 (vertices=8, convex hull=24, v0=33662)
After retessellation of defect 20 (v0=33662), euler #=-16 (106873,320357,213468) : difference with theory (-15) = 1 
CORRECTING DEFECT 21 (vertices=46, convex hull=53, v0=34797)
After retessellation of defect 21 (v0=34797), euler #=-15 (106877,320390,213498) : difference with theory (-14) = 1 
CORRECTING DEFECT 22 (vertices=40, convex hull=52, v0=35290)
After retessellation of defect 22 (v0=35290), euler #=-13 (106882,320423,213528) : difference with theory (-13) = 0 
CORRECTING DEFECT 23 (vertices=140, convex hull=122, v0=36519)
After retessellation of defect 23 (v0=36519), euler #=-12 (106905,320549,213632) : difference with theory (-12) = 0 
CORRECTING DEFECT 24 (vertices=87, convex hull=88, v0=38291)
After retessellation of defect 24 (v0=38291), euler #=-11 (106917,320621,213693) : difference with theory (-11) = 0 
CORRECTING DEFECT 25 (vertices=65, convex hull=51, v0=47497)
After retessellation of defect 25 (v0=47497), euler #=-10 (106921,320658,213727) : difference with theory (-10) = 0 
CORRECTING DEFECT 26 (vertices=5, convex hull=21, v0=55139)
After retessellation of defect 26 (v0=55139), euler #=-9 (106923,320667,213735) : difference with theory (-9) = 0 
CORRECTING DEFECT 27 (vertices=6, convex hull=14, v0=57005)
After retessellation of defect 27 (v0=57005), euler #=-8 (106925,320678,213745) : difference with theory (-8) = 0 
CORRECTING DEFECT 28 (vertices=5, convex hull=12, v0=65200)
After retessellation of defect 28 (v0=65200), euler #=-7 (106927,320686,213752) : difference with theory (-7) = 0 
CORRECTING DEFECT 29 (vertices=23, convex hull=23, v0=67431)
After retessellation of defect 29 (v0=67431), euler #=-6 (106933,320711,213772) : difference with theory (-6) = 0 
CORRECTING DEFECT 30 (vertices=8, convex hull=18, v0=67513)
After retessellation of defect 30 (v0=67513), euler #=-5 (106935,320723,213783) : difference with theory (-5) = 0 
CORRECTING DEFECT 31 (vertices=46, convex hull=32, v0=67573)
After retessellation of defect 31 (v0=67573), euler #=-4 (106946,320765,213815) : difference with theory (-4) = 0 
CORRECTING DEFECT 32 (vertices=7, convex hull=28, v0=67705)
After retessellation of defect 32 (v0=67705), euler #=-3 (106950,320784,213831) : difference with theory (-3) = 0 
CORRECTING DEFECT 33 (vertices=21, convex hull=24, v0=69541)
After retessellation of defect 33 (v0=69541), euler #=-2 (106954,320801,213845) : difference with theory (-2) = 0 
CORRECTING DEFECT 34 (vertices=21, convex hull=53, v0=69719)
After retessellation of defect 34 (v0=69719), euler #=-1 (106964,320848,213883) : difference with theory (-1) = 0 
CORRECTING DEFECT 35 (vertices=41, convex hull=43, v0=74804)
After retessellation of defect 35 (v0=74804), euler #=0 (106965,320865,213900) : difference with theory (0) = 0 
CORRECTING DEFECT 36 (vertices=25, convex hull=45, v0=83877)
After retessellation of defect 36 (v0=83877), euler #=1 (106972,320901,213930) : difference with theory (1) = 0 
CORRECTING DEFECT 37 (vertices=18, convex hull=28, v0=89148)
After retessellation of defect 37 (v0=89148), euler #=2 (106974,320916,213944) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.90 +- 0.28 (0.05-->15.60) (max @ vno 11428 --> 106605)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.90 +- 0.28 (0.05-->15.60) (max @ vno 11428 --> 106605)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
134 mutations (36.6%), 232 crossovers (63.4%), 601 vertices were eliminated
building final representation...
6286 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=106974, nf=213944, ne=320916, g=0)
writing corrected surface to /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.premesh...

0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 810 intersecting
001: 152 intersecting
002: 31 intersecting
003: 4 intersecting
terminating search with 0 intersecting
topology fixing took 773.1 minutes
FSRUNTIME@ mris_fix_topology rh 12.8842 hours 1 threads
#VMPC# mris_fix_topology VmPeak  764684
@#@FSTIME  2020:10:05:00:27:28 mris_fix_topology N 14 e 46383.06 S 60.43 U 46175.22 P 99% M 716872 F 19 R 197990 W 0 c 178529 w 25 I 3296 O 10192 L 1.38 1.43 1.21
@#@FSLOADPOST 2020:10:05:13:20:31 mris_fix_topology N 14 1.56 1.66 1.38

 mris_euler_number ../surf/lh.orig.premesh 

euler # = v-e+f = 2g-2: 111155 - 333459 + 222306 = 2 --> 0 holes
      F =2V-4:          222306 = 222310-4 (0)
      2E=3F:            666918 = 666918 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig.premesh 

euler # = v-e+f = 2g-2: 106974 - 320916 + 213944 = 2 --> 0 holes
      F =2V-4:          213944 = 213948-4 (0)
      2E=3F:            641832 = 641832 (0)

total defect index = 0
2020��� 10��� 05��� ��������� 13:20:33 CST

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer/subjects/monkey2/scripts
/usr/local/freesurfer/bin/defect2seg --s monkey2

freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
defect2seg 7.1.0
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
pid 11508
mri_label2vol --defects /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels /usr/local/freesurfer/subjects/monkey2/mri/orig.mgz 1000 0 /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mri_label2vol supposed to be reproducible but seed not set
Changing input type 0 to MRI_INT
Converting defects to volume: offset=1000, merge=0
Writing to /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mris_defects_pointset -s /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix -d /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels -o /usr/local/freesurfer/subjects/monkey2/surf/lh.defects.pointset
Reading in surface /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.nofix
Reading in defect segmentation /usr/local/freesurfer/subjects/monkey2/surf/lh.defect_labels
#VMPC# mris_defects_pointset 172588
mris_defects_pointset done
mri_label2vol --defects /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz 2000 1 /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mri_label2vol supposed to be reproducible but seed not set
Converting defects to volume: offset=2000, merge=1
Writing to /usr/local/freesurfer/subjects/monkey2/mri/surface.defects.mgz
mris_defects_pointset -s /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix -d /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels -o /usr/local/freesurfer/subjects/monkey2/surf/rh.defects.pointset
Reading in surface /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.nofix
Reading in defect segmentation /usr/local/freesurfer/subjects/monkey2/surf/rh.defect_labels
#VMPC# mris_defects_pointset 167828
mris_defects_pointset done
 
Started at 2020��� 10��� 05��� ��������� 13:20:33 CST 
Ended   at 2020��� 10��� 05��� ��������� 13:20:41 CST
Defect2seg-Run-Time-Sec 8
Defect2seg-Run-Time-Min 0.16
Defect2seg-Run-Time-Hours 0.00
 
tkmeditfv monkey2 orig.mgz -defect -c /usr/local/freesurfer/subjects/monkey2/surf/?h.defects.pointset
defect2seg Done
@#@FSTIME  2020:10:05:13:20:33 defect2seg N 2 e 7.94 S 0.29 U 6.70 P 88% M 225052 F 48 R 208345 W 0 c 2300 w 310 I 37944 O 440 L 1.56 1.66 1.38
@#@FSLOADPOST 2020:10:05:13:20:41 defect2seg N 2 1.62 1.67 1.38

 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/subjects/monkey2/surf/lh.orig.premesh --output /usr/local/freesurfer/subjects/monkey2/surf/lh.orig 

iters = 3
standard remeshing without target
   adjusted l: 0.722676
remeshing to edge length 0.722676 with 3 iterations

avg qual before   : 0.882817  after: 0.971441

Removing intersections
removing intersecting faces
000: 12 intersecting
terminating search with 0 intersecting
Remeshed surface quality stats nv0 = 111155  nv = 115085  1.03536
Area    230166  0.31229  0.03459 0.007886   0.5020
Corner  690498 60.00000  8.76341 11.956449 148.5693
Edge    345249  0.85727  0.08350 0.112504   1.2763
Hinge   345249  7.82118 10.21732 0.000008 175.0766
mris_remesh done
@#@FSTIME  2020:10:05:13:20:41 mris_remesh N 7 e 38.59 S 0.33 U 33.70 P 88% M 699876 F 19 R 250909 W 0 c 9699 w 27 I 4256 O 8096 L 1.62 1.67 1.38
@#@FSLOADPOST 2020:10:05:13:21:19 mris_remesh N 7 1.56 1.65 1.38

 mris_remesh --remesh --iters 3 --input /usr/local/freesurfer/subjects/monkey2/surf/rh.orig.premesh --output /usr/local/freesurfer/subjects/monkey2/surf/rh.orig 

iters = 3
standard remeshing without target
   adjusted l: 0.721175
remeshing to edge length 0.721175 with 3 iterations

avg qual before   : 0.884144  after: 0.971445

Removing intersections
removing intersecting faces
000: 18 intersecting
001: 15 intersecting
step 1 with no progress (num=16, old_num=15)
002: 16 intersecting
003: 14 intersecting
step 1 with no progress (num=14, old_num=14)
004: 14 intersecting
005: 13 intersecting
step 1 with no progress (num=13, old_num=13)
006: 13 intersecting
step 2 with no progress (num=13, old_num=13)
007: 13 intersecting
step 3 with no progress (num=13, old_num=13)
008: 13 intersecting
step 4 with no progress (num=13, old_num=13)
009: 13 intersecting
step 5 with no progress (num=13, old_num=13)
010: 13 intersecting
step 6 with no progress (num=13, old_num=13)
011: 13 intersecting
step 7 with no progress (num=13, old_num=13)
012: 13 intersecting
step 8 with no progress (num=13, old_num=13)
013: 13 intersecting
step 9 with no progress (num=13, old_num=13)
014: 13 intersecting
step 10 with no progress (num=13, old_num=13)
015: 13 intersecting
step 11 with no progress (num=13, old_num=13)
016: 13 intersecting
step 12 with no progress (num=13, old_num=13)
017: 13 intersecting
step 13 with no progress (num=13, old_num=13)
018: 13 intersecting
step 14 with no progress (num=13, old_num=13)
019: 13 intersecting
step 15 with no progress (num=13, old_num=13)
020: 13 intersecting
step 16 with no progress (num=13, old_num=13)
terminating search with 13 intersecting
Remeshed surface quality stats nv0 = 106974  nv = 110700  1.03483
Area    221396  0.31049  0.03442 0.028288   0.5456
Corner  664188 60.00000  8.76641 5.740801 152.4113
Edge    332094  0.85480  0.08327 0.181206   1.3560
Hinge   332094  7.86217 10.50347 0.000033 165.5073
mris_remesh done
@#@FSTIME  2020:10:05:13:21:19 mris_remesh N 7 e 73.30 S 0.34 U 63.73 P 87% M 770664 F 0 R 253141 W 0 c 18377 w 3 I 0 O 7792 L 1.56 1.65 1.38
@#@FSLOADPOST 2020:10:05:13:22:33 mris_remesh N 7 1.75 1.67 1.41
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.00 hours
writing corrected surface to ../surf/lh.orig
@#@FSTIME  2020:10:05:13:22:33 mris_remove_intersection N 2 e 3.53 S 0.09 U 3.03 P 88% M 255628 F 18 R 69996 W 0 c 914 w 25 I 3952 O 8096 L 1.75 1.67 1.41
@#@FSLOADPOST 2020:10:05:13:22:36 mris_remove_intersection N 2 1.69 1.66 1.41

 rm ../surf/lh.inflated 

rm: cannot remove '../surf/lh.inflated': No such file or directory
/usr/local/freesurfer/subjects/monkey2/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.01 hours
removing intersecting faces
000: 13 intersecting
step 1 with no progress (num=13, old_num=13)
001: 13 intersecting
step 2 with no progress (num=13, old_num=13)
002: 13 intersecting
step 3 with no progress (num=13, old_num=13)
003: 13 intersecting
step 4 with no progress (num=13, old_num=13)
004: 13 intersecting
step 5 with no progress (num=13, old_num=13)
005: 13 intersecting
step 6 with no progress (num=13, old_num=13)
006: 13 intersecting
step 7 with no progress (num=13, old_num=13)
007: 13 intersecting
step 8 with no progress (num=13, old_num=13)
008: 13 intersecting
step 9 with no progress (num=13, old_num=13)
009: 13 intersecting
step 10 with no progress (num=13, old_num=13)
010: 13 intersecting
step 11 with no progress (num=13, old_num=13)
011: 13 intersecting
step 12 with no progress (num=13, old_num=13)
012: 13 intersecting
step 13 with no progress (num=13, old_num=13)
013: 13 intersecting
step 14 with no progress (num=13, old_num=13)
014: 13 intersecting
step 15 with no progress (num=13, old_num=13)
015: 13 intersecting
step 16 with no progress (num=13, old_num=13)
terminating search with 13 intersecting
writing corrected surface to ../surf/rh.orig
@#@FSTIME  2020:10:05:13:22:36 mris_remove_intersection N 2 e 40.07 S 0.15 U 35.01 P 87% M 293392 F 0 R 88816 W 0 c 10270 w 1 I 0 O 7792 L 1.69 1.66 1.41
@#@FSLOADPOST 2020:10:05:13:23:16 mris_remove_intersection N 2 1.62 1.64 1.41

 rm ../surf/rh.inflated 

rm: cannot remove '../surf/rh.inflated': No such file or directory
#--------------------------------------------
#@# AutoDetGWStats lh 2020��� 10��� 05��� ��������� 13:23:16 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 

border white:    201470 voxels (1.20%)
border gray      250559 voxels (1.49%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/lh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=30761, wmmin=5, clip=110 
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (101.0): 100.4 +- 9.2 [70.0 --> 110.0]
CCS GM (71.0) : 71.7 +- 13.2 [30.0 --> 110.0]
white_mean = 100.376 +/- 9.16773, gray_mean = 71.7466 +/- 13.1558
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=255 nbins=256
intensity peaks found at WM=107+-5.2,    GM=70+-7.8
white_mode = 107, gray_mode = 70
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 56.8 (was 70.000000)
setting MAX_BORDER_WHITE to 116.2 (was 105.000000)
setting MIN_BORDER_WHITE to 70.0 (was 85.000000)
setting MAX_CSF to 43.7 (was 40.000000)
setting MAX_GRAY to 97.8 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 56.8 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 30.5 (was 40.000000)
When placing the white surface
  white_border_hi   = 116.168;
  white_border_low  = 70;
  white_outside_low = 56.8442;
  white_inside_hi   = 120;
  white_outside_hi  = 116.168;
When placing the pial surface
  pial_border_hi   = 56.8442;
  pial_border_low  = 30.5327;
  pial_outside_low = 10;
  pial_inside_hi   = 97.8323;
  pial_outside_hi  = 50.2663;
#VMPC# mris_autodet_gwstats VmPeak  246728
mris_autodet_gwstats done
@#@FSTIME  2020:10:05:13:23:16 mris_autodet_gwstats N 8 e 13.90 S 0.10 U 12.15 P 88% M 211036 F 17 R 62111 W 0 c 3535 w 23 I 8168 O 8 L 1.62 1.64 1.41
@#@FSLOADPOST 2020:10:05:13:23:30 mris_autodet_gwstats N 8 1.48 1.61 1.40
#--------------------------------------------
#@# AutoDetGWStats rh 2020��� 10��� 05��� ��������� 13:23:30 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 

border white:    201470 voxels (1.20%)
border gray      250559 voxels (1.49%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/rh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=30761, wmmin=5, clip=110 
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (101.0): 100.4 +- 9.2 [70.0 --> 110.0]
CCS GM (71.0) : 71.7 +- 13.2 [30.0 --> 110.0]
white_mean = 100.376 +/- 9.16773, gray_mean = 71.7466 +/- 13.1558
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=255 nbins=256
intensity peaks found at WM=106+-6.1,    GM=64+-8.7
white_mode = 106, gray_mode = 64
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 50.8 (was 70.000000)
setting MAX_BORDER_WHITE to 115.2 (was 105.000000)
setting MIN_BORDER_WHITE to 64.0 (was 85.000000)
setting MAX_CSF to 37.7 (was 40.000000)
setting MAX_GRAY to 96.8 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 50.8 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 24.5 (was 40.000000)
When placing the white surface
  white_border_hi   = 115.168;
  white_border_low  = 64;
  white_outside_low = 50.8442;
  white_inside_hi   = 120;
  white_outside_hi  = 115.168;
When placing the pial surface
  pial_border_hi   = 50.8442;
  pial_border_low  = 24.5327;
  pial_outside_low = 10;
  pial_inside_hi   = 96.8323;
  pial_outside_hi  = 44.2663;
#VMPC# mris_autodet_gwstats VmPeak  240840
mris_autodet_gwstats done
@#@FSTIME  2020:10:05:13:23:30 mris_autodet_gwstats N 8 e 13.56 S 0.09 U 11.94 P 88% M 205040 F 0 R 60382 W 0 c 3462 w 1 I 0 O 8 L 1.48 1.61 1.40
@#@FSLOADPOST 2020:10:05:13:23:44 mris_autodet_gwstats N 8 1.41 1.59 1.40
#--------------------------------------------
#@# WhitePreAparc lh 2020��� 10��� 05��� ��������� 13:23:44 CST
cd /usr/local/freesurfer/subjects/monkey2/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5
7.1.0
7.1.0

cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 

Reading in input surface ../surf/lh.orig
Smoothing surface with 5 iterations
Area    230166  0.28728  0.06614 0.000899   0.5852
Corner  690498 60.00000  9.22592 3.263084 157.1301
Edge    345249  0.81774  0.11586 0.028436   1.5900
Hinge   345249  4.79409  6.13323 0.000002 153.5438
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=30761, wmmin=5, clip=110 
MRIfindBrightNonWM(): 6937 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
ERROR: need seg for ripping
Command exited with non-zero status 1
@#@FSTIME  2020:10:05:13:23:44 mris_place_surface N 14 e 12.39 S 0.16 U 10.80 P 88% M 434260 F 25 R 126035 W 0 c 3134 w 27 I 5168 O 0 L 1.41 1.59 1.40
@#@FSLOADPOST 2020:10:05:13:23:56 mris_place_surface N 14 1.32 1.56 1.39
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s monkey2 exited with ERRORS at 2020��� 10��� 05��� ��������� 13:23:56 CST

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting