[Freesurfer] recon-all.error using T2 data to improve pial surfaces

7 Aug 2024


      External Email - Use Caution
Dear Freesurfer Expert,
I am encountering errors when attempting to run recon-all with T2 images. It
appears there are issues specifically related to the processing of the T2
files.
Could you kindly advise on the appropriate steps to resolve this issue?
Please find the recon-all.error and recon-all.log files attached for your
reference.
Thank you for your assistance.
Best regards,
-Edward
------------------------------
SUBJECT 0003
DATE 公曆 20廿四年 八月 七日 週三 十八時卅分廿五秒
USER chang
HOST chang-System-Product-Name
PROCESSOR x86_64
OS Linux
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460)
/usr/local/freesurfer/bin/recon-all
PWD /home/chang/GBM_Data/VBG/0003/0003/mri
CMD mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label
../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label
--white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf
../surf/lh.white --mmvol T2.mgz T2
公曆 20廿四年 八月 七日 週三 十一時35分37秒
cd /home/chang/GBM_Data/VBG/0003/0003
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
/usr/local/freesurfer/bin/recon-all -autorecon1 -i
/home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz -subjid 0003 -sd
/home/chang/GBM_Data/VBG/0003
subjid 0003
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 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  1048576
memorylocked 16453580 kbytes
maxproc      513872
maxlocks     unlimited
maxsignal    513872
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited
total        used        free      shared  buff/cache
available
Mem:           125Gi        16Gi       3.4Gi       2.5Gi       105Gi
104Gi
Swap:          2.0Gi       2.0Gi       0.0Ki
########################################
program versions used
7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460)
7.4.1
ProgramName: lta_convert  ProgramArguments: lta_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_compute_seg_overlap  ProgramArguments:
mri_compute_seg_overlap -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fuse_segmentations  ProgramArguments:
mri_fuse_segmentations -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_relabel_hypointensities  ProgramArguments:
mri_relabel_hypointensities -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments:
mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_register  ProgramArguments: mri_robust_register
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_template  ProgramArguments: mri_robust_template
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_divide_parcellation  ProgramArguments:
mris_divide_parcellation -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_left_right_register  ProgramArguments:
mris_left_right_register -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-03:35:37-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_register  ProgramArguments: mris_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
mri_motion_correct.fsl 7.4.1
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-03:35:37-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
/home/chang/GBM_Data/VBG/0003/0003
mri_convert /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz
mri_convert /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz
reading from /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz...
@#@FSTIME  2024:08:07:11:35:38 mri_convert N 2 e 0.97 S 0.03 U 0.93 P 99% M
42240 F 0 R 9169 W 0 c 13 w 3 I 46584 O 46368 L 10.40 10.73 10.73
@#@FSLOADPOST 2024:08:07:11:35:38 mri_convert N 2 10.40 10.73 10.73
#--------------------------------------------
#@# MotionCor 公曆 20廿四年 八月 七日 週三 十一時35分39秒
Found 1 runs
/home/chang/GBM_Data/VBG/0003/0003/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 /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
mri_info /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
rawavg.mgz ========================================
Volume information for /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
type: MGH
dimensions: 240 x 240 x 155
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 240.000
dof: 1
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -77.5, zend: 77.5
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =  -120.
0000
: x_a =   0.0000, y_a =  -1.0000, z_a =   0.0000, c_a =   119.
0000
: x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =    77.
5000
talairach xfm :
Orientation   : LPS
Primary Slice Direction: axial
voxel to ras transform:
-1.0000   0.0000   0.0000     0.0000
0.0000  -1.0000   0.0000   239.0000
0.0000   0.0000   1.0000     0.0000
0.0000   0.0000   0.0000     1.0000
voxel-to-ras determinant 1
ras to voxel transform:
-1.0000   0.0000   0.0000     0.0000
0.0000  -1.0000   0.0000   239.0000
0.0000   0.0000   1.0000     0.0000
0.0000   0.0000   0.0000     1.0000
/home/chang/GBM_Data/VBG/0003/0003
mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz --conform
mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz --conform
reading from /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram -46.4572 182.552 1000, flo=0, fhi=0.999,
dest_type=0
Reslicing using trilinear interpolation
writing to /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz...
@#@FSTIME  2024:08:07:11:35:42 mri_convert N 3 e 1.09 S 0.03 U 1.05 P 99% M
50688 F 0 R 19668 W 0 c 13 w 1 I 0 O 5872 L 10.12 10.66 10.71
@#@FSLOADPOST 2024:08:07:11:35:44 mri_convert N 3 10.12 10.66 10.71
mri_add_xform_to_header -c
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach.xfm
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
INFO: extension is mgz
@#@FSTIME  2024:08:07:11:35:44 mri_add_xform_to_header N 4 e 0.32 S 0.00 U
0.31 P 100% M 23552 F 0 R 4597 W 0 c 7 w 1 I 0 O 5872 L 10.12 10.66 10.71
@#@FSLOADPOST 2024:08:07:11:35:44 mri_add_xform_to_header N 4 10.12 10.66
10.71
mri_info /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
orig.mgz ========================================
Volume information for /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =  -120.
0000
: x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =   119.
0000
: x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =    77.
5000
talairach xfm : /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach.
xfm
Orientation   : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000   0.0000   0.0000     8.0000
0.0000   0.0000   1.0000    -9.0000
0.0000  -1.0000   0.0000   205.5000
0.0000   0.0000   0.0000     1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000  -0.0000  -0.0000     8.0000
-0.0000  -0.0000  -1.0000   205.5000
-0.0000   1.0000  -0.0000     9.0000
-0.0000  -0.0000  -0.0000     1.0000
#--------------------------------------------
#@# Talairach 公曆 20廿四年 八月 七日 週三 十一時35分44秒
/home/chang/GBM_Data/VBG/0003/0003/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
/home/chang/GBM_Data/VBG/0003/0003/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 7.4.1
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
公曆 20廿四年 八月 七日 週三 十一時35分44秒
tmpdir is ./tmp.mri_nu_correct.mni.602679
cd /home/chang/GBM_Data/VBG/0003/0003/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o
./tmp.mri_nu_correct.mni.602679/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.602679/nu0.mgz orig_nu.mgz --like orig.
mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.602679/nu0.mgz orig_nu.mgz --like orig.
mgz --conform
reading from ./tmp.mri_nu_correct.mni.602679/nu0.mgz...
TR=1000.00, 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...
公曆 20廿四年 八月 七日 週三 十一時36分58秒
mri_nu_correct.mni done
@#@FSTIME  2024:08:07:11:35:44 mri_nu_correct.mni N 12 e 73.84 S 0.15 U
73.69 P 100% M 505444 F 0 R 147801 W 0 c 362 w 101 I 0 O 10776 L 10.12 10.66
10.71
@#@FSLOADPOST 2024:08:07:11:36:58 mri_nu_correct.mni N 12 10.52 10.64 10.69
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
mv -f
/home/chang/GBM_Data/VBG/0003/0003/mri/talsrcimg_to_711-2C_as_mni_average_30
5_t4_vox2vox.txt
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talsrcimg_to_711-2C_as_mni
_average_305_t4_vox2vox.txt
Started at 公曆 20廿四年 八月 七日 週三 十一時36分58秒
Ended   at 公曆 20廿四年 八月 七日 週三 十一時37分十一秒
talairach_avi done
@#@FSTIME  2024:08:07:11:36:58 talairach_avi N 4 e 12.96 S 0.80 U 6.15 P 53%
M 254976 F 0 R 401480 W 0 c 52 w 593 I 0 O 295368 L 10.52 10.64 10.69
@#@FSLOADPOST 2024:08:07:11:37:11 talairach_avi N 4 11.01 10.74 10.73
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
7.4.1
--src: orig.mgz src image (geometry).
--trg: /usr/local/freesurfer/average/mni305.cor.mgz trg image (geometry).
--inmni: transforms/talairach.xfm input MNI/XFM transform.
--outlta: transforms/talairach.xfm.lta output LTA.
--s: fsaverage subject name
--ltavox2vox: output LTA as VOX_TO_VOX transform.
LTA read, type : 1
1.08931   0.00911  -0.03807   131.53241;
-0.00637   0.90387   0.49920  -147.69925;
0.04987  -0.48152   1.02395  -18.16597;
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 公曆 20廿四年 八月 七日 週三 十一時37分十三
秒
/home/chang/GBM_Data/VBG/0003/0003/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4547,
pval=0.1049 >= threshold=0.0050)
@#@FSTIME  2024:08:07:11:37:13 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100%
M 5888 F 0 R 253 W 0 c 0 w 1 I 0 O 0 L 11.01 10.74 10.73
@#@FSLOADPOST 2024:08:07:11:37:13 talairach_afd N 4 11.01 10.74 10.73
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach_avi.log
tal_QC_AZS
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach_avi.log
TalAviQA: 0.98085
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction 公曆 20廿四年 八月 七日 週三 十一時37分十三秒
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm
--n 2 --ants-n4
/usr/bin/bc
/home/chang/GBM_Data/VBG/0003/0003/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 7.4.1
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
公曆 20廿四年 八月 七日 週三 十一時37分十三秒
tmpdir is ./tmp.mri_nu_correct.mni.603046
cd /home/chang/GBM_Data/VBG/0003/0003/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o
./tmp.mri_nu_correct.mni.603046/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_binarize --i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --min -1 --o ./tmp.
mri_nu_correct.mni.603046/ones.mgz
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --min -1
--o ./tmp.mri_nu_correct.mni.603046/ones.mgz
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
input      ./tmp.mri_nu_correct.mni.603046/nu0.mgz
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.603046/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Starting parallel 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777215 voxels in final mask
Writing output to ./tmp.mri_nu_correct.mni.603046/ones.mgz
Count: 16777215 16777215.000000 16777216 99.999994
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz --i orig.
mgz --sum ./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf
./tmp.mri_nu_correct.mni.603046/input.mean.dat
7.4.1
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz
--i orig.mgz --sum ./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf
./tmp.mri_nu_correct.mni.603046/input.mean.dat
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
whitesurfname  white
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.603046/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.603046/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz --i
./tmp.mri_nu_correct.mni.603046/nu0.mgz --sum
./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf
./tmp.mri_nu_correct.mni.603046/output.mean.dat
7.4.1
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz
--i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --sum
./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf
./tmp.mri_nu_correct.mni.603046/output.mean.dat
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
whitesurfname  white
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.603046/ones.mgz
Loading ./tmp.mri_nu_correct.mni.603046/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.603046/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.603046/nu0.mgz
./tmp.mri_nu_correct.mni.603046/nu0.mgz mul 1.57903263683775183189
Saving result to './tmp.mri_nu_correct.mni.603046/nu0.mgz' (type = MGH )
[ ok ]
mri_convert ./tmp.mri_nu_correct.mni.603046/nu0.mgz nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.603046/nu0.mgz nu.mgz --like orig.mgz
reading from ./tmp.mri_nu_correct.mni.603046/nu0.mgz...
TR=1000.00, 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 2 seconds.
FIRST_PERCENTILE 0.010000
WM_PERCENTILE    0.900000
MAX_R 50.000000
i1 = 23, i2 = 80
#mri_make_uchar# mapping 55 190 to  3 110  :  b -40.807 m 0.794143 : thresh
51.385 maxsat 372.486 : nzero 10396308 nsat 0
公曆 20廿四年 八月 七日 週三 十一時38分39秒
mri_nu_correct.mni done
@#@FSTIME  2024:08:07:11:37:13 mri_nu_correct.mni N 9 e 85.82 S 0.53 U 85.30
P 100% M 614144 F 0 R 518305 W 0 c 354 w 171 I 0 O 26960 L 11.01 10.74 10.73
@#@FSLOADPOST 2024:08:07:11:38:39 mri_nu_correct.mni N 9 11.39 10.97 10.81
mri_add_xform_to_header -c
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach.xfm nu.mgz
nu.mgz
INFO: extension is mgz
@#@FSTIME  2024:08:07:11:38:39 mri_add_xform_to_header N 4 e 0.47 S 0.01 U
0.45 P 99% M 23552 F 0 R 4598 W 0 c 2 w 1 I 0 O 5240 L 11.39 10.97 10.81
@#@FSLOADPOST 2024:08:07:11:38:39 mri_add_xform_to_header N 4 11.39 10.97
10.81
#--------------------------------------------
#@# Intensity Normalization 公曆 20廿四年 八月 七日 週三 十一時38分39秒
/home/chang/GBM_Data/VBG/0003/0003/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...
NOT doing gentle normalization with control points/label
talairach transform
1.08931   0.00911  -0.03807   131.53241;
-0.00637   0.90387   0.49920  -147.69925;
0.04987  -0.48152   1.02395  -18.16597;
0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 15
Starting OpenSpline(): npoints = 15
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 67 (67), valley at 40 (40)
csf peak at 10, 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 66 (66), valley at 40 (40)
csf peak at 10, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 0 minutes and 36 seconds.
@#@FSTIME  2024:08:07:11:38:39 mri_normalize N 7 e 36.80 S 0.25 U 36.55 P
99% M 583648 F 0 R 263304 W 0 c 139 w 15 I 0 O 5512 L 11.39 10.97 10.81
@#@FSLOADPOST 2024:08:07:11:39:16 mri_normalize N 7 11.59 11.06 10.85
#--------------------------------------------
#@# Skull Stripping 公曆 20廿四年 八月 七日 週三 十一時39分十六秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_em_register -skull nu.mgz
/usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca
transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca'...
GCAread took 0 minutes and 1 seconds.
average std = 23.0   using min determinant for regularization = 52.8
0 singular and 9205 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.9 or > 556.0
total sample mean = 77.3 (1403 zeros)
************************************************
spacing=8, using 3292 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3292, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=16.0
skull bounding box = (50, 54, 18) --> (203, 206, 197)
finding center of left hemi white matter
using (101, 105, 108) as brain centroid of Right_Cerebral_White_Matter...
MRImask(): AllowDiffGeom = 1
mean wm in atlas = 108, using box (82,86,86) --> (119, 123,130) to find MRI
wm
before smoothing, mri peak at 107
robust fit to distribution - 108 +- 4.0
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.374
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.377367 @ (0.000, 0.000, 0.000)
max log p =    -4.320559 @ (-5.263, -5.263, -15.789)
max log p =    -4.259204 @ (2.632, -2.632, 7.895)
max log p =    -4.215544 @ (1.316, -1.316, 1.316)
max log p =    -4.215544 @ (0.000, 0.000, 0.000)
max log p =    -4.210229 @ (0.329, 0.987, -1.645)
max log p =    -4.210229 @ (0.000, 0.000, 0.000)
max log p =    -4.210229 @ (0.000, 0.000, 0.000)
Found translation: (-1.0, -8.2, -8.2): log p = -4.210
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.795, old_max_log_p =-4.210
(thresh=-4.2)
1.07500   0.00000   0.00000  -10.44355;
0.00000   1.13162   0.49132  -79.17023;
0.00000  -0.36573   0.93367   54.67687;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 57 seconds.
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.795, old_max_log_p =-3.795
(thresh=-3.8)
1.07500   0.00000   0.00000  -10.44355;
0.00000   1.13162   0.49132  -79.17023;
0.00000  -0.36573   0.93367   54.67687;
0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
iteration took 0 minutes and 55 seconds.
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.743, old_max_log_p =-3.795
(thresh=-3.8)
1.09516   0.00000   0.00000  -12.98503;
0.00000   1.06935   0.57067  -79.45934;
0.00000  -0.49134   0.91473   73.19285;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 40 seconds.
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.743, old_max_log_p =-3.743
(thresh=-3.7)
1.09516   0.00000   0.00000  -12.98503;
0.00000   1.06935   0.57067  -79.45934;
0.00000  -0.49134   0.91473   73.19285;
0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
iteration took 0 minutes and 40 seconds.
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.728, old_max_log_p =-3.743
(thresh=-3.7)
1.09127   0.00359  -0.00736  -11.66309;
0.00000   1.08237   0.53905  -78.51374;
0.00863  -0.45433   0.92968   65.93478;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 28 seconds.
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.727, old_max_log_p =-3.728
(thresh=-3.7)
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3292 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
nsamples 3292
Quasinewton: input matrix
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) =   -0.0
tol 0.000010
Resulting transform:
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
pass 1, spacing 8: log(p) = -3.727 (old=-4.374)
transform before final EM align:
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 364986 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
nsamples 364986
Quasinewton: input matrix
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) =    4.2
tol 0.000000
final transform:
1.09244   0.01734   0.00925  -15.29819;
-0.01769   1.07340   0.55346  -76.69473;
-0.00029  -0.47254   0.92184   70.62347;
0.00000   0.00000   0.00000   1.00000;
writing output transformation to transforms/talairach_with_skull.lta...
#VMPC# mri_em_register VmPeak  787448
FSRUNTIME@ mri_em_register  0.0787 hours 1 threads
registration took 4 minutes and 43 seconds.
@#@FSTIME  2024:08:07:11:39:16 mri_em_register N 4 e 283.19 S 0.32 U 282.83
P 99% M 628268 F 0 R 166964 W 0 c 871 w 336 I 0 O 32 L 11.59 11.06 10.85
@#@FSLOADPOST 2024:08:07:11:43:59 mri_em_register N 4 10.31 10.67 10.75
mri_watershed -T1 -brain_atlas
/usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode:          T1 normalized volume
Mode:          Use the information of atlas (default parms, --help for
details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=126 y=124 z=106 r=79
first estimation of the main basin volume: 2102595 voxels
Looking for seedpoints
2 found in the cerebellum
16 found in the rest of the brain
global maximum in x=107, y=120, z=69, Imax=255
CSF=14, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done.
Analyze...
main basin size=1800067864817858 voxels, voxel volume =1.000
= 1800067864817858 mmm3 = 1800067904176.128 cm3
done.
PostAnalyze...Basin Prior
7 basins merged thanks to atlas
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=129,y=132, z=111, r=136104
iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL      CSF_MIN=5, CSF_intensity=23, CSF_MAX=41 , nb = 42066
RIGHT_CER    CSF_MIN=6, CSF_intensity=16, CSF_MAX=54 , nb = 2340
LEFT_CER     CSF_MIN=5, CSF_intensity=13, CSF_MAX=76 , nb = 2628
RIGHT_BRAIN   CSF_MIN=6, CSF_intensity=23, CSF_MAX=40 , nb = 17100
LEFT_BRAIN    CSF_MIN=6, CSF_intensity=23, CSF_MAX=39 , nb = 18864
OTHER      CSF_MIN=5, CSF_intensity=10, CSF_MAX=19 , nb = 1134
Problem with the least square interpolation in GM_MIN calculation.
(2) Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX  TRANSITION  GM_MIN  GM
GLOBAL
before analyzing :    41,      37,        31,   64
after  analyzing :    33,      37,        37,   43
RIGHT_CER
before analyzing :    54,      47,        42,   70
after  analyzing :    39,      47,        47,   52
LEFT_CER
before analyzing :    76,      58,        54,   68
after  analyzing :    46,      58,        58,   60
RIGHT_BRAIN
before analyzing :    40,      36,        32,   60
after  analyzing :    32,      36,        36,   42
LEFT_BRAIN
before analyzing :    39,      36,        33,   63
after  analyzing :    32,      36,        36,   42
OTHER
before analyzing :    19,      13,        0,   23
after  analyzing :    13,      21,        25,   22
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...71 iterations
*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 69.593, std = 7.859
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 7.07, sigma = 18.44
after  rotation: sse = 7.07, sigma = 18.44
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is  8.68, its var is 21.07
before Erosion-Dilatation  6.68% 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...36 iterations
mri_strip_skull: done peeling brain
Brain Size = 1598794 voxels, voxel volume = 1.000 mm3
= 1598794 mmm3 = 1598.794 cm3
******************************
Saving brainmask.auto.mgz
done
mri_watershed done
@#@FSTIME  2024:08:07:11:43:59 mri_watershed N 6 e 7.90 S 0.23 U 7.66 P 99%
M 817432 F 0 R 207178 W 0 c 23 w 18 I 0 O 2512 L 10.31 10.67 10.75
@#@FSLOADPOST 2024:08:07:11:44:07 mri_watershed N 6 10.58 10.71 10.76
cp brainmask.auto.mgz brainmask.mgz
Started at 公曆 20廿四年 八月 七日 週三 十一時35分37秒
Ended   at 公曆 20廿四年 八月 七日 週三 十一時44分八秒
#@#%# recon-all-run-time-hours 0.142
recon-all -s 0003 finished without error at 公曆 20廿四年 八月 七日 週三 十
一時44分八秒
#New# invocation of recon-all
公曆 20廿四年 八月 七日 週三 十六時二分48秒
cd /home/chang/GBM_Data/VBG/0003/0003
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
/usr/local/freesurfer/bin/recon-all -autorecon2 -autorecon3 -subjid 0003 -sd
/home/chang/GBM_Data/VBG/0003
subjid 0003
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 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  1048576
memorylocked 16453580 kbytes
maxproc      513872
maxlocks     unlimited
maxsignal    513872
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited
total        used        free      shared  buff/cache
available
Mem:           125Gi        16Gi       2.1Gi       2.4Gi       106Gi
105Gi
Swap:          2.0Gi       2.0Gi       9.0Mi
########################################
program versions used
7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460)
7.4.1
ProgramName: lta_convert  ProgramArguments: lta_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_compute_seg_overlap  ProgramArguments:
mri_compute_seg_overlap -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fuse_segmentations  ProgramArguments:
mri_fuse_segmentations -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_relabel_hypointensities  ProgramArguments:
mri_relabel_hypointensities -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments:
mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_register  ProgramArguments: mri_robust_register
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_template  ProgramArguments: mri_robust_template
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_divide_parcellation  ProgramArguments:
mris_divide_parcellation -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
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Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_left_right_register  ProgramArguments:
mris_left_right_register -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-08:02:48-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_register  ProgramArguments: mris_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
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Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
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Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
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Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
mri_motion_correct.fsl 7.4.1
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-08:02:48-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#-------------------------------------
#@# EM Registration 公曆 20廿四年 八月 七日 週三 十六時二分48秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
/usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'...
GCAread took 0 minutes and 0 seconds.
average std = 7.2   using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 5.9 or > 519.0
total sample mean = 79.1 (1017 zeros)
************************************************
spacing=8, using 2841 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2841, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=27.9
skull bounding box = (60, 67, 28) --> (193, 202, 186)
finding center of left hemi white matter
using (104, 112, 107) as brain centroid of Right_Cerebral_White_Matter...
MRImask(): AllowDiffGeom = 1
mean wm in atlas = 107, using box (88,95,88) --> (120, 128,126) to find MRI
wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.0
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -3.964
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.964348 @ (0.000, 0.000, 0.000)
max log p =    -3.964348 @ (0.000, 0.000, 0.000)
max log p =    -3.881700 @ (-2.632, -7.895, -7.895)
max log p =    -3.839555 @ (1.316, -3.947, 3.947)
max log p =    -3.819631 @ (1.974, 0.658, -1.974)
max log p =    -3.819631 @ (0.000, 0.000, 0.000)
max log p =    -3.819631 @ (0.000, 0.000, 0.000)
max log p =    -3.819631 @ (0.000, 0.000, 0.000)
Found translation: (0.7, -11.2, -5.9): log p = -3.820
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.505, old_max_log_p =-3.820
(thresh=-3.8)
1.00000   0.00000   0.00000   0.65789;
0.00000   0.99317   0.41138  -48.59753;
0.00000  -0.38268   0.92388   59.98476;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 49 seconds.
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.505, old_max_log_p =-3.505
(thresh=-3.5)
1.00000   0.00000   0.00000   0.65789;
0.00000   0.99317   0.41138  -48.59753;
0.00000  -0.38268   0.92388   59.98476;
0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
iteration took 0 minutes and 49 seconds.
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.274, old_max_log_p =-3.505
(thresh=-3.5)
1.03694  -0.01244   0.03027  -7.38578;
0.00000   1.04862   0.43705  -62.05725;
-0.03395  -0.38011   0.92454   61.75311;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 37 seconds.
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.271, old_max_log_p =-3.274
(thresh=-3.3)
1.01692   0.02105   0.04468  -10.66427;
-0.03569   1.05489   0.47456  -62.24167;
-0.03393  -0.41422   0.90974   67.71001;
0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
iteration took 0 minutes and 36 seconds.
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.248, old_max_log_p =-3.271
(thresh=-3.3)
1.01916  -0.01475   0.00985  -2.20046;
0.00538   1.04433   0.48896  -67.64240;
-0.01676  -0.43259   0.90432   68.92675;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 27 seconds.
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.238, old_max_log_p =-3.248
(thresh=-3.2)
1.02154  -0.01478   0.00988  -2.50282;
0.00538   1.04433   0.48896  -67.64240;
-0.01682  -0.43411   0.90750   68.79836;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 26 seconds.
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.235, old_max_log_p =-3.238
(thresh=-3.2)
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
iteration took 0 minutes and 27 seconds.
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.235, old_max_log_p =-3.235
(thresh=-3.2)
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2841 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
nsamples 2841
Quasinewton: input matrix
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) =   -0.0
tol 0.000010
Resulting transform:
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
pass 1, spacing 8: log(p) = -3.235 (old=-3.964)
transform before final EM align:
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 315638 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
nsamples 315638
Quasinewton: input matrix
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) =    3.8
tol 0.000000
final transform:
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
writing output transformation to transforms/talairach.lta...
#VMPC# mri_em_register VmPeak  774892
FSRUNTIME@ mri_em_register  0.0851 hours 1 threads
registration took 5 minutes and 6 seconds.
@#@FSTIME  2024:08:07:16:02:48 mri_em_register N 7 e 306.44 S 0.44 U 305.96
P 99% M 616252 F 0 R 166997 W 0 c 941 w 328 I 2680 O 24 L 9.52 9.39 8.04
@#@FSLOADPOST 2024:08:07:16:07:54 mri_em_register N 7 10.17 9.93 8.69
#--------------------------------------
#@# CA Normalize 公曆 20廿四年 八月 七日 週三 十六時七分54秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz
/usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta
norm.mgz
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=27.9
skull bounding box = (60, 67, 28) --> (193, 202, 186)
finding center of left hemi white matter
using (104, 112, 107) as brain centroid of Right_Cerebral_White_Matter...
mean wm in atlas = 107, using box (88,95,88) --> (120, 128,126) to find MRI
wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.0
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246437 sample points...
INFO: compute sample coordinates transform
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20427;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 40230 control points for structure...
bounding box (128, 69, 33) --> (192, 185, 191)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
1 of 7761 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39478 control points for structure...
bounding box (64, 69, 33) --> (128, 178, 192)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
16 of 7713 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3105 control points for structure...
bounding box (129, 153, 69) --> (176, 195, 120)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 444 (0.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2710 control points for structure...
bounding box (84, 153, 65) --> (128, 194, 120)
Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 525 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3475 control points for structure...
bounding box (111, 139, 98) --> (145, 198, 129)
Brain_Stem: limiting intensities to 88.0 --> 132.0
1 of 886 (0.1%) samples deleted
using 17329 total control points for intensity normalization...
bias field = 0.967 +- 0.057
7 of 17309 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 40230 control points for structure...
bounding box (128, 69, 33) --> (192, 185, 191)
Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
0 of 7938 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39478 control points for structure...
bounding box (64, 69, 33) --> (128, 178, 192)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
15 of 7838 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3105 control points for structure...
bounding box (129, 153, 69) --> (176, 195, 120)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
376 of 522 (72.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2710 control points for structure...
bounding box (84, 153, 65) --> (128, 194, 120)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
224 of 572 (39.2%) samples deleted
finding control points in Brain_Stem....
found 3475 control points for structure...
bounding box (111, 139, 98) --> (145, 198, 129)
Brain_Stem: limiting intensities to 88.0 --> 132.0
491 of 965 (50.9%) samples deleted
using 17835 total control points for intensity normalization...
bias field = 1.042 +- 0.044
11 of 16665 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 40230 control points for structure...
bounding box (128, 69, 33) --> (192, 185, 191)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
1 of 7902 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39478 control points for structure...
bounding box (64, 69, 33) --> (128, 178, 192)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
18 of 7825 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3105 control points for structure...
bounding box (129, 153, 69) --> (176, 195, 120)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
479 of 548 (87.4%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2710 control points for structure...
bounding box (84, 153, 65) --> (128, 194, 120)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
394 of 570 (69.1%) samples deleted
finding control points in Brain_Stem....
found 3475 control points for structure...
bounding box (111, 139, 98) --> (145, 198, 129)
Brain_Stem: limiting intensities to 88.0 --> 132.0
664 of 972 (68.3%) samples deleted
using 17817 total control points for intensity normalization...
bias field = 1.039 +- 0.039
11 of 16171 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 0 minutes and 24 seconds.
@#@FSTIME  2024:08:07:16:07:54 mri_ca_normalize N 8 e 23.65 S 0.40 U 23.24 P
99% M 722960 F 7 R 409562 W 0 c 108 w 9 I 1440 O 3888 L 10.17 9.93 8.69
@#@FSLOADPOST 2024:08:07:16:08:18 mri_ca_normalize N 8 10.15 9.94 8.73
#--------------------------------------
#@# CA Reg 公曆 20廿四年 八月 七日 週三 十六時八分十八秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after
-mask brainmask.mgz norm.mgz
/usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.m3z
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'...
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.156
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.862135
#GCAMreg# pass 0 level1 5 level2 1 tsec 157.725 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.70885
setting smoothness cost coefficient to 0.615
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.71923
#GCAMreg# pass 0 level1 4 level2 1 tsec 70.154 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.685471
setting smoothness cost coefficient to 2.353
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.713559
#GCAMreg# pass 0 level1 3 level2 1 tsec 19.877 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.713559
setting smoothness cost coefficient to 8.000
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.798045
#GCAMreg# pass 0 level1 2 level2 1 tsec 22.471 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.769052
setting smoothness cost coefficient to 20.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.838787
#GCAMreg# pass 0 level1 1 level2 1 tsec 75.023 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.814325
resetting metric properties...
setting smoothness cost coefficient to 40.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.776136
#GCAMreg# pass 0 level1 0 level2 1 tsec 22.574 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.76882
GCAMregister done in 8.1798 min
Starting GCAmapRenormalizeWithAlignment() without scales
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10253 (16)
mri peak = 0.14690 ( 9)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (2277 voxels,
overlap=0.177)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (2277 voxels, peak =
8), gca=7.9
gca peak = 0.17690 (16)
mri peak = 0.19556 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (1742 voxels,
overlap=0.271)
Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (1742 voxels, peak =
7), gca=7.0
gca peak = 0.28275 (96)
mri peak = 0.14301 (103)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (944 voxels, overlap=0.969)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (944 voxels, peak = 102),
gca=102.2
gca peak = 0.18948 (93)
mri peak = 0.10496 (90)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (696 voxels, overlap=0.741)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (696 voxels, peak = 87),
gca=87.0
gca peak = 0.20755 (55)
mri peak = 0.11030 (58)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (866 voxels,
overlap=0.997)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (866 voxels, peak = 56),
gca=56.4
gca peak = 0.31831 (58)
mri peak = 0.09733 (60)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (978 voxels, overlap=0.997)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (978 voxels, peak = 59),
gca=59.4
gca peak = 0.11957 (102)
mri peak = 0.18524 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (56303 voxels,
overlap=0.576)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (56303 voxels,
peak = 103), gca=102.5
gca peak = 0.11429 (102)
mri peak = 0.15206 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60355 voxels,
overlap=0.663)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60355 voxels,
peak = 106), gca=105.6
gca peak = 0.14521 (59)
mri peak = 0.03967 (69)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (22949 voxels,
overlap=0.415)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (22949 voxels, peak =
69), gca=69.3
gca peak = 0.14336 (58)
mri peak = 0.03579 (62)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (24707 voxels,
overlap=0.788)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (24707 voxels, peak =
64), gca=63.5
gca peak = 0.13305 (70)
mri peak = 0.07935 (83)
Right_Caudate (50): linear fit = 1.22 x + 0.0 (704 voxels, overlap=0.141)
Right_Caudate (50): linear fit = 1.22 x + 0.0 (704 voxels, peak = 85),
gca=85.1
gca peak = 0.15761 (71)
mri peak = 0.08252 (72)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (406 voxels, overlap=0.832)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (406 voxels, peak = 71),
gca=71.0
gca peak = 0.13537 (57)
mri peak = 0.07017 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (30580 voxels,
overlap=0.721)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (30580 voxels, peak =
61), gca=60.7
gca peak = 0.13487 (56)
mri peak = 0.08278 (60)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35627 voxels,
overlap=0.745)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35627 voxels, peak
= 60), gca=59.6
gca peak = 0.19040 (84)
mri peak = 0.10666 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (9665 voxels,
overlap=0.798)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (9665 voxels,
peak = 86), gca=86.1
gca peak = 0.18871 (83)
mri peak = 0.13364 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (8255 voxels,
overlap=0.633)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (8255 voxels,
peak = 86), gca=85.9
gca peak = 0.24248 (57)
mri peak = 0.09535 (63)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (407 voxels, overlap=0.730)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (407 voxels, peak = 64),
gca=63.6
gca peak = 0.35833 (56)
mri peak = 0.15581 (63)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (401 voxels, overlap=0.912)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (401 voxels, peak = 59),
gca=58.5
gca peak = 0.12897 (85)
mri peak = 0.07222 (82)
Left_Thalamus (10): linear fit = 0.95 x + 0.0 (4765 voxels, overlap=0.872)
Left_Thalamus (10): linear fit = 0.95 x + 0.0 (4765 voxels, peak = 81),
gca=81.2
gca peak = 0.13127 (83)
mri peak = 0.06447 (80)
Right_Thalamus (49): linear fit = 1.02 x + 0.0 (3754 voxels, overlap=0.781)
Right_Thalamus (49): linear fit = 1.02 x + 0.0 (3754 voxels, peak = 85),
gca=85.1
gca peak = 0.12974 (78)
mri peak = 0.11335 (77)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2437 voxels, overlap=0.890)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2437 voxels, peak = 78),
gca=77.6
gca peak = 0.17796 (79)
mri peak = 0.09759 (81)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2271 voxels, overlap=0.938)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2271 voxels, peak = 83),
gca=82.6
gca peak = 0.10999 (80)
mri peak = 0.09912 (86)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11457 voxels, overlap=0.415)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11457 voxels, peak = 88),
gca=87.6
gca peak = 0.13215 (88)
mri peak = 0.09140 (92)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1130 voxels, overlap=0.651)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1130 voxels, peak = 94),
gca=93.7
gca peak = 0.11941 (89)
mri peak = 0.08212 (92)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1288 voxels, overlap=0.667)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1288 voxels, peak = 92),
gca=92.1
gca peak = 0.20775 (25)
mri peak = 0.11252 ( 7)
Third_Ventricle (14): linear fit = 0.25 x + 0.0 (65 voxels, overlap=0.102)
Third_Ventricle (14): linear fit = 0.25 x + 0.0 (65 voxels, peak =  6),
gca=6.4
gca peak = 0.13297 (21)
mri peak = 0.13733 ( 7)
Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (213 voxels, overlap=0.018)
Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (213 voxels, peak =  8),
gca=8.1
gca peak Unknown = 0.94777 ( 0)
gca peak Left_Inf_Lat_Vent = 0.19087 (28)
gca peak Third_Ventricle = 0.20775 (25)
gca peak Fourth_Ventricle = 0.13297 (21)
gca peak CSF = 0.16821 (33)
gca peak Left_Accumbens_area = 0.32850 (63)
gca peak Left_undetermined = 0.98480 (28)
gca peak Left_vessel = 0.40887 (53)
gca peak Left_choroid_plexus = 0.10898 (46)
gca peak Right_Inf_Lat_Vent = 0.17798 (26)
gca peak Right_Accumbens_area = 0.30137 (64)
gca peak Right_vessel = 0.47828 (52)
gca peak Right_choroid_plexus = 0.11612 (45)
gca peak Fifth_Ventricle = 0.59466 (35)
gca peak WM_hypointensities = 0.10053 (78)
gca peak non_WM_hypointensities = 0.07253 (60)
gca peak Optic_Chiasm = 0.25330 (73)
not using caudate to estimate GM means
estimating mean gm scale to be 1.08 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.47 x + 0.0
Right_Pallidum too bright - rescaling by 0.987 (from 1.065) to 100.9 (was
102.2)
saving intensity scales to talairach.label_intensities.txt
GCAmapRenormalizeWithAlignment() took 2.21097 min
noneg pre
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.008
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.78411
#GCAMreg# pass 0 level1 5 level2 1 tsec 446.91 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.665738
setting smoothness cost coefficient to 0.031
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.667395
#GCAMreg# pass 0 level1 4 level2 1 tsec 546.396 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.558268
setting smoothness cost coefficient to 0.118
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.567172
#GCAMreg# pass 0 level1 3 level2 1 tsec 354.328 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.503775
setting smoothness cost coefficient to 0.400
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.533912
#GCAMreg# pass 0 level1 2 level2 1 tsec 23.345 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.533912
setting smoothness cost coefficient to 1.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.594148
#GCAMreg# pass 0 level1 1 level2 1 tsec 22.356 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.588558
resetting metric properties...
setting smoothness cost coefficient to 2.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.517738
#GCAMreg# pass 0 level1 0 level2 1 tsec 147.863 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.484766
GCAMregister done in 29.1524 min
********************* ALLOWING NEGATIVE NODES IN
DEFORMATION********************************
noneg post
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.008
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.479493
#GCAMreg# pass 0 level1 5 level2 1 tsec 31.484 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.479148
setting smoothness cost coefficient to 0.031
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.478289
#GCAMreg# pass 0 level1 4 level2 1 tsec 65.489 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.47259
setting smoothness cost coefficient to 0.118
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.471451
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 4 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 2
after 10 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 2
after 4 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 4 iterations, nbhd size=0, neg = 0
#GCAMreg# pass 0 level1 3 level2 1 tsec 109.649 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.45082
setting smoothness cost coefficient to 0.400
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.451489
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
#GCAMreg# pass 0 level1 2 level2 1 tsec 27.467 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.451021
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 7
after 11 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 11
after 9 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 16
after 9 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 5
after 15 iterations, nbhd size=1, neg = 0
setting smoothness cost coefficient to 1.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.444784
#GCAMreg# pass 0 level1 1 level2 1 tsec 22.261 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.444784
resetting metric properties...
setting smoothness cost coefficient to 2.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.434819
iter 0, gcam->neg = 897
after 16 iterations, nbhd size=1, neg = 0
#GCAMreg# pass 0 level1 0 level2 1 tsec 29.726 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.407536
label assignment complete, 0 changed (0.00%)
GCAMregister done in 8.63605 min
Starting GCAMcomputeMaxPriorLabels()
Morphing with label term set to 0 *******************************
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.008
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.392331
#GCAMreg# pass 0 level1 5 level2 1 tsec 29.524 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.392311
setting smoothness cost coefficient to 0.031
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.392489
#GCAMreg# pass 0 level1 4 level2 1 tsec 28.203 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.392404
setting smoothness cost coefficient to 0.118
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.391893
iter 0, gcam->neg = 6
after 12 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 6
after 18 iterations, nbhd size=1, neg = 0
#GCAMreg# pass 0 level1 3 level2 1 tsec 33.347 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.390868
iter 0, gcam->neg = 3
after 14 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 3
after 8 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 5
after 9 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 7
after 11 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 8
after 10 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 11
after 13 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 14
after 3 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 8
after 8 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 6
after 11 iterations, nbhd size=1, neg = 0
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
setting smoothness cost coefficient to 0.400
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.38812
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
iter 0, gcam->neg = 1
after 4 iterations, nbhd size=0, neg = 0
#GCAMreg# pass 0 level1 2 level2 1 tsec 26.646 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.387981
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
setting smoothness cost coefficient to 1.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.395159
#GCAMreg# pass 0 level1 1 level2 1 tsec 12.209 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.395159
resetting metric properties...
setting smoothness cost coefficient to 2.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.382976
iter 0, gcam->neg = 650
after 16 iterations, nbhd size=1, neg = 0
#GCAMreg# pass 0 level1 0 level2 1 tsec 29.431 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500,
lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.374793
GCAMregister done in 6.49038 min
writing output transformation to transforms/talairach.m3z...
GCAMwrite
Calls to gcamLogLikelihoodEnergy 4055 tmin = 7.30365
Calls to gcamLabelEnergy         3476 tmin = 0.91955
Calls to gcamJacobianEnergy      4055 tmin = 3.97043
Calls to gcamSmoothnessEnergy    4055 tmin = 6.14948
Calls to gcamLogLikelihoodTerm 617 tmin = 2.5833
Calls to gcamLabelTerm         561 tmin = 3.50685
Calls to gcamJacobianTerm      617 tmin = 4.49898
Calls to gcamSmoothnessTerm    617 tmin = 1.59493
Calls to gcamComputeGradient    617 tmin = 20.6902
Calls to gcamComputeMetricProperties    5875 tmin = 7.28873
mri_ca_register took 0 hours, 54 minutes and 48 seconds.
#VMPC# mri_ca_register VmPeak  2022280
FSRUNTIME@ mri_ca_register  0.9133 hours 1 threads
@#@FSTIME  2024:08:07:16:08:18 mri_ca_register N 9 e 3287.95 S 1.31 U
3286.43 P 99% M 1330876 F 14 R 1134411 W 0 c 10171 w 424 I 2296 O 62816 L
10.15 9.94 8.73
@#@FSLOADPOST 2024:08:07:17:03:06 mri_ca_register N 9 11.78 10.80 10.55
#--------------------------------------
#@# SubCort Seg 公曆 20廿四年 八月 七日 週三 十七時三分六秒
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz
transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2020-01-02.gca
aseg.auto_noCCseg.mgz
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz
transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2020-01-02.gca
aseg.auto_noCCseg.mgz
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
== Number of threads available to for OpenMP = 1 ==
reading 1 input volumes
reading classifier array from
/usr/local/freesurfer/average/RB_all_2020-01-02.gca
reading input volume from norm.mgz
average std[0] = 7.2
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.75
Atlas used for the 3D morph was
/usr/local/freesurfer/average/RB_all_2020-01-02.gca
average std = 7.2   using min determinant for regularization = 5.2
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15521 (20)
mri peak = 0.14123 ( 9)
Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (8168 voxels,
overlap=0.092)
Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (8168 voxels, peak =
12), gca=12.1
gca peak = 0.20380 (13)
mri peak = 0.20590 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (7768 voxels,
overlap=0.406)
Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (7768 voxels, peak =
7), gca=7.2
gca peak = 0.26283 (96)
mri peak = 0.15139 (103)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (720 voxels, overlap=0.941)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (720 voxels, peak = 102),
gca=102.2
gca peak = 0.15814 (97)
mri peak = 0.11044 (90)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (499 voxels, overlap=0.731)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (499 voxels, peak = 93),
gca=92.6
gca peak = 0.27624 (56)
mri peak = 0.10739 (57)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1209 voxels,
overlap=1.009)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1209 voxels, peak = 57),
gca=57.4
gca peak = 0.28723 (59)
mri peak = 0.10453 (60)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1146 voxels,
overlap=1.009)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1146 voxels, peak = 60),
gca=60.5
gca peak = 0.07623 (103)
mri peak = 0.23320 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40003 voxels,
overlap=0.571)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40003 voxels,
peak = 102), gca=102.5
gca peak = 0.07837 (105)
mri peak = 0.17446 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33779 voxels,
overlap=0.618)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33779 voxels,
peak = 104), gca=104.5
gca peak = 0.10165 (58)
mri peak = 0.04919 (69)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (33492 voxels,
overlap=0.282)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (33492 voxels, peak =
69), gca=68.7
gca peak = 0.11113 (58)
mri peak = 0.04487 (65)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (29706 voxels,
overlap=0.747)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (29706 voxels, peak =
64), gca=63.5
gca peak = 0.27796 (67)
mri peak = 0.08893 (72)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (1095 voxels, overlap=0.527)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (1095 voxels, peak = 73),
gca=73.4
gca peak = 0.14473 (69)
mri peak = 0.07841 (73)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1024 voxels, overlap=0.920)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1024 voxels, peak = 71),
gca=71.4
gca peak = 0.14301 (56)
mri peak = 0.09727 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (30241 voxels,
overlap=0.736)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (30241 voxels, peak =
60), gca=59.6
gca peak = 0.14610 (55)
mri peak = 0.11156 (60)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (29541 voxels,
overlap=0.746)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (29541 voxels, peak
= 59), gca=58.6
gca peak = 0.16309 (85)
mri peak = 0.17077 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4606 voxels,
overlap=0.819)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4606 voxels,
peak = 86), gca=86.3
gca peak = 0.15172 (84)
mri peak = 0.18225 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4821 voxels,
overlap=0.588)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4821 voxels,
peak = 86), gca=86.1
gca peak = 0.30461 (58)
mri peak = 0.17276 (64)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (411 voxels, overlap=0.502)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (411 voxels, peak = 64),
gca=63.5
gca peak = 0.32293 (57)
mri peak = 0.17013 (63)
Right_Amygdala (54): linear fit = 1.07 x + 0.0 (529 voxels, overlap=0.607)
Right_Amygdala (54): linear fit = 1.07 x + 0.0 (529 voxels, peak = 61),
gca=60.7
gca peak = 0.11083 (90)
mri peak = 0.08271 (82)
Left_Thalamus (10): linear fit = 0.95 x + 0.0 (3762 voxels, overlap=0.917)
Left_Thalamus (10): linear fit = 0.95 x + 0.0 (3762 voxels, peak = 86),
gca=85.9
gca peak = 0.11393 (83)
mri peak = 0.06745 (86)
Right_Thalamus (49): linear fit = 1.03 x + 0.0 (2955 voxels, overlap=0.857)
Right_Thalamus (49): linear fit = 1.03 x + 0.0 (2955 voxels, peak = 86),
gca=85.9
gca peak = 0.08575 (81)
mri peak = 0.11198 (77)
Left_Putamen (12): linear fit = 0.98 x + 0.0 (1403 voxels, overlap=0.809)
Left_Putamen (12): linear fit = 0.98 x + 0.0 (1403 voxels, peak = 79),
gca=79.0
gca peak = 0.08618 (78)
mri peak = 0.10561 (81)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (1640 voxels, overlap=0.877)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (1640 voxels, peak = 79),
gca=79.2
gca peak = 0.08005 (78)
mri peak = 0.09765 (86)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (11171 voxels, overlap=0.491)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (11171 voxels, peak = 83),
gca=83.1
gca peak = 0.12854 (88)
mri peak = 0.08520 (95)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1008 voxels, overlap=0.782)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1008 voxels, peak = 94),
gca=93.7
gca peak = 0.15703 (87)
mri peak = 0.07869 (93)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1072 voxels, overlap=0.781)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1072 voxels, peak = 93),
gca=92.7
gca peak = 0.17522 (25)
mri peak = 0.10934 (11)
Third_Ventricle (14): linear fit = 0.40 x + 0.0 (172 voxels, overlap=0.118)
Third_Ventricle (14): linear fit = 0.40 x + 0.0 (172 voxels, peak = 10),
gca=9.9
gca peak = 0.17113 (14)
mri peak = 0.15791 ( 7)
Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (180 voxels, overlap=0.087)
Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (180 voxels, peak =  6),
gca=6.0
gca peak Unknown = 0.94777 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16627 (28)
gca peak Third_Ventricle = 0.17522 (25)
gca peak Fourth_Ventricle = 0.17113 (14)
gca peak CSF = 0.20346 (36)
gca peak Left_Accumbens_area = 0.70646 (62)
gca peak Left_undetermined = 1.00000 (28)
gca peak Left_vessel = 0.89917 (53)
gca peak Left_choroid_plexus = 0.11689 (35)
gca peak Right_Inf_Lat_Vent = 0.25504 (23)
gca peak Right_Accumbens_area = 0.31650 (65)
gca peak Right_vessel = 0.77268 (52)
gca peak Right_choroid_plexus = 0.13275 (38)
gca peak Fifth_Ventricle = 0.60973 (33)
gca peak WM_hypointensities = 0.11013 (77)
gca peak non_WM_hypointensities = 0.11354 (41)
gca peak Optic_Chiasm = 0.51646 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.08 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.58 x + 0.0
Right_Pallidum too bright - rescaling by 0.982 (from 1.065) to 100.4 (was
102.2)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.21508 (11)
mri peak = 0.14123 ( 9)
Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (8168 voxels,
overlap=0.913)
Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (8168 voxels, peak =
11), gca=11.5
gca peak = 0.25554 ( 7)
mri peak = 0.20590 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (7768 voxels,
overlap=0.801)
Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (7768 voxels, peak =
7), gca=6.6
gca peak = 0.21127 (97)
mri peak = 0.15139 (103)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (720 voxels, overlap=1.004)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (720 voxels, peak = 97),
gca=97.5
gca peak = 0.18013 (92)
mri peak = 0.11044 (90)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (499 voxels, overlap=0.857)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (499 voxels, peak = 93),
gca=93.4
gca peak = 0.30247 (57)
mri peak = 0.10739 (57)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1209 voxels,
overlap=1.008)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1209 voxels, peak = 57),
gca=57.0
gca peak = 0.33035 (58)
mri peak = 0.10453 (60)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1146 voxels,
overlap=1.004)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1146 voxels, peak = 57),
gca=57.1
gca peak = 0.08114 (103)
mri peak = 0.23320 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40003 voxels,
overlap=0.568)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40003 voxels,
peak = 102), gca=102.5
gca peak = 0.08124 (104)
mri peak = 0.17446 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33779 voxels,
overlap=0.597)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33779 voxels,
peak = 103), gca=103.5
gca peak = 0.08546 (69)
mri peak = 0.04919 (69)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (33492 voxels,
overlap=0.913)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (33492 voxels, peak =
68), gca=68.0
gca peak = 0.10313 (64)
mri peak = 0.04487 (65)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (29706 voxels,
overlap=0.956)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (29706 voxels, peak =
66), gca=65.6
gca peak = 0.22760 (73)
mri peak = 0.08893 (72)
Right_Caudate (50): linear fit = 1.03 x + 0.0 (1095 voxels, overlap=0.796)
Right_Caudate (50): linear fit = 1.03 x + 0.0 (1095 voxels, peak = 76),
gca=75.6
gca peak = 0.12384 (71)
mri peak = 0.07841 (73)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1024 voxels, overlap=0.842)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1024 voxels, peak = 71),
gca=71.0
gca peak = 0.13024 (60)
mri peak = 0.09727 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30241 voxels,
overlap=0.915)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30241 voxels, peak =
62), gca=61.5
gca peak = 0.14380 (59)
mri peak = 0.11156 (60)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29541 voxels,
overlap=0.937)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29541 voxels, peak
= 60), gca=60.5
gca peak = 0.15848 (86)
mri peak = 0.17077 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4606 voxels,
overlap=0.884)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4606 voxels,
peak = 86), gca=85.6
gca peak = 0.15314 (86)
mri peak = 0.18225 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4821 voxels,
overlap=0.758)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4821 voxels,
peak = 86), gca=85.6
gca peak = 0.23055 (63)
mri peak = 0.17276 (64)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (411 voxels, overlap=1.000)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (411 voxels, peak = 64),
gca=63.9
gca peak = 0.32741 (61)
mri peak = 0.17013 (63)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (529 voxels, overlap=1.003)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (529 voxels, peak = 62),
gca=61.9
gca peak = 0.12181 (86)
mri peak = 0.08271 (82)
Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3762 voxels, overlap=0.967)
Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3762 voxels, peak = 86),
gca=85.6
gca peak = 0.10629 (86)
mri peak = 0.06745 (86)
Right_Thalamus (49): linear fit = 1.00 x + 0.0 (2955 voxels, overlap=0.919)
Right_Thalamus (49): linear fit = 1.00 x + 0.0 (2955 voxels, peak = 86),
gca=85.6
gca peak = 0.08843 (77)
mri peak = 0.11198 (77)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1403 voxels, overlap=0.847)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1403 voxels, peak = 77),
gca=77.0
gca peak = 0.08736 (77)
mri peak = 0.10561 (81)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1640 voxels, overlap=0.944)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1640 voxels, peak = 77),
gca=77.0
gca peak = 0.07578 (86)
mri peak = 0.09765 (86)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (11171 voxels, overlap=0.699)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (11171 voxels, peak = 85),
gca=84.7
gca peak = 0.12327 (95)
mri peak = 0.08520 (95)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1008 voxels, overlap=0.860)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1008 voxels, peak = 96),
gca=96.4
gca peak = 0.14047 (91)
mri peak = 0.07869 (93)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1072 voxels, overlap=0.907)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1072 voxels, peak = 91),
gca=91.0
gca peak = 0.30661 (15)
mri peak = 0.10934 (11)
Third_Ventricle (14): linear fit = 0.69 x + 0.0 (172 voxels, overlap=1.028)
Third_Ventricle (14): linear fit = 0.69 x + 0.0 (172 voxels, peak = 10),
gca=10.3
gca peak = 0.29372 ( 9)
mri peak = 0.15791 ( 7)
Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (180 voxels, overlap=0.850)
Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (180 voxels, peak =  7),
gca=6.7
gca peak Unknown = 0.94777 ( 0)
gca peak Left_Inf_Lat_Vent = 0.21552 (29)
gca peak CSF = 0.33827 (21)
gca peak Left_Accumbens_area = 0.51915 (65)
gca peak Left_undetermined = 1.00000 (28)
gca peak Left_vessel = 0.89917 (53)
gca peak Left_choroid_plexus = 0.11689 (35)
gca peak Right_Inf_Lat_Vent = 0.27120 (24)
gca peak Right_Accumbens_area = 0.29187 (71)
gca peak Right_vessel = 0.77268 (52)
gca peak Right_choroid_plexus = 0.13275 (38)
gca peak Fifth_Ventricle = 0.73434 (19)
gca peak WM_hypointensities = 0.12365 (76)
gca peak non_WM_hypointensities = 0.08214 (41)
gca peak Optic_Chiasm = 0.51663 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.86 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to
aseg.auto_noCCseg.label_intensities.txt
37799 voxels changed in iteration 0 of unlikely voxel relabeling
247 voxels changed in iteration 1 of unlikely voxel relabeling
144 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
35863 gm and wm labels changed (%28 to gray, %72 to white out of all changed
labels)
377 hippocampal voxels changed.
1 amygdala voxels changed.
Reclassifying using Gibbs Priors
pass 1: 59580 changed. image ll: -2.100, PF=0.500
pass 2: 13570 changed. image ll: -2.100, PF=0.500
pass 3: 4116 changed.
29172 voxels changed in iteration 0 of unlikely voxel relabeling
254 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6910 voxels changed in iteration 0 of unlikely voxel relabeling
65 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
6614 voxels changed in iteration 0 of unlikely voxel relabeling
62 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6156 voxels changed in iteration 0 of unlikely voxel relabeling
39 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
!!!!!!!!! ventricle segment 1 with volume 22600 above threshold 100 - not
erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 0 with volume 327 above threshold 100 - not
erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 2 with volume 280 above threshold 100 - not
erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 0 with volume 281 above threshold 100 - not
erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 1 with volume 21080 above threshold 100 - not
erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 0 with volume 917 above threshold 100 - not
erasing !!!!!!!!!!
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    986.315517
mri_ca_label stimesec    1.031911
mri_ca_label ru_maxrss   2095812
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   1025163
mri_ca_label ru_majflt   13
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  2088
mri_ca_label ru_oublock  712
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    177
mri_ca_label ru_nivcsw   2964
mri_ca_label took 16 minutes and 27 seconds.
mri_ca_label done
@#@FSTIME  2024:08:07:17:03:06 mri_ca_label N 10 e 987.51 S 1.10 U 986.31 P
99% M 2095812 F 13 R 1025168 W 0 c 2965 w 178 I 2088 O 712 L 11.78 10.80 10.
55
@#@FSLOADPOST 2024:08:07:17:19:34 mri_ca_label N 10 10.07 10.34 10.44
#--------------------------------------
#@# CC Seg 公曆 20廿四年 八月 七日 週三 十七時十九分34秒
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/cc_up.lta 0003
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/cc_up.lta
reading aseg from
/home/chang/GBM_Data/VBG/0003/0003/mri/aseg.auto_noCCseg.mgz
reading norm from /home/chang/GBM_Data/VBG/0003/0003/mri/norm.mgz
18173 voxels in left wm, 21786 in right wm, xrange [123, 129]
searching rotation angles z=[-6  8], y=[-8  6]
searching scale 1 Z rot -6.3
searching scale 1 Z rot -6.1
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.6
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.1
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.6
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.1
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.6
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.1
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.7
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.7
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.7
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.7
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.7
searching scale 1 Z rot 4.9
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.4
searching scale 1 Z rot 5.7
searching scale 1 Z rot 5.9
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.4
searching scale 1 Z rot 6.7
searching scale 1 Z rot 6.9
searching scale 1 Z rot 7.2
searching scale 1 Z rot 7.4  global minimum found at slice 125.4, rotations
(-0.63, 0.68)
final transformation (x=125.4, yr=-0.629, zr=0.683):
0.99987  -0.01192  -0.01098   4.93699;
0.01192   0.99993  -0.00013   12.52455;
0.01098  -0.00000   0.99994   41.62889;
0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 131] in xformed coordinates
best xformed slice 128
min_x_fornix = 137
min_x_fornix = 137
min_x_fornix = 137
min_x_fornix = 137
min_x_fornix = 137
cc center is found at 128 114 85
eigenvectors:
0.00079   0.00244   1.00000;
-0.23427  -0.97217   0.00256;
0.97217  -0.23427  -0.00020;
error in mid anterior detected - correcting...
writing aseg with callosum to
/home/chang/GBM_Data/VBG/0003/0003/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.2 minutes
#VMPC# mri_cc VmPeak  436900
mri_cc done
@#@FSTIME  2024:08:07:17:19:34 mri_cc N 7 e 12.01 S 0.22 U 11.78 P 99% M
343560 F 8 R 277682 W 0 c 50 w 8 I 1336 O 696 L 10.07 10.34 10.44
@#@FSLOADPOST 2024:08:07:17:19:46 mri_cc N 7 9.97 10.31 10.43
#--------------------------------------
#@# Merge ASeg 公曆 20廿四年 八月 七日 週三 十七時十九分46秒
cp aseg.auto.mgz aseg.presurf.mgz
#--------------------------------------------
#@# Intensity Normalization2 公曆 20廿四年 八月 七日 週三 十七時十九分46秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz
norm.mgz brain.mgz
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src from norm.mgz...
Reading aseg aseg.presurf.mgz
aseg read with width 256 (src width 256)
************** resampling aseg to account for mismatch with source image
***************
normalizing image...
NOT doing gentle normalization with control points/label
processing with aseg
removing outliers in the aseg WM...
379 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 69 (69), valley at 37 (37)
csf peak at 34, setting threshold to 57
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 71 (71), valley at 38 (38)
csf peak at 36, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 0 minutes and 59 seconds.
@#@FSTIME  2024:08:07:17:19:46 mri_normalize N 9 e 61.80 S 0.67 U 61.12 P
99% M 1200992 F 0 R 665514 W 0 c 202 w 14 I 8 O 2520 L 9.97 10.31 10.43
@#@FSLOADPOST 2024:08:07:17:20:47 mri_normalize N 9 9.05 9.95 10.30
#--------------------------------------------
#@# Mask BFS 公曆 20廿四年 八月 七日 週三 十七時廿分47秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
DoAbs = 0
Found 1588968 voxels in mask (pct=  9.47)
maskval=0, outval=0
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2024:08:07:17:20:47 mri_mask N 5 e 0.61 S 0.01 U 0.59 P 99% M
74240 F 6 R 17283 W 0 c 4 w 7 I 1056 O 2512 L 9.05 9.95 10.30
@#@FSLOADPOST 2024:08:07:17:20:48 mri_mask N 5 9.05 9.95 10.30
cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
#--------------------------------------------
#@# WM Segmentation 公曆 20廿四年 八月 七日 週三 十七時廿分48秒
AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz
@#@FSTIME  2024:08:07:17:20:48 AntsDenoiseImageFs N 4 e 14.63 S 0.09 U 14.53
P 99% M 350720 F 23 R 86513 W 0 c 88 w 23 I 4928 O 2560 L 9.05 9.95 10.30
@#@FSLOADPOST 2024:08:07:17:21:03 AntsDenoiseImageFs N 4 9.28 9.95 10.29
mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz
wsizemm = 13, voxres = 1, wsize = 13
Widening wm low from 89 to 79
assuming input volume is MGH (Van der Kouwe) MP-RAGE
wm mean:  110
wsize:    13
wm low:   79
wm hi:    125
gray low: 30
gray hi:  99
Doing initial trinary intensity segmentation
MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99
white = 373563, nonwhite = 16121213, ambig = 282440, nmask = 0
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (104.0): 103.7 +- 5.7 [79.0 --> 125.0]
CCS GM (71.0) : 69.8 +- 11.3 [30.0 --> 95.0]
white_mean 103.715
white_sigma 5.70945
gray_mean 69.7889
gray_sigma 11.2917
setting bottom of white matter range wm_low to 81.1
setting top of gray matter range gray_hi to 92.4
wm_low 81.0806
wm_hi  125
gray_low 30
gray_hi  92.3723
Redoing initial intensity segmentation...
MRIintensitySegmentation() wm_low=81.0806, wm_hi=125, gray_hi=92.3723
white = 457273, nonwhite = 16173821, ambig = 146122, nmask = 0
Recomputing local statistics to label ambiguous voxels...
wm_low 81.0806
wm_hi  125
gray_low 30
gray_hi  92.3723
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 92.3723, wm_low = 81.0806
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=92.3723, wmlow=81.0806
135314 voxels processed (0.81%)
64383 voxels white (0.38%)
70931 voxels non-white (0.42%)
Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=76.0806, gray_hi=92.3723, wsize=13
237738 voxels tested (1.42%)
45308 voxels changed (0.27%)
50480 multi-scale searches  (0.30%)
Recovering bright white
MRIrecoverBrightWhite()
wm_low 81.0806
wm_hi 125
slack 5.70945
pct_thresh 0.33
intensity_thresh 130.709
nvox_thresh 8.58
368 voxels tested (0.00%)
325 voxels changed (0.00%)
removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=76.0806, hithr=92.3723
smoothing input volume with sigma = 0.250
93133 voxels tested (0.56%)
18543 voxels changed (0.11%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
1044 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
1070 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
20 segments, 2194 filled
MRIfindBrightNonWM(): 889 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 0.5 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2024:08:07:17:21:03 mri_segment N 5 e 29.43 S 0.20 U 29.22 P 99%
M 143024 F 7 R 295539 W 0 c 110 w 7 I 1056 O 816 L 9.28 9.95 10.29
@#@FSLOADPOST 2024:08:07:17:21:32 mri_segment N 5 9.34 9.91 10.27
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz
wm.asegedit.mgz
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz
wm.asegedit.mgz
preserving editing changes in input volume...
auto filling took 0.22 minutes
reading wm segmentation from wm.seg.mgz...
0 voxels added to wm to prevent paths from MTL structures to cortex
5212 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 93917 voxels turned on, 31197 voxels turned off.
propagating editing to output volume from wm.seg.mgz
writing edited volume to wm.asegedit.mgz....
@#@FSTIME  2024:08:07:17:21:32 mri_edit_wm_with_aseg N 5 e 13.50 S 0.23 U
13.27 P 99% M 463900 F 5 R 315082 W 0 c 42 w 6 I 960 O 760 L 9.34 9.91 10.27
@#@FSLOADPOST 2024:08:07:17:21:46 mri_edit_wm_with_aseg N 5 9.81 10.00 10.29
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1
pass   1 (xy+):  20 found -  20 modified     |    TOTAL:  20
pass   2 (xy+):   0 found -  20 modified     |    TOTAL:  20
pass   1 (xy-):   9 found -   9 modified     |    TOTAL:  29
pass   2 (xy-):   0 found -   9 modified     |    TOTAL:  29
pass   1 (yz+):  14 found -  14 modified     |    TOTAL:  43
pass   2 (yz+):   0 found -  14 modified     |    TOTAL:  43
pass   1 (yz-):  19 found -  19 modified     |    TOTAL:  62
pass   2 (yz-):   0 found -  19 modified     |    TOTAL:  62
pass   1 (xz+):  15 found -  15 modified     |    TOTAL:  77
pass   2 (xz+):   0 found -  15 modified     |    TOTAL:  77
pass   1 (xz-):  12 found -  12 modified     |    TOTAL:  89
pass   2 (xz-):   0 found -  12 modified     |    TOTAL:  89
Iteration Number : 1
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 (+++):   4 found -   4 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   8
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  14
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  14
Iteration Number : 1
pass   1 (++):  24 found -  24 modified     |    TOTAL:  24
pass   2 (++):   0 found -  24 modified     |    TOTAL:  24
pass   1 (+-):  14 found -  14 modified     |    TOTAL:  38
pass   2 (+-):   0 found -  14 modified     |    TOTAL:  38
pass   1 (--):  17 found -  17 modified     |    TOTAL:  55
pass   2 (--):   0 found -  17 modified     |    TOTAL:  55
pass   1 (-+):   9 found -   9 modified     |    TOTAL:  64
pass   2 (-+):   0 found -   9 modified     |    TOTAL:  64
Iteration Number : 2
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+):   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 : 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 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
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 = 174 (out of 573424: 0.030344)
binarizing input wm segmentation...
Ambiguous edge configurations...
mri_pretess done
@#@FSTIME  2024:08:07:17:21:46 mri_pretess N 4 e 1.49 S 0.01 U 1.47 P 99% M
56832 F 19 R 12964 W 0 c 6 w 18 I 4128 O 760 L 9.81 10.00 10.29
@#@FSLOADPOST 2024:08:07:17:21:47 mri_pretess N 4 10.07 10.05 10.31
#--------------------------------------------
#@# Fill 公曆 20廿四年 八月 七日 週三 十七時廿一分47秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.presurf.mgz -ctab
/usr/local/freesurfer/SubCorticalMassLUT.txt wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.presurf.mgz...
done.
searching for cutting planes...voxel to talairach voxel transform
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20425;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
reading input volume... wm.mgzvoxel to talairach voxel transform
1.02154  -0.01478   0.00988  -2.50282;
0.00536   1.04188   0.48781  -67.20425;
-0.01686  -0.43513   0.90963   68.71252;
0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.presurf.mgz
removing CC from segmentation
Looking for area (min, max) = (350, 1400)
area[0] = 1581 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max =
0.75)
need search nearby
using seed (125, 109, 88), TAL = (3.0, -40.0, 19.0)
talairach voxel to voxel transform
0.97863   0.00772  -0.01477   3.98269;
-0.01106   0.78408  -0.42036   81.55042;
0.01285   0.37522   0.89799  -36.45474;
0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (125,  109,  88) --> (3.0, -40.0, 19.0)
done.
filling took 0.6 minutes
talairach cc position changed to (3.00, -40.00, 19.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, -40.00, 19.00) SRC:
(108.24, 128.84, 84.84)
search lh wm seed point around talairach space (-15.00, -40.00, 19.00), SRC:
(143.47, 128.44, 85.31)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram for separating WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
Embedding colortable
mri_fill done, writing output to filled.mgz...
@#@FSTIME  2024:08:07:17:21:47 mri_fill N 10 e 34.39 S 0.55 U 33.84 P 99% M
967712 F 8 R 512484 W 0 c 158 w 8 I 1440 O 264 L 10.07 10.05 10.31
@#@FSLOADPOST 2024:08:07:17:22:22 mri_fill N 10 10.68 10.21 10.35
cp filled.mgz filled.auto.mgz
#--------------------------------------------
#@# Tessellate lh 公曆 20廿四年 八月 七日 週三 十七時廿二分廿二秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz
../mri/filled-pretess255.mgz
Iteration Number : 1
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+):   5 found -   5 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   5 modified     |    TOTAL:   7
pass   1 (yz-):   6 found -   6 modified     |    TOTAL:  13
pass   2 (yz-):   0 found -   6 modified     |    TOTAL:  13
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  15
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  15
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  16
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  16
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 (--):   2 found -   2 modified     |    TOTAL:   3
pass   2 (--):   0 found -   2 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+):   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 = 19 (out of 280395: 0.006776)
Ambiguous edge configurations...
mri_pretess done
@#@FSTIME  2024:08:07:17:22:22 mri_pretess N 4 e 0.85 S 0.00 U 0.84 P 99% M
40448 F 0 R 8833 W 0 c 4 w 0 I 0 O 256 L 10.68 10.21 10.35
@#@FSLOADPOST 2024:08:07:17:22:22 mri_pretess N 4 10.68 10.21 10.35
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
7.4.1
7.4.1
slice 40: 3157 vertices, 3372 faces
slice 50: 11715 vertices, 12071 faces
slice 60: 23505 vertices, 23965 faces
slice 70: 36140 vertices, 36564 faces
slice 80: 47809 vertices, 48236 faces
slice 90: 59176 vertices, 59577 faces
slice 100: 70387 vertices, 70817 faces
slice 110: 81044 vertices, 81462 faces
slice 120: 91301 vertices, 91727 faces
slice 130: 101530 vertices, 101931 faces
slice 140: 110558 vertices, 110932 faces
slice 150: 118275 vertices, 118586 faces
slice 160: 124610 vertices, 124867 faces
slice 170: 130090 vertices, 130299 faces
slice 180: 133577 vertices, 133707 faces
slice 190: 134332 vertices, 134394 faces
slice 200: 134332 vertices, 134394 faces
slice 210: 134332 vertices, 134394 faces
slice 220: 134332 vertices, 134394 faces
slice 230: 134332 vertices, 134394 faces
slice 240: 134332 vertices, 134394 faces
slice 250: 134332 vertices, 134394 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  2024:08:07:17:22:23 mri_tessellate N 3 e 0.68 S 0.02 U 0.65 P 99%
M 37632 F 7 R 8374 W 0 c 7 w 16 I 1024 O 6304 L 10.68 10.21 10.35
@#@FSLOADPOST 2024:08:07:17:22:23 mri_tessellate N 3 10.68 10.21 10.35
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components...
134332 voxel in cpt #1: X=-62 [v=134332,e=403182,f=268788] located at
(-25.795513, -29.102404, 6.299958)
For the whole surface: X=-62 [v=134332,e=403182,f=268788]
One single component has been found
nothing to do
done
@#@FSTIME  2024:08:07:17:22:23 mris_extract_main_component N 2 e 0.64 S 0.09
U 0.54 P 99% M 267080 F 18 R 70699 W 0 c 4 w 26 I 3440 O 9456 L 10.68 10.21
10.35
@#@FSLOADPOST 2024:08:07:17:22:24 mris_extract_main_component N 2 10.68
10.21 10.35
#--------------------------------------------
#@# Tessellate rh 公曆 20廿四年 八月 七日 週三 十七時廿二分廿四秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mri_pretess ../mri/filled.mgz 127 ../mri/norm.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+):   6 found -   6 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   6 modified     |    TOTAL:   6
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  10
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  11
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  12
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  12
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 (++):   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+):   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 = 16 (out of 274986: 0.005818)
Ambiguous edge configurations...
mri_pretess done
@#@FSTIME  2024:08:07:17:22:24 mri_pretess N 4 e 0.86 S 0.01 U 0.84 P 99% M
40448 F 0 R 8834 W 0 c 2 w 1 I 0 O 256 L 10.68 10.21 10.35
@#@FSLOADPOST 2024:08:07:17:22:25 mri_pretess N 4 10.68 10.21 10.35
mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
7.4.1
7.4.1
slice 40: 2057 vertices, 2235 faces
slice 50: 9673 vertices, 10005 faces
slice 60: 19918 vertices, 20259 faces
slice 70: 30458 vertices, 30824 faces
slice 80: 41510 vertices, 41884 faces
slice 90: 52067 vertices, 52440 faces
slice 100: 63281 vertices, 63707 faces
slice 110: 73931 vertices, 74369 faces
slice 120: 84531 vertices, 84951 faces
slice 130: 94606 vertices, 95060 faces
slice 140: 104034 vertices, 104391 faces
slice 150: 112205 vertices, 112525 faces
slice 160: 119186 vertices, 119427 faces
slice 170: 124431 vertices, 124673 faces
slice 180: 128752 vertices, 128902 faces
slice 190: 129764 vertices, 129826 faces
slice 200: 129764 vertices, 129826 faces
slice 210: 129764 vertices, 129826 faces
slice 220: 129764 vertices, 129826 faces
slice 230: 129764 vertices, 129826 faces
slice 240: 129764 vertices, 129826 faces
slice 250: 129764 vertices, 129826 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  2024:08:07:17:22:25 mri_tessellate N 3 e 0.77 S 0.01 U 0.75 P 99%
M 36608 F 0 R 8275 W 0 c 6 w 1 I 0 O 6088 L 10.68 10.21 10.35
@#@FSLOADPOST 2024:08:07:17:22:26 mri_tessellate N 3 10.68 10.21 10.35
rm -f ../mri/filled-pretess127.mgz
mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
counting number of connected components...
129764 voxel in cpt #1: X=-62 [v=129764,e=389478,f=259652] located at
(29.572609, -25.736021, 5.940870)
For the whole surface: X=-62 [v=129764,e=389478,f=259652]
One single component has been found
nothing to do
done
@#@FSTIME  2024:08:07:17:22:26 mris_extract_main_component N 2 e 0.55 S 0.10
U 0.44 P 99% M 258860 F 0 R 68280 W 0 c 5 w 4 I 8 O 9128 L 10.68 10.21 10.35
@#@FSLOADPOST 2024:08:07:17:22:26 mris_extract_main_component N 2 10.68
10.21 10.35
#--------------------------------------------
#@# Smooth1 lh 公曆 20廿四年 八月 七日 週三 十七時廿二分廿六秒
/home/chang/GBM_Data/VBG/0003/0003/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  2024:08:07:17:22:26 mris_smooth N 5 e 1.46 S 0.06 U 1.39 P 99% M
213016 F 7 R 63984 W 0 c 6 w 12 I 632 O 9456 L 10.68 10.21 10.35
@#@FSLOADPOST 2024:08:07:17:22:28 mris_smooth N 5 10.47 10.17 10.34
#--------------------------------------------
#@# Smooth1 rh 公曆 20廿四年 八月 七日 週三 十七時廿二分廿八秒
/home/chang/GBM_Data/VBG/0003/0003/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  2024:08:07:17:22:28 mris_smooth N 5 e 1.32 S 0.05 U 1.26 P 99% M
206232 F 0 R 61191 W 0 c 4 w 5 I 0 O 9136 L 10.47 10.17 10.34
@#@FSLOADPOST 2024:08:07:17:22:29 mris_smooth N 5 10.47 10.17 10.34
#--------------------------------------------
#@# Inflation1 lh 公曆 20廿四年 八月 七日 週三 十七時廿二分廿九秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix
../surf/lh.inflated.nofix
Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 47.8 mm, total surface area = 73822 mm^2
step 000: RMS=0.145 (target=0.015)
step 005: RMS=0.115 (target=0.015)
step 010: RMS=0.087 (target=0.015)
step 015: RMS=0.074 (target=0.015)
step 020: RMS=0.066 (target=0.015)
step 025: RMS=0.058 (target=0.015)
step 030: RMS=0.052 (target=0.015)
step 035: RMS=0.047 (target=0.015)
step 040: RMS=0.043 (target=0.015)
step 045: RMS=0.041 (target=0.015)
step 050: RMS=0.040 (target=0.015)
step 055: RMS=0.039 (target=0.015)
step 060: RMS=0.038 (target=0.015)   writing inflated surface to ../surf/lh.
inflated.nofix
inflation took 0.2 minutes
inflation complete.
Not saving sulc
mris_inflate utimesec    10.421465
mris_inflate stimesec    0.643843
mris_inflate ru_maxrss   213704
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   562020
mris_inflate ru_majflt   22
mris_inflate ru_nswap    0
mris_inflate ru_inblock  4016
mris_inflate ru_oublock  9456
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    24
mris_inflate ru_nivcsw   39
@#@FSTIME  2024:08:07:17:22:29 mris_inflate N 3 e 11.07 S 0.65 U 10.42 P 99%
M 213704 F 22 R 562027 W 0 c 39 w 25 I 4016 O 9456 L 10.47 10.17 10.34
@#@FSLOADPOST 2024:08:07:17:22:40 mris_inflate N 3 10.85 10.27 10.37
#--------------------------------------------
#@# Inflation1 rh 公曆 20廿四年 八月 七日 週三 十七時廿二分40秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix
../surf/rh.inflated.nofix
Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 47.1 mm, total surface area = 70773 mm^2
step 000: RMS=0.148 (target=0.015)
step 005: RMS=0.117 (target=0.015)
step 010: RMS=0.086 (target=0.015)
step 015: RMS=0.073 (target=0.015)
step 020: RMS=0.064 (target=0.015)
step 025: RMS=0.057 (target=0.015)
step 030: RMS=0.051 (target=0.015)
step 035: RMS=0.047 (target=0.015)
step 040: RMS=0.044 (target=0.015)
step 045: RMS=0.041 (target=0.015)
step 050: RMS=0.039 (target=0.015)
step 055: RMS=0.038 (target=0.015)
step 060: RMS=0.038 (target=0.015)   writing inflated surface to ../surf/rh.
inflated.nofix
inflation took 0.2 minutes
inflation complete.
Not saving sulc
mris_inflate utimesec    10.002528
mris_inflate stimesec    0.499926
mris_inflate ru_maxrss   206656
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   550105
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  9136
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2
mris_inflate ru_nivcsw   29
@#@FSTIME  2024:08:07:17:22:40 mris_inflate N 3 e 10.51 S 0.50 U 10.00 P 99%
M 206656 F 0 R 550111 W 0 c 29 w 3 I 0 O 9136 L 10.85 10.27 10.37
@#@FSLOADPOST 2024:08:07:17:22:51 mris_inflate N 3 11.02 10.32 10.39
#--------------------------------------------
#@# QSphere lh 公曆 20廿四年 八月 七日 週三 十七時廿二分51秒
/home/chang/GBM_Data/VBG/0003/0003/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
version: 7.4.1
available threads: 1
scaling brain by 0.331...
inflating...
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 0.98 +- 0.59 (0.00-->6.09) (max @ vno 57993 --> 59004)
face area 0.03 +- 0.04 (-0.15-->0.63)
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=174.378, avgs=0
005/300: dt: 0.9000, rms radial error=174.125, avgs=0
010/300: dt: 0.9000, rms radial error=173.582, avgs=0
015/300: dt: 0.9000, rms radial error=172.870, avgs=0
020/300: dt: 0.9000, rms radial error=172.059, avgs=0
025/300: dt: 0.9000, rms radial error=171.189, avgs=0
030/300: dt: 0.9000, rms radial error=170.288, avgs=0
035/300: dt: 0.9000, rms radial error=169.369, avgs=0
040/300: dt: 0.9000, rms radial error=168.442, avgs=0
045/300: dt: 0.9000, rms radial error=167.512, avgs=0
050/300: dt: 0.9000, rms radial error=166.583, avgs=0
055/300: dt: 0.9000, rms radial error=165.654, avgs=0
060/300: dt: 0.9000, rms radial error=164.728, avgs=0
065/300: dt: 0.9000, rms radial error=163.805, avgs=0
070/300: dt: 0.9000, rms radial error=162.889, avgs=0
075/300: dt: 0.9000, rms radial error=161.977, avgs=0
080/300: dt: 0.9000, rms radial error=161.070, avgs=0
085/300: dt: 0.9000, rms radial error=160.167, avgs=0
090/300: dt: 0.9000, rms radial error=159.269, avgs=0
095/300: dt: 0.9000, rms radial error=158.377, avgs=0
100/300: dt: 0.9000, rms radial error=157.490, avgs=0
105/300: dt: 0.9000, rms radial error=156.607, avgs=0
110/300: dt: 0.9000, rms radial error=155.728, avgs=0
115/300: dt: 0.9000, rms radial error=154.855, avgs=0
120/300: dt: 0.9000, rms radial error=153.986, avgs=0
125/300: dt: 0.9000, rms radial error=153.121, avgs=0
130/300: dt: 0.9000, rms radial error=152.261, avgs=0
135/300: dt: 0.9000, rms radial error=151.406, avgs=0
140/300: dt: 0.9000, rms radial error=150.555, avgs=0
145/300: dt: 0.9000, rms radial error=149.709, avgs=0
150/300: dt: 0.9000, rms radial error=148.867, avgs=0
155/300: dt: 0.9000, rms radial error=148.030, avgs=0
160/300: dt: 0.9000, rms radial error=147.197, avgs=0
165/300: dt: 0.9000, rms radial error=146.369, avgs=0
170/300: dt: 0.9000, rms radial error=145.546, avgs=0
175/300: dt: 0.9000, rms radial error=144.726, avgs=0
180/300: dt: 0.9000, rms radial error=143.912, avgs=0
185/300: dt: 0.9000, rms radial error=143.102, avgs=0
190/300: dt: 0.9000, rms radial error=142.296, avgs=0
195/300: dt: 0.9000, rms radial error=141.495, avgs=0
200/300: dt: 0.9000, rms radial error=140.698, avgs=0
205/300: dt: 0.9000, rms radial error=139.906, avgs=0
210/300: dt: 0.9000, rms radial error=139.118, avgs=0
215/300: dt: 0.9000, rms radial error=138.335, avgs=0
220/300: dt: 0.9000, rms radial error=137.556, avgs=0
225/300: dt: 0.9000, rms radial error=136.781, avgs=0
230/300: dt: 0.9000, rms radial error=136.011, avgs=0
235/300: dt: 0.9000, rms radial error=135.244, avgs=0
240/300: dt: 0.9000, rms radial error=134.483, avgs=0
245/300: dt: 0.9000, rms radial error=133.725, avgs=0
250/300: dt: 0.9000, rms radial error=132.971, avgs=0
255/300: dt: 0.9000, rms radial error=132.222, avgs=0
260/300: dt: 0.9000, rms radial error=131.477, avgs=0
265/300: dt: 0.9000, rms radial error=130.736, avgs=0
270/300: dt: 0.9000, rms radial error=129.999, avgs=0
275/300: dt: 0.9000, rms radial error=129.266, avgs=0
280/300: dt: 0.9000, rms radial error=128.538, avgs=0
285/300: dt: 0.9000, rms radial error=127.813, avgs=0
290/300: dt: 0.9000, rms radial error=127.093, avgs=0
295/300: dt: 0.9000, rms radial error=126.376, avgs=0
300/300: dt: 0.9000, rms radial error=125.664, avgs=0
spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15322.79
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00044
epoch 2 (K=40.0), pass 1, starting sse = 2434.48
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00062
epoch 3 (K=160.0), pass 1, starting sse = 241.35
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.15/16 = 0.00964
epoch 4 (K=640.0), pass 1, starting sse = 17.17
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.16/22 = 0.00711
final distance error %100000.00
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.0205 hours
FSRUNTIME@ mris_sphere  0.0205 hours 1 threads
#VMPC# mris_sphere VmPeak  476096
mris_sphere done
@#@FSTIME  2024:08:07:17:22:51 mris_sphere N 9 e 73.91 S 3.49 U 70.41 P 99%
M 217528 F 12 R 3507278 W 0 c 355 w 13 I 1600 O 9456 L 11.02 10.32 10.39
@#@FSLOADPOST 2024:08:07:17:24:05 mris_sphere N 9 10.55 10.40 10.41
#--------------------------------------------
#@# QSphere rh 公曆 20廿四年 八月 七日 週三 十七時廿四分五秒
/home/chang/GBM_Data/VBG/0003/0003/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
version: 7.4.1
available threads: 1
scaling brain by 0.337...
inflating...
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.00 +- 0.60 (0.00-->6.70) (max @ vno 59826 --> 60976)
face area 0.03 +- 0.04 (-0.07-->0.62)
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=174.539, avgs=0
005/300: dt: 0.9000, rms radial error=174.286, avgs=0
010/300: dt: 0.9000, rms radial error=173.742, avgs=0
015/300: dt: 0.9000, rms radial error=173.026, avgs=0
020/300: dt: 0.9000, rms radial error=172.209, avgs=0
025/300: dt: 0.9000, rms radial error=171.334, avgs=0
030/300: dt: 0.9000, rms radial error=170.426, avgs=0
035/300: dt: 0.9000, rms radial error=169.501, avgs=0
040/300: dt: 0.9000, rms radial error=168.567, avgs=0
045/300: dt: 0.9000, rms radial error=167.632, avgs=0
050/300: dt: 0.9000, rms radial error=166.697, avgs=0
055/300: dt: 0.9000, rms radial error=165.765, avgs=0
060/300: dt: 0.9000, rms radial error=164.836, avgs=0
065/300: dt: 0.9000, rms radial error=163.913, avgs=0
070/300: dt: 0.9000, rms radial error=162.997, avgs=0
075/300: dt: 0.9000, rms radial error=162.085, avgs=0
080/300: dt: 0.9000, rms radial error=161.178, avgs=0
085/300: dt: 0.9000, rms radial error=160.276, avgs=0
090/300: dt: 0.9000, rms radial error=159.378, avgs=0
095/300: dt: 0.9000, rms radial error=158.485, avgs=0
100/300: dt: 0.9000, rms radial error=157.597, avgs=0
105/300: dt: 0.9000, rms radial error=156.714, avgs=0
110/300: dt: 0.9000, rms radial error=155.835, avgs=0
115/300: dt: 0.9000, rms radial error=154.961, avgs=0
120/300: dt: 0.9000, rms radial error=154.092, avgs=0
125/300: dt: 0.9000, rms radial error=153.227, avgs=0
130/300: dt: 0.9000, rms radial error=152.367, avgs=0
135/300: dt: 0.9000, rms radial error=151.511, avgs=0
140/300: dt: 0.9000, rms radial error=150.661, avgs=0
145/300: dt: 0.9000, rms radial error=149.815, avgs=0
150/300: dt: 0.9000, rms radial error=148.974, avgs=0
155/300: dt: 0.9000, rms radial error=148.138, avgs=0
160/300: dt: 0.9000, rms radial error=147.307, avgs=0
165/300: dt: 0.9000, rms radial error=146.480, avgs=0
170/300: dt: 0.9000, rms radial error=145.658, avgs=0
175/300: dt: 0.9000, rms radial error=144.840, avgs=0
180/300: dt: 0.9000, rms radial error=144.027, avgs=0
185/300: dt: 0.9000, rms radial error=143.218, avgs=0
190/300: dt: 0.9000, rms radial error=142.413, avgs=0
195/300: dt: 0.9000, rms radial error=141.613, avgs=0
200/300: dt: 0.9000, rms radial error=140.817, avgs=0
205/300: dt: 0.9000, rms radial error=140.026, avgs=0
210/300: dt: 0.9000, rms radial error=139.239, avgs=0
215/300: dt: 0.9000, rms radial error=138.456, avgs=0
220/300: dt: 0.9000, rms radial error=137.677, avgs=0
225/300: dt: 0.9000, rms radial error=136.903, avgs=0
230/300: dt: 0.9000, rms radial error=136.133, avgs=0
235/300: dt: 0.9000, rms radial error=135.367, avgs=0
240/300: dt: 0.9000, rms radial error=134.606, avgs=0
245/300: dt: 0.9000, rms radial error=133.848, avgs=0
250/300: dt: 0.9000, rms radial error=133.095, avgs=0
255/300: dt: 0.9000, rms radial error=132.346, avgs=0
260/300: dt: 0.9000, rms radial error=131.601, avgs=0
265/300: dt: 0.9000, rms radial error=130.861, avgs=0
270/300: dt: 0.9000, rms radial error=130.124, avgs=0
275/300: dt: 0.9000, rms radial error=129.391, avgs=0
280/300: dt: 0.9000, rms radial error=128.663, avgs=0
285/300: dt: 0.9000, rms radial error=127.938, avgs=0
290/300: dt: 0.9000, rms radial error=127.218, avgs=0
295/300: dt: 0.9000, rms radial error=126.502, avgs=0
300/300: dt: 0.9000, rms radial error=125.789, avgs=0
spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 14716.43
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00050
epoch 2 (K=40.0), pass 1, starting sse = 2287.75
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00043
epoch 3 (K=160.0), pass 1, starting sse = 224.77
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.20/18 = 0.01101
epoch 4 (K=640.0), pass 1, starting sse = 13.78
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.25/26 = 0.00969
final distance error %100000.00
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.0214 hours
FSRUNTIME@ mris_sphere  0.0214 hours 1 threads
#VMPC# mris_sphere VmPeak  468692
mris_sphere done
@#@FSTIME  2024:08:07:17:24:05 mris_sphere N 9 e 77.02 S 3.80 U 73.20 P 99%
M 210544 F 0 R 3626328 W 0 c 307 w 25 I 0 O 9136 L 10.55 10.40 10.41
@#@FSLOADPOST 2024:08:07:17:25:22 mris_sphere N 9 11.28 10.66 10.50
#@# Fix Topology lh 公曆 20廿四年 八月 七日 週三 十七時廿五分廿二秒
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 0003 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'
7.4.1
7.4.1
before topology correction, eno=-62 (nv=134332, nf=268788, ne=403182, g=32)
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...
8322 ambiguous faces found in tessellation
segmenting defects...
26 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
26 defects to be corrected
0 vertices coincident
reading input surface
/home/chang/GBM_Data/VBG/0003/0003/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: -9.5572  (-4.7786)
-vertex     loglikelihood: -6.7775  (-3.3887)
-normal dot loglikelihood: -3.6675  (-3.6675)
-quad curv  loglikelihood: -5.7838  (-2.8919)
Total Loglikelihood : -25.7860
CORRECTING DEFECT 0 (vertices=122, convex hull=169, v0=519)
After retessellation of defect 0 (v0=519), euler #=-21
(129392,386375,256962) : difference with theory (-23) = -2
CORRECTING DEFECT 1 (vertices=1504, convex hull=796, v0=989)
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_freev
iew
After retessellation of defect 1 (v0=989), euler #=-21
(129765,387922,258136) : difference with theory (-22) = -1
CORRECTING DEFECT 2 (vertices=902, convex hull=305, v0=7739)
After retessellation of defect 2 (v0=7739), euler #=-21
(129853,388351,258477) : difference with theory (-21) = 0
CORRECTING DEFECT 3 (vertices=110, convex hull=73, v0=9937)
After retessellation of defect 3 (v0=9937), euler #=-20
(129879,388458,258559) : difference with theory (-20) = 0
CORRECTING DEFECT 4 (vertices=77, convex hull=99, v0=10732)
After retessellation of defect 4 (v0=10732), euler #=-19
(129906,388583,258658) : difference with theory (-19) = 0
CORRECTING DEFECT 5 (vertices=31, convex hull=65, v0=14128)
After retessellation of defect 5 (v0=14128), euler #=-18
(129922,388658,258718) : difference with theory (-18) = 0
CORRECTING DEFECT 6 (vertices=49, convex hull=89, v0=19640)
After retessellation of defect 6 (v0=19640), euler #=-17
(129952,388788,258819) : difference with theory (-17) = 0
CORRECTING DEFECT 7 (vertices=197, convex hull=174, v0=22045)
After retessellation of defect 7 (v0=22045), euler #=-16
(130035,389121,259070) : difference with theory (-16) = 0
CORRECTING DEFECT 8 (vertices=169, convex hull=126, v0=26189)
After retessellation of defect 8 (v0=26189), euler #=-15
(130071,389289,259203) : difference with theory (-15) = 0
CORRECTING DEFECT 9 (vertices=91, convex hull=142, v0=26866)
After retessellation of defect 9 (v0=26866), euler #=-14
(130117,389494,259363) : difference with theory (-14) = 0
CORRECTING DEFECT 10 (vertices=151, convex hull=195, v0=32544)
After retessellation of defect 10 (v0=32544), euler #=-13
(130179,389769,259577) : difference with theory (-13) = 0
CORRECTING DEFECT 11 (vertices=102, convex hull=138, v0=36049)
After retessellation of defect 11 (v0=36049), euler #=-12
(130232,389992,259748) : difference with theory (-12) = 0
CORRECTING DEFECT 12 (vertices=275, convex hull=257, v0=37633)
After retessellation of defect 12 (v0=37633), euler #=-11
(130359,390499,260129) : difference with theory (-11) = 0
CORRECTING DEFECT 13 (vertices=83, convex hull=137, v0=44132)
After retessellation of defect 13 (v0=44132), euler #=-10
(130397,390672,260265) : difference with theory (-10) = 0
CORRECTING DEFECT 14 (vertices=279, convex hull=235, v0=46527)
After retessellation of defect 14 (v0=46527), euler #=-9
(130540,391219,260670) : difference with theory (-9) = 0
CORRECTING DEFECT 15 (vertices=23, convex hull=56, v0=60200)
After retessellation of defect 15 (v0=60200), euler #=-8
(130552,391279,260719) : difference with theory (-8) = 0
CORRECTING DEFECT 16 (vertices=6, convex hull=12, v0=61082)
After retessellation of defect 16 (v0=61082), euler #=-7
(130554,391289,260728) : difference with theory (-7) = 0
CORRECTING DEFECT 17 (vertices=8, convex hull=25, v0=61123)
After retessellation of defect 17 (v0=61123), euler #=-6
(130557,391305,260742) : difference with theory (-6) = 0
CORRECTING DEFECT 18 (vertices=6, convex hull=26, v0=67901)
After retessellation of defect 18 (v0=67901), euler #=-5
(130559,391319,260755) : difference with theory (-5) = 0
CORRECTING DEFECT 19 (vertices=84, convex hull=122, v0=78033)
After retessellation of defect 19 (v0=78033), euler #=-4
(130609,391518,260905) : difference with theory (-4) = 0
CORRECTING DEFECT 20 (vertices=109, convex hull=143, v0=88396)
After retessellation of defect 20 (v0=88396), euler #=-3
(130667,391760,261090) : difference with theory (-3) = 0
CORRECTING DEFECT 21 (vertices=54, convex hull=28, v0=99495)
After retessellation of defect 21 (v0=99495), euler #=-2
(130675,391793,261116) : difference with theory (-2) = 0
CORRECTING DEFECT 22 (vertices=50, convex hull=72, v0=106668)
After retessellation of defect 22 (v0=106668), euler #=-1
(130703,391905,261201) : difference with theory (-1) = 0
CORRECTING DEFECT 23 (vertices=180, convex hull=215, v0=114064)
After retessellation of defect 23 (v0=114064), euler #=0
(130794,392281,261487) : difference with theory (0) = 0
CORRECTING DEFECT 24 (vertices=250, convex hull=94, v0=114280)
After retessellation of defect 24 (v0=114280), euler #=1
(130809,392367,261559) : difference with theory (1) = 0
CORRECTING DEFECT 25 (vertices=90, convex hull=119, v0=127382)
After retessellation of defect 25 (v0=127382), euler #=2
(130852,392550,261700) : difference with theory (2) = 0
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.25 (0.02-->13.95) (max @ vno 13606 --> 15813)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.25 (0.02-->13.95) (max @ vno 13606 --> 15813)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
69 mutations (35.6%), 125 crossovers (64.4%), 321 vertices were eliminated
building final representation...
3480 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=130852, nf=261700, ne=392550, g=0)
writing corrected surface to
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.premesh...
0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 350 intersecting
001: 37 intersecting
002: 5 intersecting
terminating search with 0 intersecting
topology fixing took 2.7 minutes
FSRUNTIME@ mris_fix_topology lh  0.0455 hours 1 threads
#VMPC# mris_fix_topology VmPeak  755536
@#@FSTIME  2024:08:07:17:25:22 mris_fix_topology N 14 e 163.65 S 0.23 U 163.
40 P 99% M 735944 F 18 R 219862 W 0 c 503 w 44 I 2112 O 12376 L 11.28 10.66
10.50
@#@FSLOADPOST 2024:08:07:17:28:05 mris_fix_topology N 14 10.48 10.58 10.50
#@# Fix Topology rh 公曆 20廿四年 八月 七日 週三 十七時廿八分五秒
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 0003 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'
7.4.1
7.4.1
before topology correction, eno=-62 (nv=129764, nf=259652, ne=389478, g=32)
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...
5716 ambiguous faces found in tessellation
segmenting defects...
31 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 14 into 12
30 defects to be corrected
0 vertices coincident
reading input surface
/home/chang/GBM_Data/VBG/0003/0003/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: -9.4820  (-4.7410)
-vertex     loglikelihood: -6.8165  (-3.4082)
-normal dot loglikelihood: -3.6692  (-3.6692)
-quad curv  loglikelihood: -5.8688  (-2.9344)
Total Loglikelihood : -25.8364
CORRECTING DEFECT 0 (vertices=222, convex hull=187, v0=62)
After retessellation of defect 0 (v0=62), euler #=-28 (126273,377339,251038)
: difference with theory (-27) = 1
CORRECTING DEFECT 1 (vertices=308, convex hull=186, v0=943)
After retessellation of defect 1 (v0=943), euler #=-27
(126359,377686,251300) : difference with theory (-26) = 1
CORRECTING DEFECT 2 (vertices=299, convex hull=243, v0=1269)
After retessellation of defect 2 (v0=1269), euler #=-26
(126426,378001,251549) : difference with theory (-25) = 1
CORRECTING DEFECT 3 (vertices=27, convex hull=28, v0=7643)
After retessellation of defect 3 (v0=7643), euler #=-25
(126429,378024,251570) : difference with theory (-24) = 1
CORRECTING DEFECT 4 (vertices=85, convex hull=111, v0=9239)
After retessellation of defect 4 (v0=9239), euler #=-24
(126483,378235,251728) : difference with theory (-23) = 1
CORRECTING DEFECT 5 (vertices=320, convex hull=267, v0=10439)
After retessellation of defect 5 (v0=10439), euler #=-23
(126632,378816,252161) : difference with theory (-22) = 1
CORRECTING DEFECT 6 (vertices=56, convex hull=63, v0=20922)
After retessellation of defect 6 (v0=20922), euler #=-22
(126653,378904,252229) : difference with theory (-21) = 1
CORRECTING DEFECT 7 (vertices=229, convex hull=221, v0=29223)
After retessellation of defect 7 (v0=29223), euler #=-21
(126726,379234,252487) : difference with theory (-20) = 1
CORRECTING DEFECT 8 (vertices=237, convex hull=197, v0=29276)
After retessellation of defect 8 (v0=29276), euler #=-20
(126839,379674,252815) : difference with theory (-19) = 1
CORRECTING DEFECT 9 (vertices=193, convex hull=189, v0=35208)
normal vector of length zero at vertex 127986 with 3 faces
normal vector of length zero at vertex 127986 with 3 faces
normal vector of length zero at vertex 127990 with 3 faces
normal vector of length zero at vertex 127998 with 4 faces
normal vector of length zero at vertex 127998 with 4 faces
normal vector of length zero at vertex 127998 with 4 faces
After retessellation of defect 9 (v0=35208), euler #=-19
(126909,379974,253046) : difference with theory (-18) = 1
CORRECTING DEFECT 10 (vertices=6, convex hull=21, v0=40311)
After retessellation of defect 10 (v0=40311), euler #=-18
(126910,379983,253055) : difference with theory (-17) = 1
CORRECTING DEFECT 11 (vertices=21, convex hull=30, v0=40553)
After retessellation of defect 11 (v0=40553), euler #=-17
(126916,380010,253077) : difference with theory (-16) = 1
CORRECTING DEFECT 12 (vertices=460, convex hull=360, v0=52977)
After retessellation of defect 12 (v0=52977), euler #=-15
(127091,380724,253618) : difference with theory (-15) = 0
CORRECTING DEFECT 13 (vertices=17, convex hull=27, v0=53691)
After retessellation of defect 13 (v0=53691), euler #=-14
(127094,380743,253635) : difference with theory (-14) = 0
CORRECTING DEFECT 14 (vertices=110, convex hull=125, v0=62704)
After retessellation of defect 14 (v0=62704), euler #=-13
(127147,380963,253803) : difference with theory (-13) = 0
CORRECTING DEFECT 15 (vertices=32, convex hull=59, v0=64095)
After retessellation of defect 15 (v0=64095), euler #=-12
(127165,381042,253865) : difference with theory (-12) = 0
CORRECTING DEFECT 16 (vertices=154, convex hull=163, v0=66535)
After retessellation of defect 16 (v0=66535), euler #=-11
(127249,381374,254114) : difference with theory (-11) = 0
CORRECTING DEFECT 17 (vertices=5, convex hull=16, v0=72365)
After retessellation of defect 17 (v0=72365), euler #=-10
(127250,381380,254120) : difference with theory (-10) = 0
CORRECTING DEFECT 18 (vertices=6, convex hull=22, v0=74779)
After retessellation of defect 18 (v0=74779), euler #=-9
(127253,381394,254132) : difference with theory (-9) = 0
CORRECTING DEFECT 19 (vertices=18, convex hull=46, v0=81334)
After retessellation of defect 19 (v0=81334), euler #=-8
(127262,381437,254167) : difference with theory (-8) = 0
CORRECTING DEFECT 20 (vertices=29, convex hull=70, v0=85891)
After retessellation of defect 20 (v0=85891), euler #=-7
(127277,381509,254225) : difference with theory (-7) = 0
CORRECTING DEFECT 21 (vertices=58, convex hull=80, v0=90055)
After retessellation of defect 21 (v0=90055), euler #=-6
(127308,381638,254324) : difference with theory (-6) = 0
CORRECTING DEFECT 22 (vertices=61, convex hull=43, v0=94515)
After retessellation of defect 22 (v0=94515), euler #=-5
(127321,381692,254366) : difference with theory (-5) = 0
CORRECTING DEFECT 23 (vertices=9, convex hull=28, v0=97415)
After retessellation of defect 23 (v0=97415), euler #=-4
(127323,381706,254379) : difference with theory (-4) = 0
CORRECTING DEFECT 24 (vertices=135, convex hull=42, v0=98383)
After retessellation of defect 24 (v0=98383), euler #=-3
(127332,381750,254415) : difference with theory (-3) = 0
CORRECTING DEFECT 25 (vertices=165, convex hull=197, v0=112537)
After retessellation of defect 25 (v0=112537), euler #=-2
(127401,382058,254655) : difference with theory (-2) = 0
CORRECTING DEFECT 26 (vertices=188, convex hull=159, v0=121916)
After retessellation of defect 26 (v0=121916), euler #=-1
(127481,382367,254885) : difference with theory (-1) = 0
CORRECTING DEFECT 27 (vertices=15, convex hull=23, v0=124765)
After retessellation of defect 27 (v0=124765), euler #=0
(127483,382379,254896) : difference with theory (0) = 0
CORRECTING DEFECT 28 (vertices=82, convex hull=99, v0=125754)
After retessellation of defect 28 (v0=125754), euler #=1
(127522,382539,255018) : difference with theory (1) = 0
CORRECTING DEFECT 29 (vertices=27, convex hull=57, v0=129230)
After retessellation of defect 29 (v0=129230), euler #=2
(127536,382602,255068) : difference with theory (2) = 0
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.02-->9.09) (max @ vno 15793 --> 21757)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.23 (0.02-->9.09) (max @ vno 15793 --> 21757)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
90 mutations (34.9%), 168 crossovers (65.1%), 78 vertices were eliminated
building final representation...
2228 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=127536, nf=255068, ne=382602, g=0)
writing corrected surface to
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.premesh...
0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 412 intersecting
001: 27 intersecting
terminating search with 0 intersecting
topology fixing took 2.4 minutes
FSRUNTIME@ mris_fix_topology rh  0.0394 hours 1 threads
#VMPC# mris_fix_topology VmPeak  750508
@#@FSTIME  2024:08:07:17:28:05 mris_fix_topology N 14 e 141.83 S 0.29 U 141.
53 P 99% M 732304 F 0 R 217954 W 0 c 370 w 20 I 0 O 12024 L 10.48 10.58
10.50
@#@FSLOADPOST 2024:08:07:17:30:27 mris_fix_topology N 14 10.19 10.49 10.48
mris_euler_number ../surf/lh.orig.premesh
euler # = v-e+f = 2g-2: 130852 - 392550 + 261700 = 2 --> 0 holes
F =2V-4:          261700 = 261704-4 (0)
2E=3F:            785100 = 785100 (0)
total defect index = 0
mris_euler_number ../surf/rh.orig.premesh
euler # = v-e+f = 2g-2: 127536 - 382602 + 255068 = 2 --> 0 holes
F =2V-4:          255068 = 255072-4 (0)
2E=3F:            765204 = 765204 (0)
total defect index = 0
公曆 20廿四年 八月 七日 週三 十七時卅分廿八秒
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/scripts
/usr/local/freesurfer/bin/defect2seg --s 0003 --cortex
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
defect2seg 7.4.1
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
pid 678883
mri_label2label --label-cortex
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix
/home/chang/GBM_Data/VBG/0003/0003/mri/aseg.presurf.mgz 0
/home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
6 non-cortical segments detected
only using segment with 7612 vertices
erasing segment 1 (vno[0] = 102116)
erasing segment 2 (vno[0] = 102166)
erasing segment 3 (vno[0] = 102199)
erasing segment 4 (vno[0] = 103023)
erasing segment 5 (vno[0] = 106757)
mri_label2vol --defects
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.defect_labels
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz 1000 0
/home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz
/home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label
mri_label2vol supposed to be reproducible but seed not set
Contraining to label
/home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label
Changing input type 0 to MRI_INT
Converting defects to volume: offset=1000, merge=0
Writing to /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz
mris_defects_pointset -s
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix -d
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.defect_labels -o
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.defects.pointset --label
/home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label
Reading in surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix
Reading in defect segmentation
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.defect_labels
Reading in label
/home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label
#VMPC# mris_defects_pointset 177600
mris_defects_pointset done
mri_label2label --label-cortex
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix
/home/chang/GBM_Data/VBG/0003/0003/mri/aseg.presurf.mgz 0
/home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
19 non-cortical segments detected
only using segment with 7828 vertices
erasing segment 0 (vno[0] = 29124)
erasing segment 1 (vno[0] = 29136)
erasing segment 2 (vno[0] = 30107)
erasing segment 3 (vno[0] = 30189)
erasing segment 4 (vno[0] = 31165)
erasing segment 5 (vno[0] = 33343)
erasing segment 7 (vno[0] = 58089)
erasing segment 8 (vno[0] = 60517)
erasing segment 9 (vno[0] = 86191)
erasing segment 10 (vno[0] = 89279)
erasing segment 11 (vno[0] = 96444)
erasing segment 12 (vno[0] = 97210)
erasing segment 13 (vno[0] = 97362)
erasing segment 14 (vno[0] = 98209)
erasing segment 15 (vno[0] = 98249)
erasing segment 16 (vno[0] = 99207)
erasing segment 17 (vno[0] = 114165)
erasing segment 18 (vno[0] = 116301)
mri_label2vol --defects
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.defect_labels
/home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz 2000 1
/home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz
/home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label
mri_label2vol supposed to be reproducible but seed not set
Contraining to label
/home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label
Converting defects to volume: offset=2000, merge=1
Writing to /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz
mris_defects_pointset -s
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix -d
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.defect_labels -o
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.defects.pointset --label
/home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label
Reading in surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix
Reading in defect segmentation
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.defect_labels
Reading in label
/home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label
#VMPC# mris_defects_pointset 172060
mris_defects_pointset done
Started at 公曆 20廿四年 八月 七日 週三 十七時卅分廿八秒
Ended   at 公曆 20廿四年 八月 七日 週三 十七時卅分44秒
Defect2seg-Run-Time-Sec 16
Defect2seg-Run-Time-Min 0.32
Defect2seg-Run-Time-Hours 0.00
tkmeditfv 0003 brain.finalsurfs.mgz -defect
defect2seg Done
@#@FSTIME  2024:08:07:17:30:28 defect2seg N 3 e 16.56 S 0.44 U 16.12 P 100%
M 379692 F 56 R 439303 W 0 c 79 w 256 I 13280 O 21904 L 10.19 10.49 10.48
@#@FSLOADPOST 2024:08:07:17:30:44 defect2seg N 3 10.15 10.47 10.48
mris_remesh --remesh --iters 3 --input
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.premesh --output
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig
iters = 3
standard remeshing without target
adjusted l: 0.715263
remeshing to edge length 0.715263 with 3 iterations
avg qual before   : 0.888071  after: 0.97149
Removing intersections
Remeshed surface quality stats nv0 = 130852  nv = 136375  1.04221
Area    272746  0.30605  0.03364 0.091724   0.4745
Corner  818238 60.00000  8.74347 16.982359 144.8765
Edge    409119  0.84866  0.08239 0.453496   1.2830
Hinge   409119  9.13168  9.22303 0.000000 164.8331
mris_remesh done
@#@FSTIME  2024:08:07:17:30:44 mris_remesh N 7 e 22.07 S 0.25 U 21.78 P 99%
M 732392 F 22 R 277722 W 0 c 71 w 250 I 3656 O 9592 L 10.15 10.47 10.48
@#@FSLOADPOST 2024:08:07:17:31:06 mris_remesh N 7 10.38 10.52 10.49
mris_remesh --remesh --iters 3 --input
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.premesh --output
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig
iters = 3
standard remeshing without target
adjusted l: 0.713047
remeshing to edge length 0.713047 with 3 iterations
avg qual before   : 0.88755  after: 0.971537
Removing intersections
Remeshed surface quality stats nv0 = 127536  nv = 132793  1.04122
Area    265582  0.30442  0.03356 0.080014   0.5220
Corner  796746 60.00000  8.74022 15.729575 147.2339
Edge    398373  0.84637  0.08211 0.473788   1.2690
Hinge   398373  9.28281  9.32584 0.000009 132.5121
mris_remesh done
@#@FSTIME  2024:08:07:17:31:06 mris_remesh N 7 e 19.82 S 0.27 U 19.53 P 99%
M 711844 F 0 R 263256 W 0 c 56 w 183 I 0 O 9344 L 10.38 10.52 10.49
@#@FSLOADPOST 2024:08:07:17:31:26 mris_remesh N 7 10.77 10.60 10.52
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
intersection removal took 0.00 hours
Found 0 intersections
writing corrected surface to ../surf/lh.orig
@#@FSTIME  2024:08:07:17:31:26 mris_remove_intersection N 2 e 2.82 S 0.09 U
2.73 P 99% M 330452 F 21 R 94642 W 0 c 10 w 26 I 3952 O 9592 L 10.77 10.60
10.52
@#@FSLOADPOST 2024:08:07:17:31:29 mris_remove_intersection N 2 10.71 10.59
10.52
rm -f ../surf/lh.inflated
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
intersection removal took 0.00 hours
Found 0 intersections
writing corrected surface to ../surf/rh.orig
@#@FSTIME  2024:08:07:17:31:29 mris_remove_intersection N 2 e 2.52 S 0.12 U
2.39 P 99% M 322292 F 0 R 92542 W 0 c 12 w 8 I 0 O 9344 L 10.71 10.59 10.52
@#@FSLOADPOST 2024:08:07:17:31:32 mris_remove_intersection N 2 10.71 10.59
10.52
rm -f ../surf/rh.inflated
#--------------------------------------------
#@# AutoDetGWStats lh 公曆 20廿四年 八月 七日 週三 十七時卅一分32秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
border white:    249897 voxels (1.49%)
border gray      269695 voxels (1.61%)
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=19640, wmmin=5, clip=110
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (99.0): 99.0 +- 8.4 [70.0 --> 110.0]
CCS GM (73.0) : 70.7 +- 12.7 [30.0 --> 110.0]
white_mean = 98.9893 +/- 8.36131, gray_mean = 70.7223 +/- 12.7089
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=168 nbins=169
intensity peaks found at WM=104+-5.2,    GM=64+-15.7
white_mode = 104, gray_mode = 64
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 51.3 (was 70.000000)
setting MAX_BORDER_WHITE to 112.4 (was 105.000000)
setting MIN_BORDER_WHITE to 64.0 (was 85.000000)
setting MAX_CSF to 38.6 (was 40.000000)
setting MAX_GRAY to 95.6 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 51.3 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 25.9 (was 40.000000)
When placing the white surface
white_border_hi   = 112.361;
white_border_low  = 64;
white_outside_low = 51.2911;
white_inside_hi   = 120;
white_outside_hi  = 112.361;
When placing the pial surface
pial_border_hi   = 51.2911;
pial_border_low  = 25.8734;
pial_outside_low = 10;
pial_inside_hi   = 95.6387;
pial_outside_hi  = 44.9367;
#VMPC# mris_autodet_gwstats VmPeak  254600
mris_autodet_gwstats done
@#@FSTIME  2024:08:07:17:31:32 mris_autodet_gwstats N 8 e 2.03 S 0.07 U 1.95
P 99% M 235796 F 24 R 65987 W 0 c 8 w 20 I 4576 O 8 L 10.81 10.61 10.53
@#@FSLOADPOST 2024:08:07:17:31:34 mris_autodet_gwstats N 8 10.81 10.61 10.53
#--------------------------------------------
#@# AutoDetGWStats rh 公曆 20廿四年 八月 七日 週三 十七時卅一分34秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
border white:    249897 voxels (1.49%)
border gray      269695 voxels (1.61%)
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=19640, wmmin=5, clip=110
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (99.0): 99.0 +- 8.4 [70.0 --> 110.0]
CCS GM (73.0) : 70.7 +- 12.7 [30.0 --> 110.0]
white_mean = 98.9893 +/- 8.36131, gray_mean = 70.7223 +/- 12.7089
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=168 nbins=169
intensity peaks found at WM=104+-6.1,    GM=62+-18.3
white_mode = 104, gray_mode = 62
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70.000000)
setting MAX_BORDER_WHITE to 112.4 (was 105.000000)
setting MIN_BORDER_WHITE to 62.0 (was 85.000000)
setting MAX_CSF to 36.6 (was 40.000000)
setting MAX_GRAY to 95.6 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 23.9 (was 40.000000)
When placing the white surface
white_border_hi   = 112.361;
white_border_low  = 62;
white_outside_low = 49.2911;
white_inside_hi   = 120;
white_outside_hi  = 112.361;
When placing the pial surface
pial_border_hi   = 49.2911;
pial_border_low  = 23.8734;
pial_outside_low = 10;
pial_inside_hi   = 95.6387;
pial_outside_hi  = 42.9367;
#VMPC# mris_autodet_gwstats VmPeak  249900
mris_autodet_gwstats done
@#@FSTIME  2024:08:07:17:31:34 mris_autodet_gwstats N 8 e 1.93 S 0.04 U 1.88
P 100% M 230612 F 0 R 64725 W 0 c 13 w 1 I 0 O 8 L 10.81 10.61 10.53
@#@FSLOADPOST 2024:08:07:17:31:36 mris_autodet_gwstats N 8 10.81 10.61 10.53
#--------------------------------------------
#@# WhitePreAparc lh 公曆 20廿四年 八月 七日 週三 十七時卅一分36秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
--threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
--threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/lh.orig
Smoothing surface before ripping with 5 iterations
Area    272746  0.27449  0.06222 0.002558   0.5929
Corner  818238 60.00000  8.91476 8.209122 160.4169
Edge    409119  0.79945  0.11110 0.053273   1.3467
Hinge   409119  6.15827  5.96714 0.000031 133.2966
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
#FML# MRISripMidline(): nmarked=6971, nmarked2=0, nripped=6971
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 68188: xyz = (-28.9837,-16.6139,32.7592) oxyz =
(-28.9837,-16.6139,32.7592) wxzy = (-28.9837,-16.6139,32.7592) pxyz =
(0,0,0)
CBVO Creating mask 136375
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6971
#FML# MRISripMidline(): nmarked=6971, nmarked2=0, nripped=6971
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 174 vertices, nripped=6971
mean border=79.9, 283 (283) missing vertices, mean dist 0.3 [0.5 (%37.7)->0.
9 (%62.3))]
%61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1092 min
Finding expansion regions
mean absolute distance = 0.74 +- 0.98
5336 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=3510442.2, rms=11.405
001: dt: 0.5000, sse=1837154.5, rms=8.085 (29.107%)
002: dt: 0.5000, sse=1161537.2, rms=6.264 (22.530%)
003: dt: 0.5000, sse=836888.6, rms=5.163 (17.571%)
004: dt: 0.5000, sse=670005.9, rms=4.490 (13.044%)
005: dt: 0.5000, sse=581758.4, rms=4.083 (9.061%)
006: dt: 0.5000, sse=537952.8, rms=3.854 (5.609%)
007: dt: 0.5000, sse=512957.6, rms=3.719 (3.488%)
008: dt: 0.5000, sse=501343.3, rms=3.645 (2.004%)
rms = 3.6070/3.6449, sse=494225.2/501343.4, time step reduction 1 of 3 to 0.
250  0 0 1
009: dt: 0.5000, sse=494225.2, rms=3.607 (1.041%)
010: dt: 0.2500, sse=254779.7, rms=1.899 (47.362%)
011: dt: 0.2500, sse=212998.3, rms=1.433 (24.544%)
012: dt: 0.2500, sse=202290.4, rms=1.270 (11.376%)
013: dt: 0.2500, sse=196069.9, rms=1.183 (6.831%)
rms = 1.1461/1.1829, sse=196967.0/196069.9, time step reduction 2 of 3 to 0.
125  0 1 1
014: dt: 0.2500, sse=196967.0, rms=1.146 (3.112%)
015: dt: 0.1250, sse=191625.9, rms=1.051 (8.311%)
rms = 1.0389/1.0509, sse=187967.0/191625.9, time step reduction 3 of 3 to 0.
062  0 0 1
016: dt: 0.1250, sse=187967.0, rms=1.039 (1.140%)
maximum number of reductions reached, breaking from loop
positioning took 0.9 minutes
done positioning surface
Iteration 1 =========================================
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6971
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=7123, nmarked2=0, nripped=7123
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 87 vertices, nripped=7123
mean border=82.2, 184 (107) missing vertices, mean dist -0.3 [0.5
(%65.6)->0.2 (%34.4))]
%64 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0759 min
Finding expansion regions
mean absolute distance = 0.41 +- 0.84
5487 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=695346.3, rms=4.334
017: dt: 0.5000, sse=476271.4, rms=3.183 (26.556%)
rms = 3.3847/3.1829, sse=511297.8/476271.4, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
018: dt: 0.2500, sse=365999.0, rms=2.412 (24.217%)
019: dt: 0.2500, sse=300724.7, rms=1.843 (23.590%)
020: dt: 0.2500, sse=271759.8, rms=1.534 (16.773%)
021: dt: 0.2500, sse=257332.0, rms=1.349 (12.079%)
022: dt: 0.2500, sse=248794.5, rms=1.220 (9.505%)
023: dt: 0.2500, sse=245329.3, rms=1.129 (7.480%)
024: dt: 0.2500, sse=242380.4, rms=1.067 (5.464%)
rms = 1.0192/1.0675, sse=253121.2/242380.4, time step reduction 2 of 3 to 0.
125  0 1 1
025: dt: 0.2500, sse=253121.2, rms=1.019 (4.520%)
rms = 0.9751/1.0192, sse=264779.5/253121.2, time step reduction 3 of 3 to 0.
062  0 1 1
026: dt: 0.1250, sse=264779.5, rms=0.975 (4.328%)
maximum number of reductions reached, breaking from loop
positioning took 0.6 minutes
done positioning surface
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=7123
removing 3 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=7124, nmarked2=0, nripped=7124
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 115 vertices, nripped=7124
mean border=84.0, 181 (94) missing vertices, mean dist -0.2 [0.4 (%64.7)->0.
2 (%35.3))]
%71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0422 min
Finding expansion regions
mean absolute distance = 0.35 +- 0.66
5037 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=479384.2, rms=3.083
027: dt: 0.5000, sse=369465.4, rms=2.480 (19.559%)
rms = 2.8765/2.4801, sse=420014.1/369465.4, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
028: dt: 0.2500, sse=282188.3, rms=1.702 (31.387%)
029: dt: 0.2500, sse=249428.6, rms=1.223 (28.135%)
030: dt: 0.2500, sse=236799.2, rms=1.029 (15.888%)
031: dt: 0.2500, sse=234373.3, rms=0.946 (8.019%)
rms = 0.9138/0.9461, sse=231459.3/234373.3, time step reduction 2 of 3 to 0.
125  0 0 1
032: dt: 0.2500, sse=231459.3, rms=0.914 (3.420%)
033: dt: 0.1250, sse=227292.4, rms=0.860 (5.877%)
rms = 0.8519/0.8601, sse=227134.7/227292.4, time step reduction 3 of 3 to 0.
062  0 0 1
034: dt: 0.1250, sse=227134.7, rms=0.852 (0.950%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
done positioning surface
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=7124
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=7132, nmarked2=0, nripped=7132
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 126 vertices, nripped=7132
mean border=84.9, 183 (88) missing vertices, mean dist -0.1 [0.4 (%56.2)->0.
2 (%43.8))]
%76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0268 min
Finding expansion regions
mean absolute distance = 0.31 +- 0.55
4538 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=293603.2, rms=1.868
rms = 1.6913/1.8683, sse=294285.6/293603.2, time step reduction 1 of 3 to 0.
250  0 1 0
035: dt: 0.5000, sse=294285.7, rms=1.691 (9.477%)
036: dt: 0.2500, sse=235204.7, rms=1.038 (38.651%)
037: dt: 0.2500, sse=224320.8, rms=0.852 (17.888%)
rms = 0.8649/0.8520, sse=231503.8/224320.8, time step reduction 2 of 3 to 0.
125  0 1 1
RMS increased, rejecting step
038: dt: 0.1250, sse=221693.5, rms=0.791 (7.141%)
rms = 0.7015/0.7911, sse=223918.3/221693.5, time step reduction 3 of 3 to 0.
062  0 1 0
039: dt: 0.1250, sse=223918.3, rms=0.702 (11.324%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface  2.61 minutes
Writing output to ../surf/lh.white.preaparc
#VMPC# mris_place_surfaces VmPeak  2181584
mris_place_surface done
@#@FSTIME  2024:08:07:17:31:36 mris_place_surface N 18 e 161.10 S 0.56 U
160.51 P 99% M 1923004 F 13 R 504279 W 0 c 522 w 100 I 1976 O 9592 L 10.81
10.61 10.53
@#@FSLOADPOST 2024:08:07:17:34:17 mris_place_surface N 18 10.60 10.65 10.56
#--------------------------------------------
#@# WhitePreAparc rh 公曆 20廿四年 八月 七日 週三 十七時34分十七秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz
--threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o
../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz
--threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o
../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/rh.orig
Smoothing surface before ripping with 5 iterations
Area    265582  0.27191  0.06213 0.009507   0.6410
Corner  796746 60.00000  8.91331 15.619468 143.3381
Edge    398373  0.79557  0.11136 0.127784   1.3356
Hinge   398373  6.33360  6.08459 0.000015 129.9691
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
#FML# MRISripMidline(): nmarked=7243, nmarked2=15, nripped=7243
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 66397: xyz = (50.0673,-13.5794,19.2827) oxyz =
(50.0673,-13.5794,19.2827) wxzy = (50.0673,-13.5794,19.2827) pxyz = (0,0,0)
CBVO Creating mask 132793
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=7243
#FML# MRISripMidline(): nmarked=7243, nmarked2=15, nripped=7243
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 197 vertices, nripped=7243
mean border=79.5, 85 (85) missing vertices, mean dist 0.3 [0.6 (%38.1)->0.9
(%61.9))]
%63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1083 min
Finding expansion regions
mean absolute distance = 0.79 +- 1.07
5662 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=3562774.8, rms=11.669
001: dt: 0.5000, sse=1944082.5, rms=8.473 (27.394%)
002: dt: 0.5000, sse=1271436.0, rms=6.709 (20.819%)
003: dt: 0.5000, sse=917817.3, rms=5.558 (17.157%)
004: dt: 0.5000, sse=729986.0, rms=4.832 (13.052%)
005: dt: 0.5000, sse=615465.8, rms=4.328 (10.429%)
006: dt: 0.5000, sse=561660.8, rms=4.062 (6.152%)
007: dt: 0.5000, sse=527542.3, rms=3.862 (4.927%)
008: dt: 0.5000, sse=512620.0, rms=3.787 (1.944%)
009: dt: 0.5000, sse=501858.6, rms=3.704 (2.200%)
rms = 3.6931/3.7036, sse=495481.9/501858.6, time step reduction 1 of 3 to 0.
250  0 0 1
010: dt: 0.5000, sse=495481.9, rms=3.693 (0.285%)
011: dt: 0.2500, sse=252359.9, rms=1.967 (46.751%)
012: dt: 0.2500, sse=211218.6, rms=1.514 (23.007%)
013: dt: 0.2500, sse=200146.5, rms=1.355 (10.506%)
014: dt: 0.2500, sse=194912.3, rms=1.268 (6.444%)
rms = 1.2262/1.2677, sse=193616.4/194912.3, time step reduction 2 of 3 to 0.
125  0 0 1
015: dt: 0.2500, sse=193616.4, rms=1.226 (3.273%)
016: dt: 0.1250, sse=185492.3, rms=1.111 (9.361%)
rms = 1.0956/1.1114, sse=185089.9/185492.3, time step reduction 3 of 3 to 0.
062  0 0 1
017: dt: 0.1250, sse=185089.9, rms=1.096 (1.429%)
maximum number of reductions reached, breaking from loop
positioning took 0.9 minutes
done positioning surface
Iteration 1 =========================================
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=7243
removing 4 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=7358, nmarked2=28, nripped=7358
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 83 vertices, nripped=7358
mean border=81.5, 155 (23) missing vertices, mean dist -0.2 [0.5 (%64.0)->0.
3 (%36.0))]
%65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0780 min
Finding expansion regions
mean absolute distance = 0.42 +- 0.86
5520 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=683148.7, rms=4.353
018: dt: 0.5000, sse=480223.1, rms=3.298 (24.239%)
rms = 3.5460/3.2979, sse=530335.2/480223.1, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
019: dt: 0.2500, sse=361994.4, rms=2.483 (24.705%)
020: dt: 0.2500, sse=298075.1, rms=1.889 (23.916%)
021: dt: 0.2500, sse=271548.9, rms=1.561 (17.400%)
022: dt: 0.2500, sse=262395.0, rms=1.366 (12.446%)
023: dt: 0.2500, sse=248962.8, rms=1.243 (9.040%)
024: dt: 0.2500, sse=248095.7, rms=1.154 (7.143%)
rms = 1.0976/1.1540, sse=249059.1/248095.7, time step reduction 2 of 3 to 0.
125  0 1 0
025: dt: 0.2500, sse=249059.1, rms=1.098 (4.890%)
rms = 1.0283/1.0976, sse=249164.9/249059.1, time step reduction 3 of 3 to 0.
062  0 1 0
026: dt: 0.1250, sse=249164.9, rms=1.028 (6.315%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
done positioning surface
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=7358
removing 3 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=7381, nmarked2=28, nripped=7381
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 118 vertices, nripped=7381
mean border=83.3, 137 (17) missing vertices, mean dist -0.2 [0.4 (%64.0)->0.
2 (%36.0))]
%72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0408 min
Finding expansion regions
mean absolute distance = 0.35 +- 0.66
5015 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=435865.3, rms=2.958
027: dt: 0.5000, sse=369905.2, rms=2.518 (14.873%)
rms = 3.0289/2.5179, sse=436262.3/369905.1, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
028: dt: 0.2500, sse=286725.1, rms=1.710 (32.099%)
029: dt: 0.2500, sse=253819.9, rms=1.259 (26.366%)
030: dt: 0.2500, sse=235221.5, rms=1.070 (15.022%)
031: dt: 0.2500, sse=230755.0, rms=0.992 (7.259%)
rms = 0.9640/0.9921, sse=230331.3/230755.0, time step reduction 2 of 3 to 0.
125  0 0 1
032: dt: 0.2500, sse=230331.3, rms=0.964 (2.836%)
033: dt: 0.1250, sse=223829.9, rms=0.896 (7.104%)
rms = 0.8850/0.8955, sse=223368.9/223829.9, time step reduction 3 of 3 to 0.
062  0 0 1
034: dt: 0.1250, sse=223368.9, rms=0.885 (1.173%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
done positioning surface
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline
structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=7381
removing 3 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=7400, nmarked2=28, nripped=7400
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 113 vertices, nripped=7400
mean border=84.1, 144 (9) missing vertices, mean dist -0.1 [0.4 (%56.1)->0.3
(%43.9))]
%76 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0291 min
Finding expansion regions
mean absolute distance = 0.32 +- 0.55
4705 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=287258.4, rms=1.879
035: dt: 0.5000, sse=284827.0, rms=1.780 (5.265%)
rms = 2.4401/1.7800, sse=351464.8/284827.0, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
036: dt: 0.2500, sse=232336.6, rms=1.083 (39.157%)
037: dt: 0.2500, sse=220988.4, rms=0.857 (20.860%)
038: dt: 0.2500, sse=219423.3, rms=0.784 (8.470%)
rms = 0.7927/0.7845, sse=223985.8/219423.3, time step reduction 2 of 3 to 0.
125  0 1 1
RMS increased, rejecting step
rms = 0.7570/0.7845, sse=218440.6/219423.3, time step reduction 3 of 3 to 0.
062  0 0 1
039: dt: 0.1250, sse=218440.7, rms=0.757 (3.506%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface  2.58 minutes
Writing output to ../surf/rh.white.preaparc
#VMPC# mris_place_surfaces VmPeak  2156700
mris_place_surface done
@#@FSTIME  2024:08:07:17:34:17 mris_place_surface N 18 e 158.93 S 0.58 U
158.34 P 99% M 1897548 F 0 R 497418 W 0 c 553 w 14 I 0 O 9344 L 10.60 10.65
10.56
@#@FSLOADPOST 2024:08:07:17:36:56 mris_place_surface N 18 11.07 10.78 10.62
#--------------------------------------------
#@# CortexLabel lh 公曆 20廿四年 八月 七日 週三 十七時36分56秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0
../label/lh.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
4 non-cortical segments detected
only using segment with 8548 vertices
erasing segment 1 (vno[0] = 85124)
erasing segment 2 (vno[0] = 116733)
erasing segment 3 (vno[0] = 126247)
@#@FSTIME  2024:08:07:17:36:56 mri_label2label N 5 e 8.38 S 0.11 U 8.27 P
100% M 315248 F 0 R 93972 W 0 c 30 w 4 I 0 O 11160 L 11.07 10.78 10.62
@#@FSLOADPOST 2024:08:07:17:37:05 mri_label2label N 5 11.67 10.92 10.67
#--------------------------------------------
#@# CortexLabel+HipAmyg lh 公曆 20廿四年 八月 七日 週三 十七時37分五秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1
../label/lh.cortex+hipamyg.label
Generating cortex label... RemoveHipAmgy=1
NucAccIsMedialWall=0
mris->useRealRAS=0
4 non-cortical segments detected
only using segment with 6801 vertices
erasing segment 1 (vno[0] = 85124)
erasing segment 2 (vno[0] = 116733)
erasing segment 3 (vno[0] = 126247)
@#@FSTIME  2024:08:07:17:37:05 mri_label2label N 5 e 8.30 S 0.11 U 8.19 P
99% M 315056 F 0 R 93994 W 0 c 22 w 2 I 0 O 11312 L 11.67 10.92 10.67
@#@FSLOADPOST 2024:08:07:17:37:13 mri_label2label N 5 11.34 10.87 10.65
#--------------------------------------------
#@# CortexLabel rh 公曆 20廿四年 八月 七日 週三 十七時37分十三秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0
../label/rh.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
7 non-cortical segments detected
only using segment with 8549 vertices
erasing segment 0 (vno[0] = 23127)
erasing segment 1 (vno[0] = 25756)
erasing segment 3 (vno[0] = 33919)
erasing segment 4 (vno[0] = 82304)
erasing segment 5 (vno[0] = 83828)
erasing segment 6 (vno[0] = 86921)
@#@FSTIME  2024:08:07:17:37:13 mri_label2label N 5 e 7.94 S 0.08 U 7.85 P
99% M 324336 F 0 R 98121 W 0 c 25 w 5 I 0 O 10616 L 11.34 10.87 10.65
@#@FSLOADPOST 2024:08:07:17:37:21 mri_label2label N 5 11.39 10.89 10.66
#--------------------------------------------
#@# CortexLabel+HipAmyg rh 公曆 20廿四年 八月 七日 週三 十七時37分廿一秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1
../label/rh.cortex+hipamyg.label
Generating cortex label... RemoveHipAmgy=1
NucAccIsMedialWall=0
mris->useRealRAS=0
8 non-cortical segments detected
only using segment with 6937 vertices
erasing segment 0 (vno[0] = 23127)
erasing segment 1 (vno[0] = 25756)
erasing segment 3 (vno[0] = 33919)
erasing segment 4 (vno[0] = 52453)
erasing segment 5 (vno[0] = 82304)
erasing segment 6 (vno[0] = 83828)
erasing segment 7 (vno[0] = 86921)
@#@FSTIME  2024:08:07:17:37:22 mri_label2label N 5 e 7.61 S 0.09 U 7.51 P
99% M 329168 F 0 R 100494 W 0 c 20 w 2 I 0 O 10736 L 11.39 10.89 10.66
@#@FSLOADPOST 2024:08:07:17:37:29 mri_label2label N 5 11.33 10.90 10.66
#--------------------------------------------
#@# Smooth2 lh 公曆 20廿四年 八月 七日 週三 十七時37分廿九秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc
../surf/lh.smoothwm
smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2024:08:07:17:37:29 mris_smooth N 7 e 1.42 S 0.08 U 1.33 P 99% M
208772 F 0 R 62525 W 0 c 13 w 7 I 0 O 9592 L 11.33 10.90 10.66
@#@FSLOADPOST 2024:08:07:17:37:31 mris_smooth N 7 11.33 10.90 10.66
#--------------------------------------------
#@# Smooth2 rh 公曆 20廿四年 八月 七日 週三 十七時37分卅一秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc
../surf/rh.smoothwm
smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
@#@FSTIME  2024:08:07:17:37:31 mris_smooth N 7 e 1.64 S 0.06 U 1.57 P 99% M
203340 F 0 R 60884 W 0 c 20 w 10 I 0 O 9344 L 11.33 10.90 10.66
@#@FSLOADPOST 2024:08:07:17:37:32 mris_smooth N 7 11.30 10.90 10.67
#--------------------------------------------
#@# Inflation2 lh 公曆 20廿四年 八月 七日 週三 十七時37分32秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
Reading ../surf/lh.smoothwm
avg radius = 47.6 mm, total surface area = 84453 mm^2
step 000: RMS=0.161 (target=0.015)
step 005: RMS=0.113 (target=0.015)
step 010: RMS=0.084 (target=0.015)
step 015: RMS=0.071 (target=0.015)
step 020: RMS=0.060 (target=0.015)
step 025: RMS=0.049 (target=0.015)
step 030: RMS=0.041 (target=0.015)
step 035: RMS=0.034 (target=0.015)
step 040: RMS=0.029 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.021 (target=0.015)
step 060: RMS=0.020 (target=0.015)   writing inflated surface to ../surf/lh.
inflated
writing sulcal depths to ../surf/lh.sulc
inflation complete.
inflation took 0.2 minutes
mris_inflate utimesec    11.422791
mris_inflate stimesec    0.439953
mris_inflate ru_maxrss   209792
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   449848
mris_inflate ru_majflt   1
mris_inflate ru_nswap    0
mris_inflate ru_inblock  184
mris_inflate ru_oublock  10672
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5
mris_inflate ru_nivcsw   32
@#@FSTIME  2024:08:07:17:37:32 mris_inflate N 2 e 11.87 S 0.44 U 11.42 P 99%
M 209792 F 1 R 449855 W 0 c 32 w 6 I 184 O 10672 L 11.30 10.90 10.67
@#@FSLOADPOST 2024:08:07:17:37:44 mris_inflate N 2 11.33 10.92 10.68
#--------------------------------------------
#@# Inflation2 rh 公曆 20廿四年 八月 七日 週三 十七時37分44秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
Reading ../surf/rh.smoothwm
avg radius = 47.0 mm, total surface area = 82720 mm^2
step 000: RMS=0.165 (target=0.015)
step 005: RMS=0.116 (target=0.015)
step 010: RMS=0.086 (target=0.015)
step 015: RMS=0.072 (target=0.015)
step 020: RMS=0.061 (target=0.015)
step 025: RMS=0.051 (target=0.015)
step 030: RMS=0.042 (target=0.015)
step 035: RMS=0.035 (target=0.015)
step 040: RMS=0.030 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.021 (target=0.015)
step 060: RMS=0.020 (target=0.015)   writing inflated surface to ../surf/rh.
inflated
writing sulcal depths to ../surf/rh.sulc
inflation complete.
inflation took 0.2 minutes
mris_inflate utimesec    11.928528
mris_inflate stimesec    0.588026
mris_inflate ru_maxrss   204564
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   522193
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10384
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5
mris_inflate ru_nivcsw   44
@#@FSTIME  2024:08:07:17:37:44 mris_inflate N 2 e 12.52 S 0.59 U 11.92 P 99%
M 204564 F 0 R 522199 W 0 c 44 w 6 I 0 O 10384 L 11.33 10.92 10.68
@#@FSLOADPOST 2024:08:07:17:37:57 mris_inflate N 2 11.44 10.96 10.69
#--------------------------------------------
#@# Curv .H and .K lh 公曆 20廿四年 八月 七日 週三 十七時37分57秒
/home/chang/GBM_Data/VBG/0003/0003/surf
mris_curvature -w -seed 1234 lh.white.preaparc
setting seed for random number generator to 1234
total integrated curvature = 20.595*4pi (258.800) --> -20 handles
ICI = 176.0, FI = 1137.6, variation=20146.676
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...mris_curvature done.
@#@FSTIME  2024:08:07:17:37:57 mris_curvature N 4 e 0.89 S 0.04 U 0.85 P 99%
M 155496 F 9 R 42029 W 0 c 6 w 8 I 968 O 2144 L 11.44 10.96 10.69
@#@FSLOADPOST 2024:08:07:17:37:58 mris_curvature N 4 11.32 10.94 10.69
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K
mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
lh.inflated
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
164 vertices thresholded to be in k1 ~ [-0.68 0.38], k2 ~ [-0.13 0.08]
total integrated curvature = 0.373*4pi (4.688) --> 1 handles
ICI = 1.4, FI = 8.6, variation=150.433
127 vertices thresholded to be in [-0.02 0.03]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at
99.90% level
curvature mean = 0.000, std = 0.001
119 vertices thresholded to be in [-0.23 0.18]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std =
0.023
mris_curvature done.
@#@FSTIME  2024:08:07:17:37:58 mris_curvature N 12 e 28.37 S 0.12 U 28.24 P
99% M 368956 F 0 R 95437 W 0 c 92 w 3 I 0 O 2144 L 11.32 10.94 10.69
@#@FSLOADPOST 2024:08:07:17:38:26 mris_curvature N 12 10.70 10.82 10.65
#--------------------------------------------
#@# Curv .H and .K rh 公曆 20廿四年 八月 七日 週三 十七時38分廿六秒
/home/chang/GBM_Data/VBG/0003/0003/surf
mris_curvature -w -seed 1234 rh.white.preaparc
setting seed for random number generator to 1234
total integrated curvature = 21.584*4pi (271.234) --> -21 handles
ICI = 185.4, FI = 1230.1, variation=21625.765
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...mris_curvature done.
@#@FSTIME  2024:08:07:17:38:26 mris_curvature N 4 e 0.94 S 0.05 U 0.89 P 99%
M 152308 F 0 R 40933 W 0 c 8 w 2 I 0 O 2080 L 10.70 10.82 10.65
@#@FSLOADPOST 2024:08:07:17:38:27 mris_curvature N 4 10.70 10.82 10.65
rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
rh.inflated
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
217 vertices thresholded to be in k1 ~ [-0.25 0.43], k2 ~ [-0.12 0.05]
total integrated curvature = 0.360*4pi (4.523) --> 1 handles
ICI = 1.4, FI = 8.6, variation=149.486
131 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at
99.90% level
curvature mean = 0.000, std = 0.001
154 vertices thresholded to be in [-0.15 0.21]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std =
0.023
mris_curvature done.
@#@FSTIME  2024:08:07:17:38:27 mris_curvature N 12 e 27.74 S 0.13 U 27.61 P
99% M 358716 F 0 R 92949 W 0 c 112 w 2 I 0 O 2080 L 10.70 10.82 10.65
@#@FSLOADPOST 2024:08:07:17:38:55 mris_curvature N 12 10.78 10.83 10.66
#--------------------------------------------
#@# Sphere lh 公曆 20廿四年 八月 七日 週三 十七時38分55秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
setting seed for random number genererator to 1234
version: 7.4.1
available threads: 1
reading original vertex positions...
projecting onto sphere...
surface projected - minimizing metric distortion...
scaling brain by 0.307...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=2, l_area=1.000,
l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
--------------------
mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.42
pass 1: epoch 2 of 3 starting distance error %21.37
unfolding complete - removing small folds...
starting distance error %21.31
removing remaining folds...
final distance error %21.36
MRISunfold() return, current seed 1234
-01: dt=0.0000,   3 negative triangles  VmPeak 537716
154: dt=0.9900,   3 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.0728 hours
FSRUNTIME@ mris_sphere  0.0728 hours 1 threads
#VMPC# mris_sphere VmPeak  537716
mris_sphere done
@#@FSTIME  2024:08:07:17:38:55 mris_sphere N 4 e 262.21 S 12.08 U 250.10 P
99% M 279856 F 0 R 11513000 W 0 c 1162 w 92 I 0 O 9600 L 10.78 10.83 10.66
@#@FSLOADPOST 2024:08:07:17:43:17 mris_sphere N 4 11.21 11.01 10.77
#--------------------------------------------
#@# Sphere rh 公曆 20廿四年 八月 七日 週三 十七時43分十七秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
setting seed for random number genererator to 1234
version: 7.4.1
available threads: 1
reading original vertex positions...
projecting onto sphere...
surface projected - minimizing metric distortion...
scaling brain by 0.310...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=2, l_area=1.000,
l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234
--------------------
mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %44.01
pass 1: epoch 2 of 3 starting distance error %22.08
unfolding complete - removing small folds...
starting distance error %21.95
removing remaining folds...
final distance error %21.99
MRISunfold() return, current seed 1234
-01: dt=0.0000,   2 negative triangles  VmPeak 530576
149: dt=0.9900,   2 negative triangles
150: dt=0.9405,   2 negative triangles
151: dt=0.9405,   1 negative triangles
152: dt=0.9405,   1 negative triangles
153: dt=0.9405,   3 negative triangles
154: dt=0.9405,   1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.0617 hours
FSRUNTIME@ mris_sphere  0.0617 hours 1 threads
#VMPC# mris_sphere VmPeak  530576
mris_sphere done
@#@FSTIME  2024:08:07:17:43:17 mris_sphere N 4 e 222.18 S 11.35 U 210.79 P
99% M 272708 F 0 R 10911357 W 0 c 911 w 249 I 0 O 9344 L 11.21 11.01 10.77
@#@FSLOADPOST 2024:08:07:17:46:59 mris_sphere N 4 9.94 10.60 10.68
#--------------------------------------------
#@# Surf Reg lh 公曆 20廿四年 八月 七日 週三 十七時46分59秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_register -curv ../surf/lh.sphere
/usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif ../surf/lh.sphere.reg
using smoothwm curvature for final alignment
cwd /home/chang/GBM_Data/VBG/0003/0003/scripts
cmdline mris_register -curv ../surf/lh.sphere
/usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif ../surf/lh.sphere.reg
0 inflated.H
1 sulc
2 smoothwm (computed)
7.4.1
7.4.1
reading surface from ../surf/lh.sphere...
reading template parameterization from
/usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0
tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
tol=1.0e+00, sigma=0.5, host=chang, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = 0.000, std = 5.720
curvature mean = 0.046, std = 0.815
curvature mean = 0.004, std = 0.858
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
new MRISrigidBodyAlignGlobal_findMinSSE min @ (5.00, -6.00, -12.50) sse =
212802.5, elapsed since starting=0.2022 min
MRISrigidBodyAlignGlobal() done   0.20 min
curvature mean = 0.029, std = 0.839
curvature mean = 0.000, std = 0.944
curvature mean = 0.027, std = 0.850
curvature mean = -0.000, std = 0.976
curvature mean = 0.027, std = 0.854
curvature mean = -0.000, std = 0.989
2 Reading smoothwm
curvature mean = -0.017, std = 0.226
curvature mean = 0.045, std = 0.247
curvature mean = 0.028, std = 0.445
curvature mean = 0.044, std = 0.302
curvature mean = 0.021, std = 0.657
curvature mean = 0.044, std = 0.328
curvature mean = 0.010, std = 0.800
curvature mean = 0.043, std = 0.340
curvature mean = 0.003, std = 0.890
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
-01: dt=0.0000,   0 negative triangles  VmPeak 519808
registration took 0.06 hours
#VMPC# mris_register VmPeak  519808
FSRUNTIME@ mris_register  0.0581 hours 1 threads
@#@FSTIME  2024:08:07:17:46:59 mris_register N 4 e 209.08 S 7.61 U 201.43 P
99% M 261452 F 18 R 7515214 W 0 c 768 w 200 I 8128 O 9600 L 9.94 10.60 10.68
@#@FSLOADPOST 2024:08:07:17:50:28 mris_register N 4 10.44 10.62 10.68
ln -sf lh.sphere.reg lh.fsaverage.sphere.reg
#--------------------------------------------
#@# Surf Reg rh 公曆 20廿四年 八月 七日 週三 十七時50分廿八秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_register -curv ../surf/rh.sphere
/usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif ../surf/rh.sphere.reg
using smoothwm curvature for final alignment
cwd /home/chang/GBM_Data/VBG/0003/0003/scripts
cmdline mris_register -curv ../surf/rh.sphere
/usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif ../surf/rh.sphere.reg
0 inflated.H
1 sulc
2 smoothwm (computed)
7.4.1
7.4.1
reading surface from ../surf/rh.sphere...
reading template parameterization from
/usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 1
randomSeed 0
tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading rh.sulc
tol=1.0e+00, sigma=0.5, host=chang, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = -0.000, std = 5.658
curvature mean = 0.050, std = 0.822
curvature mean = -0.000, std = 0.858
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
new MRISrigidBodyAlignGlobal_findMinSSE min @ (6.50, -3.50, -4.50) sse =
224771.5, elapsed since starting=0.1902 min
MRISrigidBodyAlignGlobal() done   0.19 min
curvature mean = 0.029, std = 0.830
curvature mean = -0.001, std = 0.948
curvature mean = 0.025, std = 0.839
curvature mean = -0.000, std = 0.979
curvature mean = 0.023, std = 0.840
curvature mean = -0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.015, std = 0.232
curvature mean = 0.039, std = 0.237
curvature mean = 0.023, std = 0.438
curvature mean = 0.039, std = 0.293
curvature mean = 0.019, std = 0.651
curvature mean = 0.038, std = 0.319
curvature mean = 0.009, std = 0.796
curvature mean = 0.038, std = 0.330
curvature mean = 0.002, std = 0.887
MRISregister() return, current seed 0
-01: dt=0.0000,   1 negative triangles  VmPeak 515992
112: dt=0.9900,   1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 0.06 hours
#VMPC# mris_register VmPeak  515992
FSRUNTIME@ mris_register  0.0626 hours 1 threads
@#@FSTIME  2024:08:07:17:50:28 mris_register N 4 e 225.33 S 7.68 U 217.61 P
99% M 257012 F 0 R 7460050 W 0 c 780 w 301 I 5584 O 9344 L 10.44 10.62 10.68
@#@FSLOADPOST 2024:08:07:17:54:14 mris_register N 4 11.27 10.78 10.72
ln -sf rh.sphere.reg rh.fsaverage.sphere.reg
#--------------------------------------------
#@# Jacobian white lh 公曆 20廿四年 八月 七日 週三 十七時54分十四秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg
../surf/lh.jacobian_white
reading surface from ../surf/lh.white.preaparc...
writing curvature file ../surf/lh.jacobian_white
@#@FSTIME  2024:08:07:17:54:14 mris_jacobian N 3 e 0.63 S 0.08 U 0.54 P 99%
M 209104 F 5 R 62485 W 0 c 2 w 8 I 648 O 1072 L 11.27 10.78 10.72
@#@FSLOADPOST 2024:08:07:17:54:14 mris_jacobian N 3 11.27 10.78 10.72
#--------------------------------------------
#@# Jacobian white rh 公曆 20廿四年 八月 七日 週三 十七時54分十四秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg
../surf/rh.jacobian_white
reading surface from ../surf/rh.white.preaparc...
writing curvature file ../surf/rh.jacobian_white
@#@FSTIME  2024:08:07:17:54:14 mris_jacobian N 3 e 0.50 S 0.06 U 0.43 P 99%
M 203228 F 0 R 60864 W 0 c 8 w 3 I 0 O 1040 L 11.27 10.78 10.72
@#@FSLOADPOST 2024:08:07:17:54:15 mris_jacobian N 3 11.27 10.78 10.72
#--------------------------------------------
#@# AvgCurv lh 公曆 20廿四年 八月 七日 週三 十七時54分十五秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mrisp_paint -a 5
/usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
averaging curvature patterns 5 times...
reading surface from ../surf/lh.sphere.reg...
reading template parameterization from
/usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif...
writing curvature file to ../surf/lh.avg_curv...
@#@FSTIME  2024:08:07:17:54:15 mrisp_paint N 5 e 0.42 S 0.05 U 0.37 P 99% M
160452 F 8 R 43295 W 0 c 5 w 9 I 1104 O 1072 L 11.27 10.78 10.72
@#@FSLOADPOST 2024:08:07:17:54:15 mrisp_paint N 5 11.27 10.78 10.72
#--------------------------------------------
#@# AvgCurv rh 公曆 20廿四年 八月 七日 週三 十七時54分十五秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mrisp_paint -a 5
/usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
averaging curvature patterns 5 times...
reading surface from ../surf/rh.sphere.reg...
reading template parameterization from
/usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02
.tif...
writing curvature file to ../surf/rh.avg_curv...
@#@FSTIME  2024:08:07:17:54:15 mrisp_paint N 5 e 0.42 S 0.05 U 0.36 P 99% M
156920 F 0 R 42211 W 0 c 5 w 3 I 0 O 1040 L 11.27 10.78 10.72
@#@FSLOADPOST 2024:08:07:17:54:16 mrisp_paint N 5 11.27 10.78 10.72
#-----------------------------------------
#@# Cortical Parc lh 公曆 20廿四年 八月 七日 週三 十七時54分十六秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 0003 lh ../surf/lh.sphere.reg
/usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs ../label/lh.aparc.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.4.1
7.4.1
reading atlas from
/usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs...
reading color table from GCSA file....
average std = 0.8   using min determinant for regularization = 0.006
0 singular and 342 ill-conditioned covariance matrices regularized
reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/lh.smoothwm...
GCSA::load_default_data(): ninputs=1  sulc_only=0 which_norm=0
labeling surface...
1105 labels changed using aseg
relabeling using gibbs priors...
000:   2968 changed, 136375 examined...
001:    660 changed, 12596 examined...
002:    145 changed, 3813 examined...
003:     44 changed, 903 examined...
004:      8 changed, 278 examined...
005:      1 changed, 56 examined...
006:      0 changed, 8 examined...
278 labels changed using aseg
000: 97 total segments, 56 labels (143 vertices) changed
001: 41 total segments, 1 labels (1 vertices) changed
002: 40 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1793 vertices marked for relabeling...
1793 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 6 seconds.
@#@FSTIME  2024:08:07:17:54:16 mris_ca_label N 11 e 5.66 S 0.36 U 5.28 P 99%
M 1136268 F 10 R 411388 W 0 c 25 w 98 I 64856 O 2136 L 11.27 10.78 10.72
@#@FSLOADPOST 2024:08:07:17:54:21 mris_ca_label N 11 11.01 10.73 10.70
#-----------------------------------------
#@# Cortical Parc rh 公曆 20廿四年 八月 七日 週三 十七時54分廿一秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 0003 rh ../surf/rh.sphere.reg
/usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs ../label/rh.aparc.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.4.1
7.4.1
reading atlas from
/usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs...
reading color table from GCSA file....
average std = 0.7   using min determinant for regularization = 0.004
0 singular and 309 ill-conditioned covariance matrices regularized
reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/rh.smoothwm...
GCSA::load_default_data(): ninputs=1  sulc_only=0 which_norm=0
labeling surface...
987 labels changed using aseg
relabeling using gibbs priors...
000:   2616 changed, 132793 examined...
001:    586 changed, 11348 examined...
002:    124 changed, 3422 examined...
003:     45 changed, 773 examined...
004:     21 changed, 256 examined...
005:      8 changed, 133 examined...
006:      4 changed, 44 examined...
007:      2 changed, 20 examined...
008:      1 changed, 12 examined...
009:      1 changed, 7 examined...
010:      1 changed, 6 examined...
011:      0 changed, 8 examined...
231 labels changed using aseg
000: 101 total segments, 56 labels (168 vertices) changed
001: 45 total segments, 0 labels (0 vertices) changed
9 filter iterations complete (10 requested, 0 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1340 vertices marked for relabeling...
1340 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 5 seconds.
@#@FSTIME  2024:08:07:17:54:21 mris_ca_label N 11 e 5.41 S 0.33 U 5.07 P 99%
M 1136480 F 0 R 365822 W 0 c 20 w 4 I 36352 O 2080 L 11.01 10.73 10.70
@#@FSLOADPOST 2024:08:07:17:54:27 mris_ca_label N 11 10.93 10.72 10.70
#--------------------------------------------
#@# WhiteSurfs lh 公曆 20廿四年 八月 七日 週三 十七時54分廿七秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0
--rip-label ../label/lh.cortex.label --rip-bg --rip-surf
../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0
--rip-label ../label/lh.cortex.label --rip-bg --rip-surf
../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot
Reading in input surface ../surf/lh.white.preaparc
Not smoothing input surface
Area    272746  0.33816  0.11534 0.002272   3.1832
Corner  818238 60.00000 13.02321 0.283077 178.2590
Edge    409119  0.89362  0.18737 0.015059   4.0252
Hinge   409119  9.49847 10.03758 0.000001 179.8258
Reading in aparc ../label/lh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex.label
MRISripNotLabel() ripped 8790/136375 vertices (127585 unripped)
Reading in ripping surface ../surf/lh.white.preaparc
Reading in aparc ../label/lh.aparc.annot for ripsurf
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Ripping BG
MRISripBasalGanglia(): 1 -2 2 0.5 ripped 389
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 68188: xyz = (-28.8076,-16.4404,32.5965) oxyz =
(-28.8076,-16.4404,32.5965) wxzy = (-28.8076,-16.4404,32.5965) pxyz =
(0,0,0)
CBVO Creating mask 136375
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 128 vertices, nripped=9179
mean border=79.5, 181 (181) missing vertices, mean dist 0.3 [0.7 (%20.4)->0.
6 (%79.6))]
%57 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1043 min
Finding expansion regions
mean absolute distance = 0.61 +- 1.01
5103 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=1649126.6, rms=7.539
001: dt: 0.5000, sse=930038.9, rms=5.374 (28.715%)
002: dt: 0.5000, sse=704554.6, rms=4.482 (16.595%)
003: dt: 0.5000, sse=627665.1, rms=4.094 (8.657%)
004: dt: 0.5000, sse=553975.8, rms=3.737 (8.725%)
005: dt: 0.5000, sse=540183.3, rms=3.683 (1.435%)
006: dt: 0.5000, sse=507197.3, rms=3.490 (5.250%)
rms = 3.5568/3.4899, sse=522696.2/507197.3, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
007: dt: 0.2500, sse=329416.6, rms=2.271 (34.932%)
008: dt: 0.2500, sse=270572.3, rms=1.634 (28.047%)
009: dt: 0.2500, sse=249053.9, rms=1.407 (13.920%)
010: dt: 0.2500, sse=243521.0, rms=1.325 (5.806%)
011: dt: 0.2500, sse=242632.4, rms=1.274 (3.832%)
rms = 1.2477/1.2741, sse=242299.1/242632.4, time step reduction 2 of 3 to 0.
125  0 0 1
012: dt: 0.2500, sse=242299.1, rms=1.248 (2.068%)
rms = 1.2019/1.2477, sse=238906.3/242299.1, time step reduction 3 of 3 to 0.
062  0 0 1
013: dt: 0.1250, sse=238906.3, rms=1.202 (3.670%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
done positioning surface
Iteration 1 =========================================
n_averages=2, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 101 vertices, nripped=9179
mean border=82.1, 221 (115) missing vertices, mean dist -0.3 [0.6
(%65.7)->0.2 (%34.3))]
%63 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0755 min
Finding expansion regions
mean absolute distance = 0.45 +- 0.90
5611 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=723190.6, rms=4.437
014: dt: 0.5000, sse=495846.8, rms=3.280 (26.068%)
rms = 3.4005/3.2805, sse=516489.5/495846.8, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
015: dt: 0.2500, sse=391216.1, rms=2.587 (21.138%)
016: dt: 0.2500, sse=331558.1, rms=2.024 (21.748%)
017: dt: 0.2500, sse=298149.3, rms=1.698 (16.144%)
018: dt: 0.2500, sse=286515.8, rms=1.484 (12.598%)
019: dt: 0.2500, sse=272789.6, rms=1.333 (10.131%)
020: dt: 0.2500, sse=262646.3, rms=1.226 (8.070%)
021: dt: 0.2500, sse=262408.5, rms=1.153 (5.928%)
022: dt: 0.2500, sse=258558.3, rms=1.096 (4.969%)
rms = 1.0590/1.0959, sse=256231.2/258558.3, time step reduction 2 of 3 to 0.
125  0 0 1
023: dt: 0.2500, sse=256231.2, rms=1.059 (3.365%)
rms = 1.0145/1.0590, sse=252701.9/256231.2, time step reduction 3 of 3 to 0.
062  0 0 1
024: dt: 0.1250, sse=252701.9, rms=1.014 (4.205%)
maximum number of reductions reached, breaking from loop
positioning took 0.7 minutes
done positioning surface
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 175 vertices, nripped=9179
mean border=84.1, 225 (102) missing vertices, mean dist -0.2 [0.4
(%65.3)->0.2 (%34.7))]
%71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0432 min
Finding expansion regions
mean absolute distance = 0.37 +- 0.69
5492 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=470661.5, rms=3.164
025: dt: 0.5000, sse=381812.5, rms=2.526 (20.171%)
rms = 2.8871/2.5262, sse=432543.7/381812.5, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
026: dt: 0.2500, sse=295975.0, rms=1.762 (30.263%)
027: dt: 0.2500, sse=261866.4, rms=1.279 (27.405%)
rms = 1.0708/1.2789, sse=263346.2/261866.4, time step reduction 2 of 3 to 0.
125  0 1 0
028: dt: 0.2500, sse=263346.2, rms=1.071 (16.270%)
029: dt: 0.1250, sse=243083.3, rms=0.980 (8.482%)
rms = 0.9448/0.9800, sse=242664.1/243083.3, time step reduction 3 of 3 to 0.
062  0 0 1
030: dt: 0.1250, sse=242664.1, rms=0.945 (3.588%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  64.0000000;
outside_low =  51.2911300;
outside_hi  = 112.3613130;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 113 vertices, nripped=9179
mean border=84.9, 252 (98) missing vertices, mean dist -0.1 [0.4 (%56.7)->0.
3 (%43.3))]
%75 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0286 min
Finding expansion regions
mean absolute distance = 0.33 +- 0.56
4436 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=309507.7, rms=1.932
031: dt: 0.5000, sse=302431.8, rms=1.724 (10.756%)
rms = 2.2850/1.7245, sse=349086.6/302431.8, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
032: dt: 0.2500, sse=245943.4, rms=1.091 (36.716%)
033: dt: 0.2500, sse=236383.9, rms=0.850 (22.068%)
034: dt: 0.2500, sse=232593.1, rms=0.773 (9.144%)
rms = 0.7675/0.7727, sse=234206.4/232593.1, time step reduction 2 of 3 to 0.
125  0 1 1
035: dt: 0.2500, sse=234206.4, rms=0.767 (0.681%)
036: dt: 0.1250, sse=228430.4, rms=0.716 (6.663%)
rms = 0.7074/0.7163, sse=225214.3/228430.4, time step reduction 3 of 3 to 0.
062  0 0 1
037: dt: 0.1250, sse=225214.3, rms=0.707 (1.250%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface  2.51 minutes
Writing output to ../surf/lh.white
#VMPC# mris_place_surfaces VmPeak  2164264
mris_place_surface done
@#@FSTIME  2024:08:07:17:54:27 mris_place_surface N 25 e 155.65 S 0.59 U
155.05 P 99% M 1905528 F 0 R 538708 W 0 c 546 w 42 I 0 O 9592 L 10.93 10.72
10.70
@#@FSLOADPOST 2024:08:07:17:57:03 mris_place_surface N 25 10.39 10.47 10.61
#--------------------------------------------
#@# WhiteSurfs rh 公曆 20廿四年 八月 七日 週三 十七時57分三秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh
--i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0
--rip-label ../label/rh.cortex.label --rip-bg --rip-surf
../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh
--i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0
--rip-label ../label/rh.cortex.label --rip-bg --rip-surf
../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot
Reading in input surface ../surf/rh.white.preaparc
Not smoothing input surface
Area    265582  0.34259  0.12168 0.002037   2.5951
Corner  796746 60.00000 13.24604 0.376281 176.7460
Edge    398373  0.89985  0.19702 0.016821   3.4749
Hinge   398373  9.84040 10.71187 0.000003 179.8247
Reading in aparc ../label/rh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/rh.cortex.label
MRISripNotLabel() ripped 8892/132793 vertices (123901 unripped)
Reading in ripping surface ../surf/rh.white.preaparc
Reading in aparc ../label/rh.aparc.annot for ripsurf
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Ripping BG
MRISripBasalGanglia(): 1 -2 2 0.5 ripped 409
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 66397: xyz = (50.1364,-13.7269,19.1954) oxyz =
(50.1364,-13.7269,19.1954) wxzy = (50.1364,-13.7269,19.1954) pxyz = (0,0,0)
CBVO Creating mask 132793
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 184 vertices, nripped=9301
mean border=78.9, 179 (179) missing vertices, mean dist 0.3 [0.7 (%22.0)->0.
6 (%78.0))]
%59 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1039 min
Finding expansion regions
mean absolute distance = 0.63 +- 1.07
4567 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=1608454.8, rms=7.559
001: dt: 0.5000, sse=959092.6, rms=5.574 (26.270%)
002: dt: 0.5000, sse=758160.2, rms=4.740 (14.953%)
003: dt: 0.5000, sse=665441.2, rms=4.365 (7.906%)
004: dt: 0.5000, sse=594201.2, rms=3.979 (8.844%)
005: dt: 0.5000, sse=582043.4, rms=3.919 (1.513%)
006: dt: 0.5000, sse=531500.7, rms=3.683 (6.015%)
rms = 3.7380/3.6834, sse=542452.8/531500.7, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
007: dt: 0.2500, sse=352007.8, rms=2.502 (32.080%)
008: dt: 0.2500, sse=287511.7, rms=1.897 (24.172%)
009: dt: 0.2500, sse=266896.0, rms=1.654 (12.798%)
010: dt: 0.2500, sse=263011.6, rms=1.548 (6.444%)
011: dt: 0.2500, sse=256604.5, rms=1.471 (4.967%)
rms = 1.4230/1.4708, sse=249419.5/256604.5, time step reduction 2 of 3 to 0.
125  0 0 1
012: dt: 0.2500, sse=249419.5, rms=1.423 (3.249%)
013: dt: 0.1250, sse=248150.6, rms=1.365 (4.091%)
rms = 1.3476/1.3648, sse=249619.6/248150.6, time step reduction 3 of 3 to 0.
062  0 1 1
014: dt: 0.1250, sse=249619.6, rms=1.348 (1.261%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
done positioning surface
Iteration 1 =========================================
n_averages=2, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 138 vertices, nripped=9301
mean border=81.3, 205 (96) missing vertices, mean dist -0.3 [0.6 (%64.7)->0.
3 (%35.3))]
%64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0756 min
Finding expansion regions
mean absolute distance = 0.46 +- 0.93
5906 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=735868.4, rms=4.545
015: dt: 0.5000, sse=518800.8, rms=3.441 (24.293%)
rms = 3.5340/3.4405, sse=532536.9/518800.7, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
016: dt: 0.2500, sse=407538.5, rms=2.712 (21.181%)
017: dt: 0.2500, sse=337413.7, rms=2.108 (22.255%)
018: dt: 0.2500, sse=299869.5, rms=1.757 (16.681%)
019: dt: 0.2500, sse=289669.3, rms=1.534 (12.693%)
020: dt: 0.2500, sse=272518.7, rms=1.383 (9.804%)
021: dt: 0.2500, sse=267529.3, rms=1.271 (8.087%)
022: dt: 0.2500, sse=264880.4, rms=1.198 (5.740%)
rms = 1.1380/1.1984, sse=265182.1/264880.4, time step reduction 2 of 3 to 0.
125  0 1 0
023: dt: 0.2500, sse=265182.2, rms=1.138 (5.040%)
024: dt: 0.1250, sse=262272.7, rms=1.084 (4.758%)
rms = 1.0650/1.0839, sse=264757.5/262272.7, time step reduction 3 of 3 to 0.
062  0 1 1
025: dt: 0.1250, sse=264757.5, rms=1.065 (1.744%)
maximum number of reductions reached, breaking from loop
positioning took 0.7 minutes
done positioning surface
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 186 vertices, nripped=9301
mean border=83.2, 188 (80) missing vertices, mean dist -0.2 [0.5 (%64.9)->0.
3 (%35.1))]
%71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0397 min
Finding expansion regions
mean absolute distance = 0.38 +- 0.70
5070 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=461516.9, rms=3.088
026: dt: 0.5000, sse=395712.1, rms=2.600 (15.801%)
rms = 3.0407/2.5998, sse=469765.1/395712.1, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
027: dt: 0.2500, sse=314416.0, rms=1.806 (30.516%)
028: dt: 0.2500, sse=276677.0, rms=1.348 (25.371%)
029: dt: 0.2500, sse=256800.5, rms=1.143 (15.193%)
030: dt: 0.2500, sse=249938.3, rms=1.052 (8.025%)
rms = 1.0139/1.0516, sse=242593.3/249938.3, time step reduction 2 of 3 to 0.
125  0 0 1
031: dt: 0.2500, sse=242593.2, rms=1.014 (3.586%)
032: dt: 0.1250, sse=237817.3, rms=0.951 (6.155%)
rms = 0.9405/0.9515, sse=238283.0/237817.3, time step reduction 3 of 3 to 0.
062  0 1 1
033: dt: 0.1250, sse=238283.0, rms=0.940 (1.154%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
done positioning surface
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   = 120.0000000;
border_hi   = 112.3613130;
border_low  =  62.0000000;
outside_low =  49.2911300;
outside_hi  = 112.3613130;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 127 vertices, nripped=9301
mean border=84.1, 220 (71) missing vertices, mean dist -0.1 [0.4 (%56.4)->0.
3 (%43.6))]
%76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0280 min
Finding expansion regions
mean absolute distance = 0.33 +- 0.57
4475 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=304504.8, rms=1.949
034: dt: 0.5000, sse=296084.3, rms=1.807 (7.289%)
rms = 2.4378/1.8072, sse=354140.3/296084.3, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
035: dt: 0.2500, sse=241556.9, rms=1.150 (36.374%)
036: dt: 0.2500, sse=232064.5, rms=0.920 (19.978%)
037: dt: 0.2500, sse=224740.8, rms=0.842 (8.469%)
rms = 0.8400/0.8422, sse=222657.9/224740.8, time step reduction 2 of 3 to 0.
125  0 0 1
038: dt: 0.2500, sse=222657.9, rms=0.840 (0.270%)
039: dt: 0.1250, sse=220650.0, rms=0.771 (8.155%)
rms = 0.7644/0.7715, sse=220726.5/220649.9, time step reduction 3 of 3 to 0.
062  0 1 1
040: dt: 0.1250, sse=220726.5, rms=0.764 (0.914%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface  2.63 minutes
Writing output to ../surf/rh.white
#VMPC# mris_place_surfaces VmPeak  2174856
mris_place_surface done
@#@FSTIME  2024:08:07:17:57:03 mris_place_surface N 25 e 162.20 S 0.55 U
161.63 P 99% M 1916156 F 0 R 517087 W 0 c 559 w 140 I 0 O 9344 L 10.39 10.47
10.61
@#@FSLOADPOST 2024:08:07:17:59:45 mris_place_surface N 25 10.78 10.46 10.57
#--------------------------------------------
#@# T1PialSurf lh 公曆 20廿四年 八月 七日 週三 十七時59分45秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label
../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label
--aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf
../surf/lh.white
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label
../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label
--aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf
../surf/lh.white
Reading in input surface ../surf/lh.white
Not smoothing input surface
Area    272746  0.34084  0.13137 0.001104   3.1137
Corner  818238 60.00000 14.68941 0.256211 179.1172
Edge    409119  0.89911  0.21080 0.018905   3.5050
Hinge   409119  9.83579 11.02995 0.000006 179.9860
Reading white surface coordinates from ../surf/lh.white
Reading repulsion surface coordinates from ../surf/lh.white
Reading in aparc ../label/lh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 60.756
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex+hipamyg.label
MRISripNotLabel() ripped 7099/136375 vertices (129276 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 68188: xyz = (-28.7963,-16.4263,32.6041) oxyz =
(-28.7963,-16.4263,32.6041) wxzy = (-28.7963,-16.4263,32.6041) pxyz =
(-28.7963,-16.4263,32.6041)
CBVO Creating mask 136375
n_averages 16
Iteration 0 =========================================
n_averages=16, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  51.2911300;
border_low  =  25.8733980;
outside_low =  10.0000000;
outside_hi  =  44.9366990;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 193 vertices, nripped=7099
mean border=50.5, 235 (235) missing vertices, mean dist 1.8 [3.5 (%0.0)->2.9
(%100.0))]
%11 local maxima, %49 large gradients and %35 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0859 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=chang, nav=16, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=32054922.0, rms=35.135
001: dt: 0.5000, sse=23047766.0, rms=29.756 (15.309%)
002: dt: 0.5000, sse=16248795.0, rms=24.938 (16.191%)
003: dt: 0.5000, sse=11582516.0, rms=21.001 (15.790%)
004: dt: 0.5000, sse=8732515.0, rms=18.179 (13.435%)
005: dt: 0.5000, sse=7042099.5, rms=16.276 (10.471%)
006: dt: 0.5000, sse=5795407.0, rms=14.714 (9.598%)
007: dt: 0.5000, sse=4917989.0, rms=13.505 (8.213%)
008: dt: 0.5000, sse=4178076.2, rms=12.393 (8.231%)
009: dt: 0.5000, sse=3623495.2, rms=11.489 (7.297%)
010: dt: 0.5000, sse=3114657.2, rms=10.591 (7.818%)
011: dt: 0.5000, sse=2738036.0, rms=9.873 (6.777%)
012: dt: 0.5000, sse=2378002.0, rms=9.134 (7.486%)
013: dt: 0.5000, sse=2122419.2, rms=8.570 (6.177%)
014: dt: 0.5000, sse=1861151.5, rms=7.952 (7.212%)
015: dt: 0.5000, sse=1684708.1, rms=7.505 (5.622%)
016: dt: 0.5000, sse=1505404.0, rms=7.022 (6.439%)
017: dt: 0.5000, sse=1405290.0, rms=6.735 (4.080%)
018: dt: 0.5000, sse=1295281.2, rms=6.406 (4.886%)
019: dt: 0.5000, sse=1255644.8, rms=6.281 (1.949%)
020: dt: 0.5000, sse=1192210.8, rms=6.078 (3.231%)
rms = 6.0467/6.0782, sse=1183253.1/1192210.8, time step reduction 1 of 3 to
0.250  0 0 1
021: dt: 0.5000, sse=1183253.1, rms=6.047 (0.517%)
022: dt: 0.2500, sse=1003253.0, rms=5.424 (10.304%)
023: dt: 0.2500, sse=970316.9, rms=5.302 (2.244%)
rms = 5.2785/5.3019, sse=964385.9/970316.9, time step reduction 2 of 3 to 0.
125  0 0 1
024: dt: 0.2500, sse=964385.9, rms=5.278 (0.443%)
025: dt: 0.1250, sse=930701.1, rms=5.150 (2.436%)
rms = 5.1288/5.1499, sse=925395.8/930701.1, time step reduction 3 of 3 to 0.
062  0 0 1
026: dt: 0.1250, sse=925395.8, rms=5.129 (0.409%)
maximum number of reductions reached, breaking from loop
positioning took 1.3 minutes
done positioning surface
Iteration 1 =========================================
n_averages=8, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  51.2911300;
border_low  =  25.8733980;
outside_low =  10.0000000;
outside_hi  =  44.9366990;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 10620 vertices, nripped=7099
mean border=50.4, 1984 (52) missing vertices, mean dist 0.2 [0.1 (%55.2)->0.
8 (%44.8))]
%20 local maxima, %42 large gradients and %32 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0320 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=chang, nav=8, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=916715.8, rms=4.806
rms = 4.8533/4.8065, sse=927440.3/916715.8, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
027: dt: 0.2500, sse=871876.8, rms=4.621 (3.863%)
028: dt: 0.2500, sse=839656.2, rms=4.483 (2.984%)
029: dt: 0.2500, sse=825045.9, rms=4.420 (1.408%)
rms = 4.4004/4.4198, sse=820530.0/825045.9, time step reduction 2 of 3 to 0.
125  0 0 1
030: dt: 0.2500, sse=820530.0, rms=4.400 (0.440%)
031: dt: 0.1250, sse=803860.4, rms=4.323 (1.750%)
rms = 4.3035/4.3234, sse=799592.2/803860.4, time step reduction 3 of 3 to 0.
062  0 0 1
032: dt: 0.1250, sse=799592.1, rms=4.304 (0.459%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Iteration 2 =========================================
n_averages=4, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  51.2911300;
border_low  =  25.8733980;
outside_low =  10.0000000;
outside_hi  =  44.9366990;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 10489 vertices, nripped=7099
mean border=49.8, 2600 (42) missing vertices, mean dist 0.2 [0.1 (%49.6)->0.
7 (%50.4))]
%29 local maxima, %32 large gradients and %31 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0167 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=chang, nav=4, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=860412.1, rms=4.562
rms = 4.7047/4.5625, sse=893308.5/860412.0, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
033: dt: 0.2500, sse=823442.2, rms=4.402 (3.518%)
034: dt: 0.2500, sse=799969.7, rms=4.299 (2.344%)
rms = 4.2575/4.2987, sse=790532.7/799969.7, time step reduction 2 of 3 to 0.
125  0 0 1
035: dt: 0.2500, sse=790532.7, rms=4.257 (0.960%)
rms = 4.2120/4.2575, sse=781022.3/790532.7, time step reduction 3 of 3 to 0.
062  0 0 1
036: dt: 0.1250, sse=781022.3, rms=4.212 (1.068%)
maximum number of reductions reached, breaking from loop
positioning took 0.2 minutes
done positioning surface
Iteration 3 =========================================
n_averages=2, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  51.2911300;
border_low  =  25.8733980;
outside_low =  10.0000000;
outside_hi  =  44.9366990;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=136375
Gdiag_no=-1
vno start=0, stop=136375
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 8152 vertices, nripped=7099
mean border=48.9, 5501 (37) missing vertices, mean dist 0.2 [0.1 (%48.3)->0.
6 (%51.7))]
%35 local maxima, %26 large gradients and %30 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0100 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=chang, nav=2, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=828618.9, rms=4.425
rms = 4.5791/4.4247, sse=862726.1/828618.9, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
037: dt: 0.2500, sse=798232.6, rms=4.289 (3.065%)
038: dt: 0.2500, sse=775404.8, rms=4.189 (2.345%)
rms = 4.1457/4.1885, sse=765501.3/775404.7, time step reduction 2 of 3 to 0.
125  0 0 1
039: dt: 0.2500, sse=765501.4, rms=4.146 (1.023%)
040: dt: 0.1250, sse=753654.8, rms=4.089 (1.377%)
rms = 4.0643/4.0886, sse=748361.4/753654.8, time step reduction 3 of 3 to 0.
062  0 0 1
041: dt: 0.1250, sse=748361.4, rms=4.064 (0.593%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
done positioning surface
Pinning medial wall to white surface
Removing intersections
removing intersecting faces
000: 4 intersecting
step 1 with no progress (num=5, old_num=4)
001: 5 intersecting
terminating search with 0 intersecting
#ET# mris_place_surface  2.45 minutes
Writing output to ../surf/lh.pial.T1
#VMPC# mris_place_surfaces VmPeak  1359888
mris_place_surface done
@#@FSTIME  2024:08:07:17:59:45 mris_place_surface N 28 e 151.41 S 0.39 U
151.00 P 99% M 1102040 F 0 R 303927 W 0 c 506 w 101 I 0 O 9592 L 10.78 10.46
10.57
@#@FSLOADPOST 2024:08:07:18:02:17 mris_place_surface N 28 9.94 10.20 10.45
#--------------------------------------------
#@# T1PialSurf rh 公曆 20廿四年 八月 七日 週三 十八時二分十七秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh
--i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label
../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label
--aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf
../surf/rh.white
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg
aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh
--i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label
../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label
--aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf
../surf/rh.white
Reading in input surface ../surf/rh.white
Not smoothing input surface
Area    265582  0.34629  0.13997 0.000323   3.8735
Corner  796746 60.00000 14.67677 0.116431 179.7091
Edge    398373  0.90606  0.21889 0.029829   4.4605
Hinge   398373 10.07644 11.42100 0.000069 179.9864
Reading white surface coordinates from ../surf/rh.white
Reading repulsion surface coordinates from ../surf/rh.white
Reading in aparc ../label/rh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 59.756
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/rh.cortex+hipamyg.label
MRISripNotLabel() ripped 7437/132793 vertices (125356 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 66397: xyz = (50.097,-13.6992,19.1422) oxyz =
(50.097,-13.6992,19.1422) wxzy = (50.097,-13.6992,19.1422) pxyz =
(50.097,-13.6992,19.1422)
CBVO Creating mask 132793
n_averages 16
Iteration 0 =========================================
n_averages=16, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  49.2911300;
border_low  =  23.8733980;
outside_low =  10.0000000;
outside_hi  =  42.9366990;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 181 vertices, nripped=7437
mean border=49.2, 199 (199) missing vertices, mean dist 1.7 [6.5 (%0.0)->2.8
(%100.0))]
% 9 local maxima, %47 large gradients and %38 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0838 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=chang, nav=16, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=32014970.0, rms=35.655
001: dt: 0.5000, sse=23031894.0, rms=30.205 (15.284%)
002: dt: 0.5000, sse=16270871.0, rms=25.341 (16.103%)
003: dt: 0.5000, sse=11645042.0, rms=21.384 (15.616%)
004: dt: 0.5000, sse=8802490.0, rms=18.536 (13.318%)
005: dt: 0.5000, sse=7115731.5, rms=16.617 (10.357%)
006: dt: 0.5000, sse=5865234.0, rms=15.035 (9.521%)
007: dt: 0.5000, sse=4949200.0, rms=13.760 (8.480%)
008: dt: 0.5000, sse=4153327.5, rms=12.546 (8.820%)
009: dt: 0.5000, sse=3542935.8, rms=11.529 (8.111%)
010: dt: 0.5000, sse=2991820.8, rms=10.525 (8.704%)
011: dt: 0.5000, sse=2581933.5, rms=9.711 (7.733%)
012: dt: 0.5000, sse=2207837.2, rms=8.903 (8.323%)
013: dt: 0.5000, sse=1952614.8, rms=8.306 (6.706%)
014: dt: 0.5000, sse=1716964.6, rms=7.713 (7.138%)
015: dt: 0.5000, sse=1582487.5, rms=7.352 (4.676%)
016: dt: 0.5000, sse=1443075.6, rms=6.958 (5.362%)
017: dt: 0.5000, sse=1377451.9, rms=6.764 (2.796%)
018: dt: 0.5000, sse=1292741.0, rms=6.504 (3.839%)
019: dt: 0.5000, sse=1269601.9, rms=6.429 (1.148%)
020: dt: 0.5000, sse=1214033.4, rms=6.250 (2.785%)
rms = 6.2391/6.2502, sse=1211384.8/1214033.3, time step reduction 1 of 3 to
0.250  0 0 1
021: dt: 0.5000, sse=1211384.8, rms=6.239 (0.178%)
022: dt: 0.2500, sse=1035584.1, rms=5.633 (9.718%)
023: dt: 0.2500, sse=1003745.6, rms=5.516 (2.068%)
rms = 5.4824/5.5163, sse=994897.9/1003745.6, time step reduction 2 of 3 to
0.125  0 0 1
024: dt: 0.2500, sse=994897.9, rms=5.482 (0.614%)
025: dt: 0.1250, sse=963334.8, rms=5.363 (2.183%)
rms = 5.3400/5.3628, sse=957516.0/963334.7, time step reduction 3 of 3 to 0.
062  0 0 1
026: dt: 0.1250, sse=957516.0, rms=5.340 (0.424%)
maximum number of reductions reached, breaking from loop
positioning took 1.3 minutes
done positioning surface
Iteration 1 =========================================
n_averages=8, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  49.2911300;
border_low  =  23.8733980;
outside_low =  10.0000000;
outside_hi  =  42.9366990;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 10496 vertices, nripped=7437
mean border=49.2, 2207 (71) missing vertices, mean dist 0.2 [0.1 (%57.0)->0.
9 (%43.0))]
%16 local maxima, %43 large gradients and %34 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0277 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=chang, nav=8, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=922258.7, rms=4.927
rms = 4.9731/4.9268, sse=932681.6/922258.7, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
027: dt: 0.2500, sse=879512.6, rms=4.749 (3.611%)
028: dt: 0.2500, sse=846388.3, rms=4.607 (2.990%)
029: dt: 0.2500, sse=831249.0, rms=4.541 (1.426%)
rms = 4.5147/4.5413, sse=825042.8/831249.0, time step reduction 2 of 3 to 0.
125  0 0 1
030: dt: 0.2500, sse=825042.8, rms=4.515 (0.585%)
031: dt: 0.1250, sse=807034.6, rms=4.431 (1.850%)
rms = 4.4059/4.4312, sse=801523.7/807034.6, time step reduction 3 of 3 to 0.
062  0 0 1
032: dt: 0.1250, sse=801523.7, rms=4.406 (0.571%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
done positioning surface
Iteration 2 =========================================
n_averages=4, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  49.2911300;
border_low  =  23.8733980;
outside_low =  10.0000000;
outside_hi  =  42.9366990;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 10618 vertices, nripped=7437
mean border=48.7, 2785 (62) missing vertices, mean dist 0.2 [0.1 (%53.9)->0.
7 (%46.1))]
%24 local maxima, %34 large gradients and %34 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0166 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=chang, nav=4, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=839688.4, rms=4.567
rms = 4.6865/4.5672, sse=865966.7/839688.4, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
033: dt: 0.2500, sse=812164.3, rms=4.445 (2.683%)
034: dt: 0.2500, sse=793196.5, rms=4.360 (1.899%)
rms = 4.3242/4.3603, sse=785038.4/793196.5, time step reduction 2 of 3 to 0.
125  0 0 1
035: dt: 0.2500, sse=785038.4, rms=4.324 (0.827%)
rms = 4.2764/4.3242, sse=775138.5/785038.4, time step reduction 3 of 3 to 0.
062  0 0 1
036: dt: 0.1250, sse=775138.4, rms=4.276 (1.106%)
maximum number of reductions reached, breaking from loop
positioning took 0.2 minutes
done positioning surface
Iteration 3 =========================================
n_averages=2, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi   =  95.6386870;
border_hi   =  49.2911300;
border_low  =  23.8733980;
outside_low =  10.0000000;
outside_hi  =  42.9366990;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=132793
Gdiag_no=-1
vno start=0, stop=132793
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 8190 vertices, nripped=7437
mean border=47.9, 5858 (54) missing vertices, mean dist 0.2 [0.1 (%50.8)->0.
6 (%49.2))]
%31 local maxima, %27 large gradients and %33 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0102 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100
l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=chang, nav=2, nbrs=2, l_surf_repulse=5.000,
l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=819963.5, rms=4.480
rms = 4.6214/4.4800, sse=850271.0/819963.5, time step reduction 1 of 3 to 0.
250  0 1 1
RMS increased, rejecting step
037: dt: 0.2500, sse=791578.9, rms=4.351 (2.877%)
038: dt: 0.2500, sse=769586.8, rms=4.253 (2.247%)
039: dt: 0.2500, sse=757910.2, rms=4.201 (1.222%)
rms = 4.1760/4.2014, sse=751819.4/757910.2, time step reduction 2 of 3 to 0.
125  0 0 1
040: dt: 0.2500, sse=751819.4, rms=4.176 (0.605%)
041: dt: 0.1250, sse=739447.6, rms=4.115 (1.472%)
rms = 4.0920/4.1145, sse=734682.5/739447.5, time step reduction 3 of 3 to 0.
062  0 0 1
042: dt: 0.1250, sse=734682.5, rms=4.092 (0.546%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
done positioning surface
Pinning medial wall to white surface
Removing intersections
removing intersecting faces
000: 33 intersecting
terminating search with 0 intersecting
#ET# mris_place_surface  2.41 minutes
Writing output to ../surf/rh.pial.T1
#VMPC# mris_place_surfaces VmPeak  1340224
mris_place_surface done
@#@FSTIME  2024:08:07:18:02:17 mris_place_surface N 28 e 149.24 S 0.37 U
148.85 P 99% M 1081700 F 0 R 298663 W 0 c 547 w 112 I 0 O 9344 L 9.94 10.20
10.45
@#@FSLOADPOST 2024:08:07:18:04:46 mris_place_surface N 28 10.19 10.14 10.39
#@# white curv lh 公曆 20廿四年 八月 七日 週三 十八時四分46秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
insurf  ../surf/lh.white, nbrs 2, curvature_avgs 10
writing curvature file ../surf/lh.curv
@#@FSTIME  2024:08:07:18:04:46 mris_place_surface N 5 e 1.08 S 0.07 U 1.01 P
99% M 187416 F 0 R 49954 W 0 c 7 w 1 I 0 O 1072 L 10.19 10.14 10.39
@#@FSLOADPOST 2024:08:07:18:04:47 mris_place_surface N 5 10.19 10.14 10.39
#@# white area lh 公曆 20廿四年 八月 七日 週三 十八時四分47秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
writing curvature file ../surf/lh.area
@#@FSTIME  2024:08:07:18:04:47 mris_place_surface N 3 e 0.50 S 0.05 U 0.44 P
99% M 187736 F 0 R 49954 W 0 c 1 w 2 I 0 O 1072 L 10.19 10.14 10.39
@#@FSLOADPOST 2024:08:07:18:04:48 mris_place_surface N 3 10.19 10.14 10.39
#@# pial curv lh 公曆 20廿四年 八月 七日 週三 十八時四分48秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
insurf  ../surf/lh.pial, nbrs 2, curvature_avgs 10
writing curvature file ../surf/lh.curv.pial
@#@FSTIME  2024:08:07:18:04:48 mris_place_surface N 5 e 1.02 S 0.05 U 0.96 P
99% M 187484 F 0 R 49954 W 0 c 7 w 2 I 0 O 1072 L 10.19 10.14 10.39
@#@FSLOADPOST 2024:08:07:18:04:49 mris_place_surface N 5 10.09 10.12 10.38
#@# pial area lh 公曆 20廿四年 八月 七日 週三 十八時四分49秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
writing curvature file ../surf/lh.area.pial
@#@FSTIME  2024:08:07:18:04:49 mris_place_surface N 3 e 0.50 S 0.05 U 0.44 P
99% M 187484 F 0 R 49951 W 0 c 5 w 1 I 0 O 1072 L 10.09 10.12 10.38
@#@FSLOADPOST 2024:08:07:18:04:50 mris_place_surface N 3 10.09 10.12 10.38
#@# thickness lh 公曆 20廿四年 八月 七日 週三 十八時四分50秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
../surf/lh.thickness
0 of 136375 vertices processed
25000 of 136375 vertices processed
50000 of 136375 vertices processed
75000 of 136375 vertices processed
100000 of 136375 vertices processed
125000 of 136375 vertices processed
0 of 136375 vertices processed
25000 of 136375 vertices processed
50000 of 136375 vertices processed
75000 of 136375 vertices processed
100000 of 136375 vertices processed
125000 of 136375 vertices processed
thickness calculation complete, 964:5945 truncations.
68597 vertices at 0 distance
107371 vertices at 1 distance
55213 vertices at 2 distance
22895 vertices at 3 distance
10159 vertices at 4 distance
4347 vertices at 5 distance
1851 vertices at 6 distance
858 vertices at 7 distance
425 vertices at 8 distance
241 vertices at 9 distance
144 vertices at 10 distance
116 vertices at 11 distance
85 vertices at 12 distance
71 vertices at 13 distance
71 vertices at 14 distance
62 vertices at 15 distance
48 vertices at 16 distance
40 vertices at 17 distance
42 vertices at 18 distance
47 vertices at 19 distance
67 vertices at 20 distance
writing curvature file ../surf/lh.thickness
@#@FSTIME  2024:08:07:18:04:50 mris_place_surface N 6 e 18.60 S 0.07 U 18.53
P 100% M 186824 F 0 R 57137 W 0 c 52 w 1 I 0 O 1072 L 10.09 10.12 10.38
@#@FSLOADPOST 2024:08:07:18:05:08 mris_place_surface N 6 9.91 10.07 10.36
#@# area and vertex vol lh 公曆 20廿四年 八月 七日 週三 十八時五分九秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
../surf/lh.thickness
/home/chang/GBM_Data/VBG/0003/0003/surf
mris_calc -o lh.area.mid lh.area add lh.area.pial
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)
[ ok ]
mris_calc -o lh.area.mid lh.area.mid div 2
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)
[ ok ]
mris_convert --volume 0003 lh
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.volume
masking with /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Total face volume 252503
Total vertex volume 252258 (mask=0)
#@# 0003 lh 252258
vertexvol Done
@#@FSTIME  2024:08:07:18:05:09 vertexvol N 4 e 1.08 S 0.10 U 0.97 P 99% M
311652 F 8 R 91540 W 0 c 9 w 32 I 1088 O 3216 L 9.91 10.07 10.36
@#@FSLOADPOST 2024:08:07:18:05:10 vertexvol N 4 9.91 10.07 10.36
#@# white curv rh 公曆 20廿四年 八月 七日 週三 十八時五分十秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
insurf  ../surf/rh.white, nbrs 2, curvature_avgs 10
writing curvature file ../surf/rh.curv
@#@FSTIME  2024:08:07:18:05:10 mris_place_surface N 5 e 1.16 S 0.07 U 1.08 P
99% M 182808 F 0 R 48655 W 0 c 5 w 5 I 0 O 1040 L 9.91 10.07 10.36
@#@FSLOADPOST 2024:08:07:18:05:11 mris_place_surface N 5 9.91 10.07 10.36
#@# white area rh 公曆 20廿四年 八月 七日 週三 十八時五分十一秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
writing curvature file ../surf/rh.area
@#@FSTIME  2024:08:07:18:05:11 mris_place_surface N 3 e 0.60 S 0.07 U 0.53 P
99% M 183060 F 0 R 48694 W 0 c 2 w 44 I 0 O 1040 L 9.91 10.07 10.36
@#@FSLOADPOST 2024:08:07:18:05:12 mris_place_surface N 3 9.91 10.07 10.36
#@# pial curv rh 公曆 20廿四年 八月 七日 週三 十八時五分十二秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
insurf  ../surf/rh.pial, nbrs 2, curvature_avgs 10
writing curvature file ../surf/rh.curv.pial
@#@FSTIME  2024:08:07:18:05:12 mris_place_surface N 5 e 1.06 S 0.04 U 1.01 P
99% M 182456 F 0 R 48652 W 0 c 5 w 2 I 0 O 1040 L 9.91 10.07 10.36
@#@FSLOADPOST 2024:08:07:18:05:13 mris_place_surface N 5 9.91 10.07 10.36
#@# pial area rh 公曆 20廿四年 八月 七日 週三 十八時五分十三秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
writing curvature file ../surf/rh.area.pial
@#@FSTIME  2024:08:07:18:05:13 mris_place_surface N 3 e 0.50 S 0.04 U 0.46 P
99% M 182456 F 0 R 48654 W 0 c 3 w 3 I 0 O 1040 L 10.15 10.12 10.37
@#@FSLOADPOST 2024:08:07:18:05:14 mris_place_surface N 3 10.15 10.12 10.37
#@# thickness rh 公曆 20廿四年 八月 七日 週三 十八時五分十四秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
../surf/rh.thickness
0 of 132793 vertices processed
25000 of 132793 vertices processed
50000 of 132793 vertices processed
75000 of 132793 vertices processed
100000 of 132793 vertices processed
125000 of 132793 vertices processed
0 of 132793 vertices processed
25000 of 132793 vertices processed
50000 of 132793 vertices processed
75000 of 132793 vertices processed
100000 of 132793 vertices processed
125000 of 132793 vertices processed
thickness calculation complete, 585:4335 truncations.
65093 vertices at 0 distance
102863 vertices at 1 distance
55087 vertices at 2 distance
23493 vertices at 3 distance
10439 vertices at 4 distance
4374 vertices at 5 distance
1809 vertices at 6 distance
779 vertices at 7 distance
422 vertices at 8 distance
290 vertices at 9 distance
206 vertices at 10 distance
145 vertices at 11 distance
87 vertices at 12 distance
86 vertices at 13 distance
77 vertices at 14 distance
77 vertices at 15 distance
64 vertices at 16 distance
47 vertices at 17 distance
51 vertices at 18 distance
46 vertices at 19 distance
51 vertices at 20 distance
writing curvature file ../surf/rh.thickness
@#@FSTIME  2024:08:07:18:05:14 mris_place_surface N 6 e 18.56 S 0.06 U 18.50
P 99% M 182804 F 0 R 55652 W 0 c 42 w 3 I 0 O 1040 L 10.15 10.12 10.37
@#@FSLOADPOST 2024:08:07:18:05:33 mris_place_surface N 6 9.92 10.06 10.35
#@# area and vertex vol rh 公曆 20廿四年 八月 七日 週三 十八時五分33秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
../surf/rh.thickness
/home/chang/GBM_Data/VBG/0003/0003/surf
mris_calc -o rh.area.mid rh.area add rh.area.pial
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)
[ ok ]
mris_calc -o rh.area.mid rh.area.mid div 2
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)
[ ok ]
mris_convert --volume 0003 rh
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.volume
masking with /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Total face volume 244738
Total vertex volume 244461 (mask=0)
#@# 0003 rh 244461
vertexvol Done
@#@FSTIME  2024:08:07:18:05:33 vertexvol N 4 e 0.96 S 0.10 U 0.86 P 99% M
303864 F 0 R 89215 W 0 c 6 w 26 I 0 O 3120 L 9.92 10.06 10.35
@#@FSLOADPOST 2024:08:07:18:05:34 vertexvol N 4 10.08 10.10 10.36
#-----------------------------------------
#@# Curvature Stats lh 公曆 20廿四年 八月 七日 週三 十八時五分34秒
/home/chang/GBM_Data/VBG/0003/0003/surf
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats
-F smoothwm 0003 lh curv sulc
Toggling save flag on curvature files                       [
ok ]
Outputting results using filestem   [
../stats/lh.curv.stats ]
Toggling save flag on curvature files                       [
ok ]
Setting surface    [ 0003/lh.smoothwm ]
Reading surface...                       [
ok ]
Setting texture                     [
curv ]
Reading texture...                       [
ok ]
Setting texture                     [
sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [####################] [
ok ]
Determining KH curvatures... [####################] [
ok ]
Determining k1k2 curvatures... [####################] [
ok ]
deltaViolations                      [
333 ]
Gb_filter = 0
@#@FSTIME  2024:08:07:18:05:34 mris_curvature_stats N 11 e 1.37 S 0.06 U
1.31 P 99% M 187292 F 13 R 50116 W 0 c 8 w 16 I 1504 O 8616 L 10.08 10.10
10.36
@#@FSLOADPOST 2024:08:07:18:05:35 mris_curvature_stats N 11 10.08 10.10
10.36
#-----------------------------------------
#@# Curvature Stats rh 公曆 20廿四年 八月 七日 週三 十八時五分35秒
/home/chang/GBM_Data/VBG/0003/0003/surf
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats
-F smoothwm 0003 rh curv sulc
Toggling save flag on curvature files                       [
ok ]
Outputting results using filestem   [
../stats/rh.curv.stats ]
Toggling save flag on curvature files                       [
ok ]
Setting surface    [ 0003/rh.smoothwm ]
Reading surface...                       [
ok ]
Setting texture                     [
curv ]
Reading texture...                       [
ok ]
Setting texture                     [
sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [####################] [
ok ]
Determining KH curvatures... [####################] [
ok ]
Determining k1k2 curvatures... [####################] [
ok ]
deltaViolations                      [
307 ]
Gb_filter = 0
WARN:    S lookup   min:                          -0.075386
WARN:    S explicit min:                          0.000000          vertex =
378
@#@FSTIME  2024:08:07:18:05:35 mris_curvature_stats N 11 e 1.39 S 0.06 U
1.32 P 99% M 182856 F 0 R 48857 W 0 c 8 w 4 I 0 O 8360 L 10.08 10.10 10.36
@#@FSLOADPOST 2024:08:07:18:05:37 mris_curvature_stats N 11 10.08 10.10
10.36
#--------------------------------------------
#@# Cortical ribbon mask 公曆 20廿四年 八月 七日 週三 十八時五分37秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mris_volmask --aseg_name aseg.presurf --label_left_white 2
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42
--save_ribbon 0003
SUBJECTS_DIR is /home/chang/GBM_Data/VBG/0003
loading input data...
Running hemis serially
Processing left hemi
computing distance to left white surface
computing distance to left pial surface
Processing right hemi
computing distance to right white surface
computing distance to right pial surface
hemi masks overlap voxels = 206
writing volume /home/chang/GBM_Data/VBG/0003/0003/mri/ribbon.mgz
mris_volmask took 4.57 minutes
writing ribbon files
@#@FSTIME  2024:08:07:18:05:37 mris_volmask N 12 e 273.96 S 0.59 U 273.30 P
99% M 980936 F 8 R 526315 W 0 c 763 w 326 I 952 O 888 L 10.08 10.10 10.36
@#@FSLOADPOST 2024:08:07:18:10:11 mris_volmask N 12 10.76 10.50 10.48
#-----------------------------------------
#@# Cortical Parc 2 lh 公曆 20廿四年 八月 七日 週三 十八時十分十一秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 0003 lh ../surf/lh.sphere.reg
/usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs ../label/lh.aparc.a2009s.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.4.1
7.4.1
reading atlas from
/usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs...
reading color table from GCSA file....
average std = 3.0   using min determinant for regularization = 0.088
0 singular and 0 ill-conditioned covariance matrices regularized
reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/lh.smoothwm...
GCSA::load_default_data(): ninputs=1  sulc_only=0 which_norm=0
labeling surface...
94 labels changed using aseg
relabeling using gibbs priors...
000:   8994 changed, 136375 examined...
001:   2021 changed, 34698 examined...
002:    591 changed, 10861 examined...
003:    239 changed, 3354 examined...
004:    122 changed, 1389 examined...
005:     63 changed, 696 examined...
006:     29 changed, 337 examined...
007:     12 changed, 159 examined...
008:      9 changed, 71 examined...
009:      6 changed, 46 examined...
010:      2 changed, 30 examined...
011:      1 changed, 10 examined...
012:      0 changed, 6 examined...
23 labels changed using aseg
000: 238 total segments, 156 labels (1779 vertices) changed
001: 92 total segments, 10 labels (18 vertices) changed
002: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 34 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
relabeling unknown label...
1205 vertices marked for relabeling...
1205 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 8 seconds.
@#@FSTIME  2024:08:07:18:10:11 mris_ca_label N 11 e 7.58 S 0.69 U 6.88 P 99%
M 1831100 F 0 R 696459 W 0 c 24 w 6 I 42432 O 2144 L 10.76 10.50 10.48
@#@FSLOADPOST 2024:08:07:18:10:18 mris_ca_label N 11 10.22 10.39 10.44
#-----------------------------------------
#@# Cortical Parc 2 rh 公曆 20廿四年 八月 七日 週三 十八時十分十八秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 0003 rh ../surf/rh.sphere.reg
/usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs ../label/rh.aparc.a2009s.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.4.1
7.4.1
reading atlas from
/usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02
.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.021
0 singular and 0 ill-conditioned covariance matrices regularized
reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/rh.smoothwm...
GCSA::load_default_data(): ninputs=1  sulc_only=0 which_norm=0
labeling surface...
149 labels changed using aseg
relabeling using gibbs priors...
000:   8867 changed, 132793 examined...
001:   1937 changed, 34353 examined...
002:    557 changed, 10408 examined...
003:    221 changed, 3235 examined...
004:     95 changed, 1277 examined...
005:     44 changed, 548 examined...
006:     25 changed, 273 examined...
007:      9 changed, 136 examined...
008:      6 changed, 55 examined...
009:      2 changed, 30 examined...
010:      1 changed, 13 examined...
011:      2 changed, 8 examined...
012:      1 changed, 11 examined...
013:      0 changed, 7 examined...
17 labels changed using aseg
000: 247 total segments, 160 labels (2134 vertices) changed
001: 91 total segments, 4 labels (19 vertices) changed
002: 87 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 30 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
relabeling unknown label...
1005 vertices marked for relabeling...
1005 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 8 seconds.
@#@FSTIME  2024:08:07:18:10:18 mris_ca_label N 11 e 8.26 S 0.75 U 7.50 P 99%
M 1839540 F 0 R 697586 W 0 c 50 w 24 I 42776 O 2088 L 10.22 10.39 10.44
@#@FSLOADPOST 2024:08:07:18:10:27 mris_ca_label N 11 9.96 10.33 10.42
#-----------------------------------------
#@# Cortical Parc 3 lh 公曆 20廿四年 八月 七日 週三 十八時十分廿七秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 0003 lh ../surf/lh.sphere.reg
/usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0
2.gcs ../label/lh.aparc.DKTatlas.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.4.1
7.4.1
reading atlas from
/usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0
2.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 383 ill-conditioned covariance matrices regularized
reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/lh.smoothwm...
GCSA::load_default_data(): ninputs=1  sulc_only=0 which_norm=0
labeling surface...
1352 labels changed using aseg
relabeling using gibbs priors...
000:   1884 changed, 136375 examined...
001:    454 changed, 9043 examined...
002:    142 changed, 2601 examined...
003:     76 changed, 829 examined...
004:     52 changed, 409 examined...
005:     40 changed, 271 examined...
006:     31 changed, 215 examined...
007:     22 changed, 179 examined...
008:     12 changed, 117 examined...
009:      7 changed, 66 examined...
010:      6 changed, 42 examined...
011:      7 changed, 32 examined...
012:      3 changed, 41 examined...
013:      4 changed, 24 examined...
014:      4 changed, 18 examined...
015:      3 changed, 22 examined...
016:      3 changed, 17 examined...
017:      2 changed, 17 examined...
018:      1 changed, 17 examined...
019:      1 changed, 6 examined...
020:      1 changed, 7 examined...
021:      0 changed, 6 examined...
465 labels changed using aseg
000: 44 total segments, 11 labels (175 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
744 vertices marked for relabeling...
744 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 6 seconds.
@#@FSTIME  2024:08:07:18:10:27 mris_ca_label N 11 e 5.88 S 0.29 U 5.58 P 99%
M 895172 F 0 R 292399 W 0 c 17 w 6 I 42976 O 2136 L 9.96 10.33 10.42
@#@FSLOADPOST 2024:08:07:18:10:32 mris_ca_label N 11 9.81 10.29 10.41
#-----------------------------------------
#@# Cortical Parc 3 rh 公曆 20廿四年 八月 七日 週三 十八時十分32秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 0003 rh ../surf/rh.sphere.reg
/usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0
2.gcs ../label/rh.aparc.DKTatlas.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.4.1
7.4.1
reading atlas from
/usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0
2.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.009
0 singular and 325 ill-conditioned covariance matrices regularized
reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/rh.smoothwm...
GCSA::load_default_data(): ninputs=1  sulc_only=0 which_norm=0
labeling surface...
1462 labels changed using aseg
relabeling using gibbs priors...
000:   1941 changed, 132793 examined...
001:    491 changed, 9038 examined...
002:    152 changed, 2697 examined...
003:     75 changed, 859 examined...
004:     33 changed, 417 examined...
005:     22 changed, 193 examined...
006:     16 changed, 113 examined...
007:     16 changed, 91 examined...
008:     16 changed, 94 examined...
009:     12 changed, 78 examined...
010:      9 changed, 59 examined...
011:      8 changed, 46 examined...
012:     12 changed, 46 examined...
013:      7 changed, 59 examined...
014:      7 changed, 42 examined...
015:      7 changed, 37 examined...
016:      7 changed, 38 examined...
017:      5 changed, 38 examined...
018:      5 changed, 25 examined...
019:      3 changed, 27 examined...
020:      2 changed, 21 examined...
021:      3 changed, 13 examined...
022:      2 changed, 20 examined...
023:      3 changed, 12 examined...
024:      2 changed, 13 examined...
025:      2 changed, 15 examined...
026:      1 changed, 14 examined...
027:      0 changed, 7 examined...
446 labels changed using aseg
000: 54 total segments, 21 labels (323 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
9 filter iterations complete (10 requested, 0 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
607 vertices marked for relabeling...
607 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 6 seconds.
@#@FSTIME  2024:08:07:18:10:32 mris_ca_label N 11 e 5.91 S 0.27 U 5.64 P 99%
M 931196 F 0 R 300341 W 0 c 19 w 3 I 42952 O 2080 L 9.81 10.29 10.41
@#@FSLOADPOST 2024:08:07:18:10:38 mris_ca_label N 11 9.74 10.27 10.40
#-----------------------------------------
#@# WM/GM Contrast lh 公曆 20廿四年 八月 七日 週三 十八時十分38秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
pctsurfcon --s 0003 --lh-only
Log file is /home/chang/GBM_Data/VBG/0003/0003/scripts/pctsurfcon.log
公曆 20廿四年 八月 七日 週三 十八時十分38秒
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/scripts
/usr/local/freesurfer/bin/pctsurfcon
pctsurfcon 7.4.1
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi
lh --noreshape --interp trilinear --projdist -1 --o
/home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.wm.mgh
--regheader 0003 --cortex
srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference.
-------- original matrix -----------
1.00000   0.00000   0.00000   0.00000;
0.00000   0.00000   1.00000   0.00000;
0.00000   1.00000   0.00000   0.00000;
0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
Projecting -1 -1 1
1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 82565
Masking with /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.
wm.mgh
Dim: 136375 1 1
mri_vol2surf done
mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi
lh --noreshape --interp trilinear --o
/home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.gm.mgh
--projfrac 0.3 --regheader 0003 --cortex
srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference.
-------- original matrix -----------
1.00000   0.00000   0.00000   0.00000;
0.00000   0.00000   1.00000   0.00000;
0.00000   1.00000   0.00000   0.00000;
0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Done reading source surface
Reading thickness /home/chang/GBM_Data/VBG/0003/0003/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
Projecting 0.3 0.3 1
1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 91251
Masking with /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.
gm.mgh
Dim: 136375 1 1
mri_vol2surf done
mri_concat /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.
wm.mgh
/home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.gm.mgh
--paired-diff-norm --mul 100 --o /home/chang/GBM_Data/VBG/0003/0003/surf/lh.
w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh
mri_segstats --in /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh
--annot 0003 lh aparc --sum /home/chang/GBM_Data/VBG/0003/0003/stats/lh.w-g.
pct.stats --snr
7.4.1
cwd
cmdline mri_segstats --in
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh --annot 0003 lh aparc
--sum /home/chang/GBM_Data/VBG/0003/0003/stats/lh.w-g.pct.stats --snr
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
whitesurfname  white
UseRobust  0
Constructing seg from annotation
Reading annotation /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot
Seg base 1000
MRISannot2seg(): nhits = 127585
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh
Vertex Area is 0.681666 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
@#@FSTIME  2024:08:07:18:10:38 pctsurfcon N 3 e 1.94 S 0.19 U 1.74 P 99% M
232776 F 19 R 171874 W 0 c 19 w 87 I 47384 O 3328 L 9.74 10.27 10.40
@#@FSLOADPOST 2024:08:07:18:10:40 pctsurfcon N 3 10.08 10.33 10.42
#-----------------------------------------
#@# WM/GM Contrast rh 公曆 20廿四年 八月 七日 週三 十八時十分40秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
pctsurfcon --s 0003 --rh-only
Log file is /home/chang/GBM_Data/VBG/0003/0003/scripts/pctsurfcon.log
公曆 20廿四年 八月 七日 週三 十八時十分40秒
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/scripts
/usr/local/freesurfer/bin/pctsurfcon
pctsurfcon 7.4.1
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi
rh --noreshape --interp trilinear --projdist -1 --o
/home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.wm.mgh
--regheader 0003 --cortex
srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference.
-------- original matrix -----------
1.00000   0.00000   0.00000   0.00000;
0.00000   0.00000   1.00000   0.00000;
0.00000   1.00000   0.00000   0.00000;
0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
Projecting -1 -1 1
1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 81281
Masking with /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.
wm.mgh
Dim: 132793 1 1
mri_vol2surf done
mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi
rh --noreshape --interp trilinear --o
/home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.gm.mgh
--projfrac 0.3 --regheader 0003 --cortex
srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference.
-------- original matrix -----------
1.00000   0.00000   0.00000   0.00000;
0.00000   0.00000   1.00000   0.00000;
0.00000   1.00000   0.00000   0.00000;
0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Done reading source surface
Reading thickness /home/chang/GBM_Data/VBG/0003/0003/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
Projecting 0.3 0.3 1
1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 88541
Masking with /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.
gm.mgh
Dim: 132793 1 1
mri_vol2surf done
mri_concat /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.
wm.mgh
/home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.gm.mgh
--paired-diff-norm --mul 100 --o /home/chang/GBM_Data/VBG/0003/0003/surf/rh.
w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh
mri_segstats --in /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh
--annot 0003 rh aparc --sum /home/chang/GBM_Data/VBG/0003/0003/stats/rh.w-g.
pct.stats --snr
7.4.1
cwd
cmdline mri_segstats --in
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh --annot 0003 rh aparc
--sum /home/chang/GBM_Data/VBG/0003/0003/stats/rh.w-g.pct.stats --snr
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
whitesurfname  white
UseRobust  0
Constructing seg from annotation
Reading annotation /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot
Seg base 2000
MRISannot2seg(): nhits = 123901
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh
Vertex Area is 0.692561 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
@#@FSTIME  2024:08:07:18:10:40 pctsurfcon N 3 e 1.86 S 0.17 U 1.69 P 100% M
228936 F 0 R 176581 W 0 c 18 w 68 I 8 O 3256 L 10.08 10.33 10.42
@#@FSLOADPOST 2024:08:07:18:10:42 pctsurfcon N 3 10.08 10.33 10.42
#-----------------------------------------
#@# Relabel Hypointensities 公曆 20廿四年 八月 七日 週三 十八時十分42秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
reading input surface ../surf/lh.white...
relabeling lh hypointensities...
5774 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
4516 voxels changed to hypointensity...
9889 hypointense voxels neighboring cortex changed
@#@FSTIME  2024:08:07:18:10:42 mri_relabel_hypointensities N 3 e 8.01 S 0.29
U 7.71 P 99% M 470264 F 12 R 331528 W 0 c 31 w 10 I 1880 O 688 L 10.08 10.33
10.42
@#@FSLOADPOST 2024:08:07:18:10:50 mri_relabel_hypointensities N 3 10.07
10.32 10.41
#-----------------------------------------
#@# APas-to-ASeg 公曆 20廿四年 八月 七日 週三 十八時十分50秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz
--fix-presurf-with-ribbon /home/chang/GBM_Data/VBG/0003/0003/mri/ribbon.mgz
--threads 1 --lh-cortex-mask
/home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label --lh-white
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-cortex-mask
/home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label --rh-white
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
outvol aseg.mgz
32 avail.processors, using 1
Loading aseg.presurf.hypos.mgz
Loading /home/chang/GBM_Data/VBG/0003/0003/mri/ribbon.mgz
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Done loading
0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
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nrelabeled = 0
ndotcheck = 0
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak  913940
mri_surf2volseg done
@#@FSTIME  2024:08:07:18:10:50 mri_surf2volseg N 20 e 10.06 S 0.24 U 9.76 P
99% M 894616 F 9 R 252796 W 0 c 59 w 404 I 1392 O 720 L 10.07 10.32 10.41
@#@FSLOADPOST 2024:08:07:18:11:01 mri_surf2volseg N 20 9.97 10.29 10.40
mri_brainvol_stats --subject 0003
ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1
#CBVS2 MaskVol              1595656.0
#CBVS2 BrainSegVol          1211438.0
#CBVS2 BrainSegVolNotVent   1158705.0
#CBVS2 SupraTentVol         1081389.0
#CBVS2 SupraTentVolNotVent  1028656.0
#CBVS2 lhCtxGM               251396.0
#CBVS2 rhCtxGM               243553.7
#CBVS2 lhCerebralWM          241703.5
#CBVS2 rhCerebralWM          241770.5
#CBVS2 SubCortGMVol           51153.0
#CBVS2 CerebellumVol         130049.0
#CBVS2 CerebellumGMVol       107015.0
#CBVS2 VentChorVol            47962.0
#CBVS2 3rd4th5thCSF            4771.0
#CBVS2 AllCSF                 52733.0
#CBVS2 CCVol                   3379.0
@#@FSTIME  2024:08:07:18:11:01 mri_brainvol_stats N 2 e 2.99 S 0.13 U 2.85 P
99% M 223188 F 25 R 123971 W 0 c 18 w 35 I 4312 O 8 L 9.97 10.29 10.40
@#@FSLOADPOST 2024:08:07:18:11:04 mri_brainvol_stats N 2 9.97 10.29 10.40
#-----------------------------------------
#@# AParc-to-ASeg aparc 公曆 20廿四年 八月 七日 週三 十八時十一分四秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1
--lh-annot /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot 1000
--lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
--lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot
/home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot 2000
--rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
--rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
outvol aparc+aseg.mgz
32 avail.processors, using 1
Loading aseg.mgz
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8790 vertices from lh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
ripped 8892 vertices from rh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot
Done loading
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nrelabeled = 0
ndotcheck = 31232
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak  897072
mri_surf2volseg done
@#@FSTIME  2024:08:07:18:11:04 mri_surf2volseg N 25 e 111.80 S 0.30 U 111.49
P 99% M 877596 F 0 R 244170 W 0 c 323 w 21 I 0 O 832 L 10.22 10.34 10.42
@#@FSLOADPOST 2024:08:07:18:12:55 mri_surf2volseg N 25 10.68 10.48 10.46
#-----------------------------------------
#@# AParc-to-ASeg aparc.a2009s 公曆 20廿四年 八月 七日 週三 十八時十二分55秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz
--threads 1 --lh-annot
/home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.a2009s.annot 11100
--lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
--lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot
/home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.a2009s.annot 12100
--rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
--rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
outvol aparc.a2009s+aseg.mgz
32 avail.processors, using 1
Loading aseg.mgz
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8790 vertices from lh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.a2009s.annot
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
ripped 8892 vertices from rh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.a2009s.annot
Done loading
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nrelabeled = 0
ndotcheck = 31232
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak  897160
mri_surf2volseg done
@#@FSTIME  2024:08:07:18:12:56 mri_surf2volseg N 25 e 112.68 S 0.24 U 112.41
P 99% M 878312 F 0 R 244380 W 0 c 427 w 206 I 0 O 896 L 10.68 10.48 10.46
@#@FSLOADPOST 2024:08:07:18:14:48 mri_surf2volseg N 25 11.28 10.71 10.55
#-----------------------------------------
#@# AParc-to-ASeg aparc.DKTatlas 公曆 20廿四年 八月 七日 週三 十八時十四分48
秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz
--threads 1 --lh-annot
/home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.DKTatlas.annot 1000
--lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
--lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot
/home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.DKTatlas.annot 2000
--rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
--rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
outvol aparc.DKTatlas+aseg.mgz
32 avail.processors, using 1
Loading aseg.mgz
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8790 vertices from lh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.DKTatlas.annot
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
ripped 8892 vertices from rh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.DKTatlas.annot
Done loading
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nrelabeled = 0
ndotcheck = 31232
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak  897072
mri_surf2volseg done
@#@FSTIME  2024:08:07:18:14:48 mri_surf2volseg N 25 e 110.19 S 0.25 U 109.87
P 99% M 877636 F 0 R 244522 W 0 c 223 w 370 I 0 O 832 L 11.28 10.71 10.55
@#@FSLOADPOST 2024:08:07:18:16:39 mri_surf2volseg N 25 10.87 10.78 10.59
#-----------------------------------------
#@# WMParc 公曆 20廿四年 八月 七日 週三 十八時十六分39秒
/home/chang/GBM_Data/VBG/0003/0003/mri
mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1
--lh-annot /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot 3000
--lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
--lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot
/home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot 4000
--rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
--rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
outvol wmparc.mgz
32 avail.processors, using 1
Loading aparc+aseg.mgz
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8790 vertices from lh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
ripped 8892 vertices from rh hemi
Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot
Done loading
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nrelabeled = 0
ndotcheck = 3713
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak  897084
mri_surf2volseg done
@#@FSTIME  2024:08:07:18:16:39 mri_surf2volseg N 25 e 25.16 S 0.29 U 24.86 P
99% M 877484 F 0 R 244184 W 0 c 98 w 1 I 0 O 928 L 10.87 10.78 10.59
@#@FSLOADPOST 2024:08:07:18:17:04 mri_surf2volseg N 25 10.64 10.74 10.58
mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --subject 0003
--surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv
setting seed for random number genererator to 1234
7.4.1
cwd
cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum
stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --subject 0003 --surf-wm-vol --ctab
/usr/local/freesurfer/WMParcStatsLUT.txt --etiv
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
whitesurfname  white
UseRobust  0
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 390 segmentations
Computing statistics for each segmentation
Reporting on  70 segmentations
Using PrintSegStat
mri_segstats done
@#@FSTIME  2024:08:07:18:17:04 mri_segstats N 24 e 261.79 S 0.37 U 261.40 P
99% M 239872 F 0 R 1207400 W 0 c 1035 w 80 I 56 O 24 L 10.64 10.74 10.58
@#@FSLOADPOST 2024:08:07:18:21:26 mri_segstats N 24 9.90 10.36 10.47
#-----------------------------------------
#@# Parcellation Stats lh 公曆 20廿四年 八月 七日 週三 十八時廿一分廿六秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab 0003 lh white
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 252503
Total vertex volume 252258 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
1304    892   1817  2.190 0.719     0.105     0.028        9     1.4
bankssts
1245    843   2068  2.199 0.808     0.109     0.017       13     1.0
caudalanteriorcingulate
3778   2473   5494  2.344 0.747     0.117     0.032       28     5.1
caudalmiddlefrontal
2203   1629   3520  2.169 0.611     0.144     0.040       21     3.9  cuneus
667    501   2183  2.889 1.022     0.135     0.036        6     1.1
entorhinal
4001   2849   8385  2.477 0.829     0.126     0.030       40     5.3
fusiform
5117   3504  10274  2.511 0.873     0.118     0.031       42     6.7
inferiorparietal
4310   3127  11690  2.728 1.045     0.135     0.040       45     6.8
inferiortemporal
1648   1104   3009  2.356 1.005     0.102     0.023       12     1.4
isthmuscingulate
6682   4516  14585  2.522 0.930     0.125     0.034       65     9.6
lateraloccipital
2572   1780   7036  3.051 1.115     0.106     0.028       20     2.5
lateralorbitofrontal
4366   3132   7497  2.097 0.772     0.129     0.040       47     7.0
lingual
2443   1824   7304  3.044 1.053     0.125     0.029       30     2.9
medialorbitofrontal
4260   3036  11963  2.707 0.992     0.133     0.037       44     7.0
middletemporal
973    599   1879  2.550 0.928     0.075     0.015        5     0.5
parahippocampal
1925   1276   2564  1.995 0.615     0.120     0.034       14     2.8
paracentral
2259   1449   4971  2.719 0.921     0.097     0.025       15     2.0
parsopercularis
980    775   3628  2.824 1.130     0.174     0.051       16     2.2
parsorbitalis
1791   1185   3570  2.258 0.873     0.114     0.029       16     2.0
parstriangularis
1893   1530   2587  1.853 0.566     0.157     0.049       19     4.5
pericalcarine
7502   4922  10684  1.886 0.765     0.111     0.029       58     8.9
postcentral
1196    766   1720  2.029 0.687     0.101     0.020       10     1.0
posteriorcingulate
9510   6119  13990  2.166 0.788     0.112     0.030       67    12.4
precentral
6453   4548  10700  2.207 0.735     0.121     0.028       52     7.5
precuneus
1226    854   2888  2.633 1.091     0.108     0.024       11     1.2
rostralanteriorcingulate
8682   5889  18865  2.454 0.958     0.121     0.033       81    11.7
rostralmiddlefrontal
10940   7300  23050  2.658 0.888     0.123     0.035      102    15.7
superiorfrontal
10345   7133  14862  1.911 0.700     0.119     0.030       86    13.5
superiorparietal
5851   4029  13885  2.665 1.022     0.097     0.022       50     5.1
superiortemporal
5967   4130  11744  2.340 0.874     0.116     0.032       49     7.7
supramarginal
356    285   1990  3.659 1.207     0.163     0.038        6     0.5
frontalpole
696    561   2628  3.376 0.832     0.122     0.028        7     0.9
temporalpole
643    450   1197  2.344 0.673     0.122     0.030        6     0.7
transversetemporal
3801   2621   8030  2.934 1.016     0.107     0.027       30     4.2  insula
@#@FSTIME  2024:08:07:18:21:26 mris_anatomical_stats N 14 e 6.59 S 0.16 U 6.
42 P 99% M 482384 F 9 R 138973 W 0 c 18 w 36 I 1464 O 24 L 9.90 10.36 10.47
@#@FSLOADPOST 2024:08:07:18:21:32 mris_anatomical_stats N 14 9.99 10.37
10.47
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab 0003 lh pial
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 252503
Total vertex volume 252258 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
1304    880   1817  2.190 0.719     0.123     0.040       26     1.7
bankssts
1245   1050   2068  2.199 0.808     0.165     0.038       40     2.2
caudalanteriorcingulate
3778   2476   5494  2.344 0.747     0.112     0.028       74     4.4
caudalmiddlefrontal
2203   1807   3520  2.169 0.611     0.149     0.045      108     4.0  cuneus
667    981   2183  2.889 1.022     0.361     0.111       34     4.0
entorhinal
4001   3678   8385  2.477 0.829     0.160     0.044       86     7.2
fusiform
5117   4605  10274  2.511 0.873     0.153     0.039     3421     8.7
inferiorparietal
4310   5034  11690  2.728 1.045     0.199     0.049       97     9.5
inferiortemporal
1648   1348   3009  2.356 1.005     0.134     0.037       38     2.4
isthmuscingulate
6682   6605  14585  2.522 0.930     0.161     0.042      143    12.4
lateraloccipital
2572   2596   7036  3.051 1.115     0.174     0.045       55     5.5
lateralorbitofrontal
4366   4043   7497  2.097 0.772     0.159     0.040       79     8.4
lingual
2443   2786   7304  3.044 1.053     0.198     0.045       46     5.1
medialorbitofrontal
4260   5269  11963  2.707 0.992     0.192     0.044       77     8.9
middletemporal
973    897   1879  2.550 0.928     0.157     0.042       13     2.2
parahippocampal
1925   1418   2564  1.995 0.615     0.117     0.030       19     2.3
paracentral
2259   2056   4971  2.719 0.921     0.133     0.028       23     2.8
parsopercularis
980   1614   3628  2.824 1.130     0.256     0.057       19     2.9
parsorbitalis
1791   1721   3570  2.258 0.873     0.159     0.032       27     3.0
parstriangularis
1893   1344   2587  1.853 0.566     0.130     0.039       31     2.8
pericalcarine
7502   6237  10684  1.886 0.765     0.122     0.027       66     8.1
postcentral
1196    909   1720  2.029 0.687     0.116     0.032       23     1.5
posteriorcingulate
9510   6748  13990  2.166 0.788     0.109     0.028      141    10.8
precentral
6453   5271  10700  2.207 0.735     0.145     0.040      117    10.6
precuneus
1226   1218   2888  2.633 1.091     0.172     0.047       28     2.2
rostralanteriorcingulate
8682   8401  18865  2.454 0.958     0.160     0.038      147    14.6
rostralmiddlefrontal
10940   9382  23050  2.658 0.888     0.140     0.036      404    15.5
superiorfrontal
10345   8736  14862  1.911 0.700     0.130     0.031      119    13.5
superiorparietal
5851   5791  13885  2.665 1.022     0.147     0.032       71     8.7
superiortemporal
5967   5625  11744  2.340 0.874     0.155     0.037      118    10.1
supramarginal
356    677   1990  3.659 1.207     0.259     0.040        5     0.8
frontalpole
696   1013   2628  3.376 0.832     0.200     0.038       10     1.2
temporalpole
643    640   1197  2.344 0.673     0.174     0.047       12     1.5
transversetemporal
3801   2768   8030  2.934 1.016     0.170     0.052      129    10.6  insula
@#@FSTIME  2024:08:07:18:21:32 mris_anatomical_stats N 14 e 6.53 S 0.21 U 6.
30 P 99% M 482160 F 0 R 139017 W 0 c 36 w 68 I 0 O 24 L 9.99 10.37 10.47
@#@FSLOADPOST 2024:08:07:18:21:39 mris_anatomical_stats N 14 10.07 10.38 10.
48
#-----------------------------------------
#@# Parcellation Stats rh 公曆 20廿四年 八月 七日 週三 十八時廿一分39秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f
../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c
../label/aparc.annot.ctab 0003 rh white
computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 244738
Total vertex volume 244461 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
1065    756   1907  2.829 0.675     0.105     0.025        8     0.9
bankssts
1123    757   2363  2.443 0.858     0.122     0.024       11     1.2
caudalanteriorcingulate
4355   3012   7349  2.354 0.790     0.139     0.038       45     7.6
caudalmiddlefrontal
2344   1693   3608  2.024 0.694     0.146     0.040       23     4.1  cuneus
534    473   2074  2.904 0.962     0.185     0.054        8     1.5
entorhinal
3760   2876   8824  2.550 0.830     0.148     0.044       48     6.9
fusiform
6063   4287  13987  2.670 0.831     0.123     0.034       58     8.1
inferiorparietal
3434   2556   9856  2.808 0.967     0.147     0.047       39     6.4
inferiortemporal
1246    816   2552  2.738 1.020     0.109     0.031        9     1.5
isthmuscingulate
8091   6001  16825  2.344 0.854     0.144     0.046       90    15.7
lateraloccipital
2905   2036   6628  2.751 0.892     0.121     0.031       25     3.8
lateralorbitofrontal
3598   2753   7600  2.224 0.806     0.141     0.045       44     7.1
lingual
2315   1620   6326  2.831 1.186     0.115     0.024       23     2.2
medialorbitofrontal
4064   3005  11573  2.789 0.900     0.132     0.033       46     5.7
middletemporal
938    572   1717  2.346 0.834     0.088     0.018        6     0.6
parahippocampal
2283   1420   2936  2.003 0.608     0.111     0.026       16     2.4
paracentral
2181   1464   3828  2.381 0.716     0.113     0.030       20     2.8
parsopercularis
967    672   3041  3.020 1.041     0.135     0.032       10     1.4
parsorbitalis
1780   1220   3577  2.347 0.963     0.122     0.032       17     2.3
parstriangularis
1890   1361   2455  2.003 0.541     0.152     0.056      123     5.4
pericalcarine
6564   4165   9082  1.923 0.838     0.099     0.024       46     6.4
postcentral
1660   1118   2573  2.159 0.788     0.129     0.037       15     2.6
posteriorcingulate
9064   5712  12212  2.015 0.748     0.116     0.031       77    12.1
precentral
6185   4358  10614  2.286 0.860     0.125     0.034       54     8.5
precuneus
692    495   2113  3.293 0.916     0.097     0.019        6     0.5
rostralanteriorcingulate
8417   5885  15312  2.103 0.863     0.132     0.038       84    13.2
rostralmiddlefrontal
12088   8265  23709  2.480 0.844     0.126     0.034      107    16.6
superiorfrontal
9409   6658  13995  1.939 0.725     0.129     0.037       88    15.1
superiorparietal
5340   3739  12789  2.733 1.021     0.106     0.024       41     5.4
superiortemporal
4534   3145   9172  2.397 0.936     0.112     0.030       37     5.5
supramarginal
361    268   1955  3.713 1.060     0.153     0.043        6     0.7
frontalpole
648    523   3312  3.939 0.662     0.156     0.044       10     1.0
temporalpole
511    346   1036  2.492 0.659     0.114     0.030        5     0.6
transversetemporal
3492   2507   7560  2.933 0.831     0.113     0.027       29     3.7  insula
@#@FSTIME  2024:08:07:18:21:39 mris_anatomical_stats N 14 e 5.77 S 0.15 U 5.
61 P 99% M 470024 F 0 R 135436 W 0 c 31 w 1 I 0 O 48 L 10.07 10.38 10.48
@#@FSLOADPOST 2024:08:07:18:21:45 mris_anatomical_stats N 14 9.76 10.30
10.45
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f
../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c
../label/aparc.annot.ctab 0003 rh pial
computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 244738
Total vertex volume 244461 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
1065    661   1907  2.829 0.675     0.124     0.043       27     1.5
bankssts
1123   1054   2363  2.443 0.858     0.186     0.048       40     2.3
caudalanteriorcingulate
4355   3345   7349  2.354 0.790     0.128     0.033       74     6.3
caudalmiddlefrontal
2344   2004   3608  2.024 0.694     0.143     0.041       31     4.2  cuneus
534    945   2074  2.904 0.962     0.349     0.081       15     2.4
entorhinal
3760   3936   8824  2.550 0.830     0.182     0.049      106     7.5
fusiform
6063   5916  13987  2.670 0.831     0.171     0.044      137    11.6
inferiorparietal
3434   4086   9856  2.808 0.967     0.204     0.052       81     8.1
inferiortemporal
1246   1068   2552  2.738 1.020     0.143     0.042       18     2.0
isthmuscingulate
8091   8079  16825  2.344 0.854     0.167     0.044      250    15.4
lateraloccipital
2905   2702   6628  2.751 0.892     0.199     0.062      179     8.6
lateralorbitofrontal
3598   3995   7600  2.224 0.806     0.182     0.044       61     7.4
lingual
2315   2551   6326  2.831 1.186     0.199     0.048       49     5.2
medialorbitofrontal
4064   5010  11573  2.789 0.900     0.216     0.053      141    10.1
middletemporal
938    881   1717  2.346 0.834     0.174     0.045       16     2.3
parahippocampal
2283   1579   2936  2.003 0.608     0.116     0.029       28     2.8
paracentral
2181   1862   3828  2.381 0.716     0.136     0.035       26     3.1
parsopercularis
967   1239   3041  3.020 1.041     0.204     0.048       18     2.6
parsorbitalis
1780   1768   3577  2.347 0.963     0.169     0.037       25     3.2
parstriangularis
1890   1213   2455  2.003 0.541     0.148     0.058       75     4.2
pericalcarine
6564   5221   9082  1.923 0.838     0.118     0.024       64     6.9
postcentral
1660   1290   2573  2.159 0.788     0.137     0.043       30     3.0
posteriorcingulate
9064   6464  12212  2.015 0.748     0.112     0.027      113    10.4
precentral
6185   4912  10614  2.286 0.860     0.142     0.040      114    10.7
precuneus
692    738   2113  3.293 0.916     0.161     0.042       12     1.0
rostralanteriorcingulate
8417   7898  15312  2.103 0.863     0.160     0.038      135    14.6
rostralmiddlefrontal
12088  10399  23709  2.480 0.844     0.149     0.038      241    19.3
superiorfrontal
9409   8212  13995  1.939 0.725     0.141     0.034      135    13.9
superiorparietal
5340   5208  12789  2.733 1.021     0.149     0.031       68     7.3
superiortemporal
4534   4429   9172  2.397 0.936     0.157     0.032       64     7.0
supramarginal
361    687   1955  3.713 1.060     0.265     0.051        6     1.0
frontalpole
648   1137   3312  3.939 0.662     0.286     0.061       19     2.0
temporalpole
511    506   1036  2.492 0.659     0.131     0.032        4     0.7
transversetemporal
3492   2641   7560  2.933 0.831     0.163     0.044       85     6.3  insula
@#@FSTIME  2024:08:07:18:21:45 mris_anatomical_stats N 14 e 6.37 S 0.16 U 6.
20 P 100% M 470528 F 0 R 135437 W 0 c 18 w 1 I 0 O 24 L 9.76 10.30 10.45
@#@FSLOADPOST 2024:08:07:18:21:51 mris_anatomical_stats N 14 9.78 10.30
10.45
#-----------------------------------------
#@# Parcellation Stats 2 lh 公曆 20廿四年 八月 七日 週三 十八時廿一分51秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c
../label/aparc.annot.a2009s.ctab 0003 lh white
computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 252503
Total vertex volume 252258 (mask=0)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
953    670   2462  2.514 1.070     0.120     0.028        8     1.1
G_and_S_frontomargin
1352    891   3563  2.734 0.943     0.126     0.034       14     1.7
G_and_S_occipital_inf
1644   1091   2194  1.850 0.537     0.121     0.035       13     2.3
G_and_S_paracentral
1641   1127   4308  2.714 0.914     0.122     0.032       15     2.0
G_and_S_subcentral
703    552   3178  3.361 1.182     0.154     0.044       10     1.2
G_and_S_transv_frontopol
2302   1680   4750  2.419 0.893     0.122     0.027       22     2.5
G_and_S_cingul-Ant
1420    981   2231  2.161 0.655     0.117     0.024       13     1.4
G_and_S_cingul-Mid-Ant
1015    672   1598  2.389 0.750     0.106     0.023        6     0.9
G_and_S_cingul-Mid-Post
532    368   1356  2.928 0.940     0.125     0.031        6     0.7
G_cingul-Post-dorsal
372    267    867  2.616 0.763     0.125     0.027        5     0.3
G_cingul-Post-ventral
1927   1449   3314  2.114 0.700     0.150     0.045       21     3.8
G_cuneus
1283    820   3828  3.077 0.914     0.112     0.034       12     1.5
G_front_inf-Opercular
508    355   1970  3.069 0.911     0.142     0.036        6     0.9
G_front_inf-Orbital
1081    751   2959  2.502 0.944     0.133     0.040       14     1.6
G_front_inf-Triangul
5007   3439  12255  2.537 0.938     0.145     0.044       63     9.3
G_front_middle
7142   4761  17818  2.813 0.932     0.131     0.041       80    11.9
G_front_sup
705    532   1879  3.037 1.059     0.144     0.043       10     1.1
G_Ins_lg_and_S_cent_ins
792    597   2605  3.456 0.993     0.134     0.040       11     1.6
G_insular_short
1924   1279   6478  3.010 1.012     0.134     0.041       23     2.9
G_occipital_middle
1708   1250   3329  2.394 0.842     0.134     0.036       15     2.8
G_occipital_sup
1578   1199   3539  2.323 0.803     0.145     0.044       23     2.9
G_oc-temp_lat-fusifor
2993   2236   6202  2.254 0.822     0.148     0.050       40     6.1
G_oc-temp_med-Lingual
1451    977   4433  2.969 0.955     0.111     0.026       12     1.6
G_oc-temp_med-Parahip
1781   1320   6854  3.379 1.071     0.138     0.042       23     2.7
G_orbital
2045   1495   4942  2.528 0.932     0.138     0.041       24     3.8
G_pariet_inf-Angular
3351   2400   8834  2.524 1.027     0.133     0.037       38     5.4
G_pariet_inf-Supramar
4069   2803   6711  1.989 0.739     0.126     0.034       40     6.1
G_parietal_sup
2845   1809   4370  1.985 0.684     0.130     0.040       28     4.8
G_postcentral
3970   2474   6253  2.106 0.806     0.122     0.037       34     6.6
G_precentral
3057   2299   6837  2.264 0.858     0.137     0.034       34     4.2
G_precuneus
746    635   3711  3.613 0.781     0.165     0.037       16     1.3
G_rectus
678    418   1117  2.935 1.139     0.096     0.033        5     0.8
G_subcallosal
499    344   1101  2.441 0.801     0.123     0.032        5     0.7
G_temp_sup-G_T_transv
2052   1479   7818  3.348 1.095     0.132     0.036       35     2.8
G_temp_sup-Lateral
683    511   1556  2.938 0.907     0.079     0.020        3     0.6
G_temp_sup-Plan_polar
901    626   1767  2.504 0.954     0.095     0.026        5     0.8
G_temp_sup-Plan_tempo
2126   1610   7803  3.062 1.134     0.146     0.050       28     4.1
G_temporal_inf
2569   1860   9006  2.956 1.021     0.142     0.042       32     4.8
G_temporal_middle
302    198    364  2.191 0.473     0.096     0.018        2     0.3
Lat_Fis-ant-Horizont
205    139    236  1.662 0.476     0.087     0.013        1     0.1
Lat_Fis-ant-Vertical
1111    700   1222  2.175 0.512     0.097     0.020        5     0.9
Lat_Fis-post
1842   1311   3162  2.158 0.858     0.122     0.038       19     2.9
Pole_occipital
1351   1126   5150  3.066 0.982     0.158     0.042       18     2.6
Pole_temporal
2757   2076   3312  1.798 0.536     0.130     0.038       21     5.0
S_calcarine
3832   2513   3678  1.737 0.603     0.096     0.021       18     3.8
S_central
997    660   1098  1.891 0.478     0.093     0.017        5     0.7
S_cingul-Marginalis
568    382    742  2.164 0.750     0.093     0.016        2     0.4
S_circular_insula_ant
1679   1093   2418  2.770 0.862     0.075     0.011        5     0.8
S_circular_insula_inf
1959   1246   2466  2.207 0.786     0.086     0.017        7     1.2
S_circular_insula_sup
851    553   1573  2.790 0.650     0.105     0.016        5     0.7
S_collat_transv_ant
503    338    563  2.396 0.468     0.135     0.029        4     0.8
S_collat_transv_post
2291   1466   2626  2.033 0.725     0.088     0.019       12     1.7
S_front_inf
1863   1266   2837  2.285 0.681     0.115     0.026       12     2.4
S_front_middle
3425   2204   5150  2.426 0.744     0.100     0.026       20     3.5
S_front_sup
127     93    130  1.451 0.272     0.091     0.013        0     0.1
S_interm_prim-Jensen
2990   1975   3421  1.998 0.727     0.100     0.021       16     2.5
S_intrapariet_and_P_trans
751    495    929  2.112 0.571     0.115     0.027        4     0.8
S_oc_middle_and_Lunatus
1317    869   1651  2.211 0.503     0.107     0.021        8     1.1
S_oc_sup_and_transversal
785    524   1466  2.401 0.799     0.128     0.035        7     1.4
S_occipital_ant
1002    665   1326  2.463 0.508     0.099     0.019        5     0.8
S_oc-temp_lat
1697   1097   2042  2.031 0.658     0.089     0.017        8     1.0
S_oc-temp_med_and_Lingual
251    174    343  2.116 0.679     0.115     0.032        1     0.3
S_orbital_lateral
397    280   1257  3.290 1.026     0.087     0.022        3     0.2
S_orbital_med-olfact
837    579   1958  2.968 1.223     0.110     0.030        6     0.9
S_orbital-H_Shaped
2652   1790   3595  2.292 0.627     0.114     0.025       16     3.0
S_parieto_occipital
1347    782   1347  2.016 0.898     0.078     0.012        7     0.5
S_pericallosal
4404   2974   4353  1.606 0.514     0.103     0.024       28     4.1
S_postcentral
1449    937   2016  2.634 0.779     0.086     0.018        6     1.0
S_precentral-inf-part
2156   1402   2639  2.324 0.701     0.099     0.021       11     2.0
S_precentral-sup-part
645    433    915  2.502 0.885     0.097     0.013        3     0.3
S_suborbital
1267    837   1601  2.076 0.697     0.110     0.023        8     1.2
S_subparietal
1459    993   2016  2.062 0.735     0.112     0.027        9     1.5
S_temporal_inf
4876   3259   6533  2.183 0.676     0.097     0.022       27     4.6
S_temporal_sup
235    175    328  2.130 0.661     0.130     0.029        2     0.2
S_temporal_transverse
@#@FSTIME  2024:08:07:18:21:51 mris_anatomical_stats N 14 e 7.16 S 0.15 U 7.
01 P 99% M 482288 F 0 R 138312 W 0 c 31 w 1 I 0 O 40 L 9.78 10.30 10.45
@#@FSLOADPOST 2024:08:07:18:21:58 mris_anatomical_stats N 14 10.04 10.34 10.
46
#-----------------------------------------
#@# Parcellation Stats 2 rh 公曆 20廿四年 八月 七日 週三 十八時廿一分58秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f
../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c
../label/aparc.annot.a2009s.ctab 0003 rh white
computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 244738
Total vertex volume 244461 (mask=0)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
840    627   2112  2.582 0.973     0.152     0.045       12     1.8
G_and_S_frontomargin
1379    988   3671  2.751 0.885     0.133     0.041       13     2.3
G_and_S_occipital_inf
1248    815   2143  2.112 0.716     0.128     0.041       10     2.0
G_and_S_paracentral
1463    963   3142  2.717 0.934     0.117     0.032       12     1.6
G_and_S_subcentral
1127    844   3264  2.595 1.151     0.150     0.041       15     2.0
G_and_S_transv_frontopol
2592   1799   6095  2.904 1.000     0.109     0.023       18     2.5
G_and_S_cingul-Ant
1578   1095   2634  2.229 0.635     0.134     0.032       14     2.2
G_and_S_cingul-Mid-Ant
1437    932   1999  2.061 0.752     0.110     0.024        9     1.4
G_and_S_cingul-Mid-Post
465    297   1317  3.234 0.951     0.118     0.037        4     0.6
G_cingul-Post-dorsal
379    260    909  2.982 0.927     0.127     0.024        4     0.4
G_cingul-Post-ventral
2284   1703   4033  2.090 0.772     0.154     0.048       24     4.6
G_cuneus
1456   1031   3501  2.428 0.884     0.138     0.042       20     2.7
G_front_inf-Opercular
264    189   1063  3.100 1.088     0.154     0.040        4     0.4
G_front_inf-Orbital
745    524   2016  2.586 1.042     0.132     0.043       10     1.2
G_front_inf-Triangul
5022   3598  11623  2.342 0.954     0.159     0.051       69    11.4
G_front_middle
7838   5371  17684  2.509 0.888     0.136     0.038       83    12.1
G_front_sup
652    525   1574  2.976 0.673     0.161     0.050        8     1.4
G_Ins_lg_and_S_cent_ins
778    640   2636  3.163 0.863     0.150     0.040       12     1.2
G_insular_short
2110   1611   6670  2.839 0.926     0.161     0.056       32     4.8
G_occipital_middle
1867   1437   3329  2.035 0.713     0.159     0.054       27     4.4
G_occipital_sup
1768   1414   4735  2.632 0.761     0.166     0.054       27     4.0
G_oc-temp_lat-fusifor
1975   1628   5532  2.512 0.872     0.159     0.054       34     4.7
G_oc-temp_med-Lingual
1212    895   3889  2.832 0.919     0.147     0.043       16     2.3
G_oc-temp_med-Parahip
2002   1468   6814  3.133 0.908     0.132     0.034       23     2.9
G_orbital
1795   1369   5037  2.570 0.897     0.151     0.050       24     3.5
G_pariet_inf-Angular
2262   1677   6567  2.673 0.968     0.136     0.041       27     4.0
G_pariet_inf-Supramar
3320   2419   5627  1.910 0.718     0.147     0.046       39     6.3
G_parietal_sup
2278   1374   3715  2.146 0.864     0.114     0.032       24     3.1
G_postcentral
3550   2170   5582  2.130 0.817     0.118     0.037       36     5.5
G_precentral
2682   2035   5771  2.252 0.944     0.149     0.040       30     4.7
G_precuneus
587    458   2875  3.515 0.905     0.144     0.034        9     0.8
G_rectus
420    275    839  2.811 1.339     0.088     0.028        3     0.3
G_subcallosal
398    259    956  2.673 0.623     0.132     0.039        5     0.7
G_temp_sup-G_T_transv
1721   1276   6268  3.413 1.013     0.137     0.037       21     2.7
G_temp_sup-Lateral
753    541   2122  3.387 0.874     0.073     0.017        3     0.3
G_temp_sup-Plan_polar
809    560   1496  2.315 0.879     0.078     0.014        3     0.5
G_temp_sup-Plan_tempo
1797   1441   6556  3.018 1.017     0.174     0.061       28     4.5
G_temporal_inf
2469   1897   9012  2.999 0.987     0.149     0.040       36     4.1
G_temporal_middle
309    207    349  2.020 0.569     0.114     0.023        2     0.3
Lat_Fis-ant-Horizont
198    134    234  2.130 0.812     0.127     0.032        1     0.3
Lat_Fis-ant-Vertical
1348    850   1828  2.802 0.621     0.075     0.015        4     0.7
Lat_Fis-post
3616   2726   6895  2.120 0.805     0.145     0.046       36     7.8
Pole_occipital
1271   1041   6112  3.426 0.943     0.164     0.044       17     2.4
Pole_temporal
2223   1576   2647  1.970 0.567     0.130     0.043      122     5.4
S_calcarine
3089   1988   2717  1.595 0.497     0.091     0.019       16     2.6
S_central
1216    830   1240  1.627 0.391     0.118     0.034        9     2.0
S_cingul-Marginalis
618    411    787  2.332 0.449     0.094     0.019        2     0.6
S_circular_insula_ant
1447    917   1844  2.257 0.829     0.074     0.010        4     0.7
S_circular_insula_inf
1577    996   2234  2.747 0.898     0.086     0.017        6     1.0
S_circular_insula_sup
950    617   1747  2.820 0.655     0.098     0.024        6     0.7
S_collat_transv_ant
546    357    685  2.507 0.481     0.117     0.028        3     0.7
S_collat_transv_post
2050   1360   1989  1.743 0.521     0.113     0.028       15     2.2
S_front_inf
2345   1544   2495  1.755 0.511     0.103     0.023       12     2.2
S_front_middle
3294   2206   4954  2.545 0.729     0.106     0.025       19     3.2
S_front_sup
291    196    443  1.775 0.692     0.065     0.013        1     0.1
S_interm_prim-Jensen
3387   2203   4152  2.108 0.799     0.099     0.021       19     3.2
S_intrapariet_and_P_trans
889    644   1275  2.140 0.558     0.132     0.042        8     1.3
S_oc_middle_and_Lunatus
1462   1005   1647  1.914 0.534     0.114     0.028       11     1.7
S_oc_sup_and_transversal
705    474   1060  2.721 0.704     0.125     0.037        6     1.0
S_occipital_ant
716    517   1118  2.265 0.687     0.128     0.033        7     0.9
S_oc-temp_lat
1694   1152   2030  1.909 0.521     0.106     0.026       13     1.7
S_oc-temp_med_and_Lingual
542    366    661  1.861 0.656     0.125     0.028        4     0.8
S_orbital_lateral
545    398    846  2.134 0.724     0.148     0.039        6     1.0
S_orbital_med-olfact
947    635   1983  2.916 0.876     0.099     0.023        5     0.9
S_orbital-H_Shaped
2511   1666   3262  2.355 0.638     0.111     0.026       16     2.7
S_parieto_occipital
1191    717   1258  2.135 0.709     0.104     0.029        9     1.4
S_pericallosal
3049   1976   2836  1.583 0.461     0.093     0.018       17     2.2
S_postcentral
2247   1454   2793  2.148 0.601     0.106     0.023       15     2.1
S_precentral-inf-part
1910   1218   2022  1.970 0.588     0.113     0.027       13     2.3
S_precentral-sup-part
352    229    465  2.172 1.001     0.092     0.012        2     0.2
S_suborbital
1465   1019   2097  2.002 0.897     0.126     0.034       11     2.1
S_subparietal
981    661   1733  2.432 0.791     0.106     0.026        5     0.9
S_temporal_inf
5304   3631   8903  2.570 0.707     0.103     0.022       36     4.7
S_temporal_sup
294    206    315  1.762 0.620     0.113     0.012        2     0.2
S_temporal_transverse
@#@FSTIME  2024:08:07:18:21:58 mris_anatomical_stats N 14 e 6.67 S 0.13 U 6.
53 P 99% M 470488 F 0 R 134816 W 0 c 31 w 1 I 0 O 40 L 10.04 10.34 10.46
@#@FSLOADPOST 2024:08:07:18:22:05 mris_anatomical_stats N 14 9.65 10.25
10.43
#-----------------------------------------
#@# Parcellation Stats 3 lh 公曆 20廿四年 八月 七日 週三 十八時廿二分五秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c
../label/aparc.annot.DKTatlas.ctab 0003 lh white
computing statistics for each annotation in
../label/lh.aparc.DKTatlas.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 252503
Total vertex volume 252258 (mask=0)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
2025   1374   3305  2.241 0.771     0.115     0.021       21     1.8
caudalanteriorcingulate
4057   2654   5935  2.336 0.749     0.118     0.033       31     5.7
caudalmiddlefrontal
3132   2253   4914  2.232 0.636     0.135     0.036       28     4.7  cuneus
603    444   1983  2.866 1.043     0.135     0.034        5     0.9
entorhinal
3695   2612   7243  2.398 0.791     0.125     0.031       37     4.9
fusiform
5181   3535  10314  2.501 0.879     0.119     0.032       43     6.9
inferiorparietal
4257   3136  12385  2.824 1.039     0.137     0.040       45     6.9
inferiortemporal
1656   1111   2981  2.360 0.998     0.105     0.023       12     1.4
isthmuscingulate
6807   4612  14781  2.515 0.923     0.125     0.034       67     9.5
lateraloccipital
2869   2003   8225  3.066 1.129     0.114     0.032       25     3.3
lateralorbitofrontal
4425   3171   7572  2.102 0.770     0.128     0.039       47     7.1
lingual
1839   1396   6094  3.234 0.990     0.127     0.029       24     2.1
medialorbitofrontal
5548   3920  13897  2.623 0.950     0.129     0.036       54     8.9
middletemporal
1055    655   2062  2.548 0.933     0.074     0.014        5     0.5
parahippocampal
2370   1579   3337  2.100 0.688     0.121     0.034       19     3.5
paracentral
2124   1344   4634  2.744 0.933     0.098     0.026       15     2.0
parsopercularis
1113    828   3279  2.624 1.000     0.139     0.038       13     1.7
parsorbitalis
2167   1429   3991  2.204 0.847     0.114     0.029       19     2.4
parstriangularis
1889   1522   2569  1.852 0.561     0.157     0.049       19     4.5
pericalcarine
8674   5701  12060  1.868 0.754     0.111     0.028       66    10.2
postcentral
1298    832   1825  2.078 0.682     0.104     0.023       11     1.2
posteriorcingulate
9349   6012  13938  2.180 0.788     0.113     0.030       68    12.4
precentral
6219   4451  10754  2.180 0.743     0.125     0.029       52     7.8
precuneus
1722   1176   3687  2.584 1.079     0.107     0.025       14     1.7
rostralanteriorcingulate
6508   4442  14357  2.435 0.977     0.124     0.034       64     9.2
rostralmiddlefrontal
11777   7944  27056  2.692 0.928     0.122     0.035      109    16.6
superiorfrontal
8370   5751  11847  1.891 0.700     0.116     0.030       68    10.9
superiorparietal
7503   5244  17872  2.670 1.021     0.100     0.023       65     6.8
superiortemporal
5581   3869  11048  2.354 0.871     0.117     0.032       46     7.3
supramarginal
629    441   1180  2.354 0.672     0.121     0.030        5     0.7
transversetemporal
3143   2191   7132  3.062 1.010     0.105     0.026       24     3.3  insula
@#@FSTIME  2024:08:07:18:22:05 mris_anatomical_stats N 14 e 6.66 S 0.15 U 6.
50 P 99% M 482132 F 0 R 138330 W 0 c 24 w 17 I 0 O 24 L 9.65 10.25 10.43
@#@FSLOADPOST 2024:08:07:18:22:12 mris_anatomical_stats N 14 9.43 10.19
10.41
#-----------------------------------------
#@# Parcellation Stats 3 rh 公曆 20廿四年 八月 七日 週三 十八時廿二分十二秒
/home/chang/GBM_Data/VBG/0003/0003/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f
../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c
../label/aparc.annot.DKTatlas.ctab 0003 rh white
computing statistics for each annotation in
../label/rh.aparc.DKTatlas.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert,
SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 244738
Total vertex volume 244461 (mask=0)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
1210    815   2531  2.463 0.849     0.121     0.024       12     1.2
caudalanteriorcingulate
4551   3145   7605  2.338 0.795     0.138     0.037       46     7.7
caudalmiddlefrontal
2868   2052   4423  2.059 0.719     0.143     0.042       27     5.0  cuneus
497    447   1845  2.793 0.906     0.193     0.058        7     1.5
entorhinal
3543   2707   8029  2.510 0.810     0.148     0.045       45     6.6
fusiform
6010   4239  13643  2.643 0.816     0.124     0.034       57     8.2
inferiorparietal
3676   2738  10922  2.859 0.949     0.145     0.045       41     6.6
inferiortemporal
1252    818   2588  2.723 1.032     0.106     0.028        9     1.4
isthmuscingulate
8173   6105  16919  2.331 0.854     0.145     0.046       92    16.1
lateraloccipital
3084   2207   7582  2.812 0.905     0.130     0.035       32     4.8
lateralorbitofrontal
3514   2685   7434  2.224 0.813     0.141     0.045       46     7.0
lingual
1611   1145   5205  3.065 1.240     0.119     0.027       16     1.7
medialorbitofrontal
4842   3557  13265  2.826 0.891     0.126     0.031       50     6.3
middletemporal
991    620   1872  2.375 0.859     0.091     0.019        6     0.8
parahippocampal
2366   1475   3093  2.015 0.611     0.111     0.027       16     2.5
paracentral
2404   1615   4129  2.360 0.738     0.112     0.030       21     3.1
parsopercularis
935    654   2740  2.820 1.040     0.124     0.029        9     1.2
parsorbitalis
1711   1151   3372  2.350 0.971     0.119     0.030       17     2.0
parstriangularis
1838   1331   2389  1.981 0.524     0.153     0.056      119     5.3
pericalcarine
7211   4608   9881  1.897 0.818     0.100     0.024       51     7.2
postcentral
1737   1159   2605  2.134 0.781     0.131     0.038       15     2.8
posteriorcingulate
8568   5402  11753  2.031 0.764     0.115     0.031       73    11.3
precentral
6364   4548  11022  2.253 0.866     0.128     0.035       57     9.5
precuneus
964    657   2591  3.067 1.090     0.091     0.019        7     0.7
rostralanteriorcingulate
6238   4296  11281  2.089 0.878     0.134     0.041       64    10.5
rostralmiddlefrontal
14895  10275  29674  2.441 0.864     0.126     0.033      134    20.1
superiorfrontal
7890   5514  11656  1.957 0.729     0.126     0.035       73    11.7
superiorparietal
6814   4816  17356  2.846 1.016     0.112     0.026       58     7.2
superiortemporal
4382   3045   8898  2.411 0.939     0.113     0.031       37     5.5
supramarginal
508    345   1041  2.458 0.683     0.109     0.030        5     0.6
transversetemporal
3254   2362   7116  2.928 0.836     0.114     0.027       27     3.5  insula
@#@FSTIME  2024:08:07:18:22:12 mris_anatomical_stats N 14 e 5.81 S 0.12 U 5.
68 P 99% M 470448 F 0 R 134816 W 0 c 30 w 1 I 0 O 24 L 9.43 10.19 10.41
@#@FSLOADPOST 2024:08:07:18:22:18 mris_anatomical_stats N 14 9.64 10.22
10.42
#--------------------------------------------
#@# ASeg Stats 公曆 20廿四年 八月 七日 週三 十八時廿二分十八秒
/home/chang/GBM_Data/VBG/0003/0003
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
--surf-ctx-vol --totalgray --euler --ctab
/usr/local/freesurfer/ASegStatsLUT.txt --subject 0003
setting seed for random number genererator to 1234
7.4.1
cwd
cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats
--pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
--surf-ctx-vol --totalgray --euler --ctab
/usr/local/freesurfer/ASegStatsLUT.txt --subject 0003
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
whitesurfname  white
UseRobust  0
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
Computing euler number
orig.nofix lheno =  -62, rheno = -62
orig.nofix lhholes =   32, rhholes = 32
Loading mri/aseg.mgz
Getting Brain Volume Statistics
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation
Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
@#@FSTIME  2024:08:07:18:22:18 mri_segstats N 32 e 143.11 S 0.34 U 142.75 P
99% M 290072 F 0 R 753890 W 0 c 481 w 66 I 0 O 24 L 9.64 10.22 10.42
@#@FSLOADPOST 2024:08:07:18:24:41 mri_segstats N 32 10.18 10.29 10.42
/home/chang/GBM_Data/VBG/0003/0003/label
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...
cd /home/chang/GBM_Data/VBG/0003; ln -s
/usr/local/freesurfer/subjects/fsaverage; cd -
#--------------------------------------------
#@# BA_exvivo Labels lh 公曆 20廿四年 八月 七日 週三 十八時廿四分41秒
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA1_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4129 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 343
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4472
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:41 mri_label2label N 12 e 2.25 S 0.16 U 2.08 P
99% M 557012 F 0 R 165787 W 0 c 15 w 11 I 16720 O 312 L 10.18 10.29 10.42
@#@FSLOADPOST 2024:08:07:18:24:43 mri_label2label N 12 10.18 10.29 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA2_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7909 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 1619
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9528
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:43 mri_label2label N 12 e 3.17 S 0.13 U 3.04 P
99% M 556908 F 0 R 165867 W 0 c 24 w 3 I 632 O 696 L 10.18 10.29 10.42
@#@FSLOADPOST 2024:08:07:18:24:46 mri_label2label N 12 10.24 10.30 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA3a_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4077 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 195
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4272
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:46 mri_label2label N 12 e 2.75 S 0.18 U 2.57 P
99% M 557620 F 0 R 165781 W 0 c 14 w 3 I 320 O 272 L 10.24 10.30 10.42
@#@FSLOADPOST 2024:08:07:18:24:49 mri_label2label N 12 10.24 10.30 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA3b_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5983 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 395
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6378
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:49 mri_label2label N 12 e 2.75 S 0.18 U 2.57 P
99% M 557736 F 0 R 165817 W 0 c 12 w 2 I 472 O 432 L 10.24 10.30 10.42
@#@FSLOADPOST 2024:08:07:18:24:52 mri_label2label N 12 10.06 10.26 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA4a_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5784 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 894
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6678
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:52 mri_label2label N 12 e 2.90 S 0.20 U 2.69 P
99% M 557164 F 0 R 165818 W 0 c 29 w 2 I 456 O 472 L 10.06 10.26 10.41
@#@FSLOADPOST 2024:08:07:18:24:55 mri_label2label N 12 10.14 10.27 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA4p_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4070 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 385
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4455
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:55 mri_label2label N 12 e 2.70 S 0.18 U 2.52 P
99% M 557824 F 0 R 165786 W 0 c 9 w 2 I 320 O 312 L 10.14 10.27 10.41
@#@FSLOADPOST 2024:08:07:18:24:57 mri_label2label N 12 10.14 10.27 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA6_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  13589 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 2204
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15793
mri_label2label: Done
@#@FSTIME  2024:08:07:18:24:57 mri_label2label N 12 e 3.43 S 0.18 U 3.24 P
99% M 558504 F 0 R 165970 W 0 c 11 w 4 I 1056 O 1136 L 10.14 10.27 10.41
@#@FSLOADPOST 2024:08:07:18:25:01 mri_label2label N 12 10.05 10.25 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA44_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4181 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 233
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4414
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:01 mri_label2label N 12 e 2.78 S 0.20 U 2.58 P
99% M 557264 F 0 R 165787 W 0 c 16 w 2 I 328 O 264 L 10.05 10.25 10.41
@#@FSLOADPOST 2024:08:07:18:25:04 mri_label2label N 12 10.05 10.25 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.label
--trgsubject 0003 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA45_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3422 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 455
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 3877
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:04 mri_label2label N 12 e 2.65 S 0.15 U 2.49 P
99% M 556904 F 0 R 165768 W 0 c 28 w 3 I 272 O 280 L 10.05 10.25 10.41
@#@FSLOADPOST 2024:08:07:18:25:06 mri_label2label N 12 9.96 10.23 10.40
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.label
--trgsubject 0003 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.V1_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4641 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 866
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5507
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:06 mri_label2label N 12 e 2.98 S 0.17 U 2.80 P
99% M 557624 F 0 R 165858 W 0 c 15 w 62 I 376 O 432 L 9.96 10.23 10.40
@#@FSLOADPOST 2024:08:07:18:25:09 mri_label2label N 12 9.96 10.23 10.40
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.label
--trgsubject 0003 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.V2_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8114 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 2231
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10345
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:09 mri_label2label N 12 e 3.04 S 0.15 U 2.88 P
99% M 557516 F 0 R 165874 W 0 c 14 w 5 I 664 O 848 L 9.97 10.23 10.40
@#@FSLOADPOST 2024:08:07:18:25:12 mri_label2label N 12 9.97 10.23 10.40
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.label
--trgsubject 0003 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.MT_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2018 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 217
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2235
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:12 mri_label2label N 12 e 2.52 S 0.19 U 2.32 P
100% M 557644 F 0 R 166517 W 0 c 15 w 2 I 168 O 168 L 9.97 10.23 10.40
@#@FSLOADPOST 2024:08:07:18:25:15 mri_label2label N 12 9.81 10.19 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.label
--trgsubject 0003 --trglabel ./lh.entorhinal_exvivo.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.entorhinal_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1290 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1290 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 68
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1358
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:15 mri_label2label N 12 e 2.60 S 0.21 U 2.39 P
99% M 557008 F 0 R 165729 W 0 c 9 w 3 I 264 O 88 L 9.81 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:17 mri_label2label N 12 9.81 10.19 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.label
--trgsubject 0003 --trglabel ./lh.perirhinal_exvivo.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.perirhinal_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1199 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 69
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1268
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:17 mri_label2label N 12 e 2.66 S 0.20 U 2.45 P
99% M 557208 F 0 R 165725 W 0 c 10 w 4 I 112 O 88 L 9.81 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:20 mri_label2label N 12 9.82 10.19 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG1.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.FG1.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 414 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  414 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 41
Checking for and removing duplicates
Writing label file ./lh.FG1.mpm.vpnl.label 455
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:20 mri_label2label N 12 e 2.90 S 0.18 U 2.71 P
99% M 557340 F 0 R 165725 W 0 c 10 w 2 I 40 O 40 L 9.82 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:23 mri_label2label N 12 9.82 10.19 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG2.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.FG2.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 703 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  703 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 48
Checking for and removing duplicates
Writing label file ./lh.FG2.mpm.vpnl.label 751
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:23 mri_label2label N 12 e 2.57 S 0.20 U 2.36 P
99% M 557272 F 0 R 165717 W 0 c 10 w 3 I 72 O 56 L 9.82 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:26 mri_label2label N 12 10.00 10.22 10.39
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG3.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG3.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.FG3.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1873 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1873 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 73
Checking for and removing duplicates
Writing label file ./lh.FG3.mpm.vpnl.label 1946
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:26 mri_label2label N 12 e 2.05 S 0.19 U 1.86 P
99% M 557668 F 0 R 165743 W 0 c 8 w 2 I 176 O 136 L 10.00 10.22 10.39
@#@FSLOADPOST 2024:08:07:18:25:28 mri_label2label N 12 10.00 10.22 10.39
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG4.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG4.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.FG4.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2101 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2101 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 358
Checking for and removing duplicates
Writing label file ./lh.FG4.mpm.vpnl.label 2459
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:28 mri_label2label N 12 e 2.42 S 0.16 U 2.26 P
100% M 557468 F 0 R 165745 W 0 c 10 w 3 I 200 O 200 L 10.00 10.22 10.39
@#@FSLOADPOST 2024:08:07:18:25:30 mri_label2label N 12 9.84 10.18 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc1.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.hOc1.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3877 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3877 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 694
Checking for and removing duplicates
Writing label file ./lh.hOc1.mpm.vpnl.label 4571
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:30 mri_label2label N 12 e 2.76 S 0.17 U 2.59 P
99% M 557836 F 0 R 165787 W 0 c 9 w 3 I 360 O 360 L 9.84 10.18 10.38
@#@FSLOADPOST 2024:08:07:18:25:33 mri_label2label N 12 9.84 10.18 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc2.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.hOc2.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2919 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2919 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 951
Checking for and removing duplicates
Writing label file ./lh.hOc2.mpm.vpnl.label 3870
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:33 mri_label2label N 12 e 2.64 S 0.18 U 2.46 P
100% M 557352 F 0 R 166535 W 0 c 14 w 4 I 272 O 320 L 9.84 10.18 10.38
@#@FSLOADPOST 2024:08:07:18:25:36 mri_label2label N 12 10.01 10.21 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc3v.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc3v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.hOc3v.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1286 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1286 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 496
Checking for and removing duplicates
Writing label file ./lh.hOc3v.mpm.vpnl.label 1782
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:36 mri_label2label N 12 e 2.67 S 0.21 U 2.46 P
100% M 557240 F 0 R 165733 W 0 c 14 w 2 I 128 O 160 L 10.01 10.21 10.38
@#@FSLOADPOST 2024:08:07:18:25:38 mri_label2label N 12 10.01 10.21 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc4v.mpm.vpnl.label
--trgsubject 0003 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc4v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.hOc4v.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1006 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1006 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./lh.hOc4v.mpm.vpnl.label 1180
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:38 mri_label2label N 12 e 2.60 S 0.21 U 2.39 P
99% M 557468 F 0 R 165728 W 0 c 10 w 3 I 96 O 96 L 10.01 10.21 10.38
@#@FSLOADPOST 2024:08:07:18:25:41 mri_label2label N 12 9.93 10.19 10.38
mris_label2annot --s 0003 --ctab
/usr/local/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl
--maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l
lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label
--l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.
label --l lh.hOc4v.mpm.vpnl.label
Reading ctab /usr/local/freesurfer/average/colortable_vpnl.txt
Number of ctab entries 9
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/label
cmdline mris_label2annot --s 0003 --ctab
/usr/local/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl
--maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l
lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label
--l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.
label --l lh.hOc4v.mpm.vpnl.label
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
subject 0003
hemi    lh
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
ColorTable /usr/local/freesurfer/average/colortable_vpnl.txt
AnnotName  mpm.vpnl
nlables 8
LabelThresh 0 0.000000
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig
Index Offset 0
0 reading lh.FG1.mpm.vpnl.label
1 1376057 FG1
1 reading lh.FG2.mpm.vpnl.label
2 16711935 FG2
2 reading lh.FG3.mpm.vpnl.label
3 16711680 FG3
3 reading lh.FG4.mpm.vpnl.label
4 1705837 FG4
4 reading lh.hOc1.mpm.vpnl.label
5 25600 hOc1
5 reading lh.hOc2.mpm.vpnl.label
6 255 hOc2
6 reading lh.hOc3v.mpm.vpnl.label
7 16776960 hOc3v
7 reading lh.hOc4v.mpm.vpnl.label
8 65535 hOc4v
Mapping unhit to unknown
Found 121569 unhit vertices
Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/lh.mpm.vpnl.annot
@#@FSTIME  2024:08:07:18:25:41 mris_label2annot N 26 e 0.40 S 0.06 U 0.33 P
99% M 158036 F 8 R 42714 W 0 c 3 w 7 I 1328 O 2136 L 9.93 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:41 mris_label2annot N 26 9.93 10.19 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA1_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1014 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 44
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1058
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:41 mri_label2label N 12 e 2.73 S 0.16 U 2.55 P
99% M 557732 F 0 R 165810 W 0 c 11 w 87 I 96 O 80 L 9.93 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:44 mri_label2label N 12 9.93 10.19 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA2_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2092 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 511
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2603
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:44 mri_label2label N 12 e 2.73 S 0.16 U 2.56 P
99% M 556856 F 0 R 165750 W 0 c 20 w 3 I 192 O 208 L 9.93 10.19 10.38
@#@FSLOADPOST 2024:08:07:18:25:47 mri_label2label N 12 10.10 10.22 10.39
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA3a_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1504 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 27
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1531
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:47 mri_label2label N 12 e 2.51 S 0.21 U 2.29 P
99% M 556712 F 0 R 166505 W 0 c 15 w 3 I 136 O 96 L 10.10 10.22 10.39
@#@FSLOADPOST 2024:08:07:18:25:49 mri_label2label N 12 10.09 10.22 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA3b_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1996 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 70
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2066
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:49 mri_label2label N 12 e 2.48 S 0.17 U 2.31 P
99% M 557284 F 0 R 165746 W 0 c 10 w 3 I 184 O 144 L 10.09 10.22 10.38
@#@FSLOADPOST 2024:08:07:18:25:52 mri_label2label N 12 10.09 10.22 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA4a_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2319 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 346
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2665
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:52 mri_label2label N 12 e 2.67 S 0.17 U 2.49 P
99% M 557416 F 0 R 165750 W 0 c 10 w 4 I 208 O 192 L 10.09 10.22 10.38
@#@FSLOADPOST 2024:08:07:18:25:55 mri_label2label N 12 10.24 10.25 10.39
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA4p_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1549 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 158
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1707
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:55 mri_label2label N 12 e 2.60 S 0.18 U 2.42 P
100% M 557748 F 0 R 165736 W 0 c 11 w 5 I 144 O 128 L 10.24 10.25 10.39
@#@FSLOADPOST 2024:08:07:18:25:57 mri_label2label N 12 10.24 10.25 10.39
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA6_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7035 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 1215
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8250
mri_label2label: Done
@#@FSTIME  2024:08:07:18:25:57 mri_label2label N 12 e 3.27 S 0.18 U 3.09 P
100% M 557944 F 0 R 165842 W 0 c 16 w 3 I 616 O 608 L 10.24 10.25 10.39
@#@FSLOADPOST 2024:08:07:18:26:00 mri_label2label N 12 10.14 10.22 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA44_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1912 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 28
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 1940
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:00 mri_label2label N 12 e 2.57 S 0.18 U 2.38 P
100% M 557760 F 0 R 165737 W 0 c 8 w 3 I 168 O 112 L 10.14 10.22 10.38
@#@FSLOADPOST 2024:08:07:18:26:03 mri_label2label N 12 10.14 10.22 10.38
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.BA45_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1151 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 194
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1345
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:03 mri_label2label N 12 e 2.86 S 0.19 U 2.67 P
99% M 557452 F 0 R 165723 W 0 c 8 w 3 I 104 O 104 L 10.14 10.22 10.38
@#@FSLOADPOST 2024:08:07:18:26:06 mri_label2label N 12 10.61 10.32 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.V1_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3405 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 616
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4021
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:06 mri_label2label N 12 e 2.91 S 0.16 U 2.74 P
99% M 557816 F 0 R 165769 W 0 c 14 w 3 I 304 O 320 L 10.61 10.32 10.41
@#@FSLOADPOST 2024:08:07:18:26:09 mri_label2label N 12 10.61 10.32 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.V2_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3334 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 1050
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4384
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:09 mri_label2label N 12 e 2.72 S 0.21 U 2.51 P
99% M 557052 F 0 R 165774 W 0 c 21 w 4 I 296 O 368 L 10.61 10.32 10.41
@#@FSLOADPOST 2024:08:07:18:26:12 mri_label2label N 12 10.64 10.33 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.thresh.label
--trgsubject 0003 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.MT_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  513 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 543
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:12 mri_label2label N 12 e 1.94 S 0.17 U 1.77 P
99% M 557104 F 0 R 165713 W 0 c 9 w 2 I 48 O 40 L 10.64 10.33 10.42
@#@FSLOADPOST 2024:08:07:18:26:14 mri_label2label N 12 10.64 10.33 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.thresh.la
bel --trgsubject 0003 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi
lh --regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.thresh.la
bel
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.entorhinal_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 470 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  470 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 35
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 505
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:14 mri_label2label N 12 e 2.26 S 0.19 U 2.06 P
100% M 556700 F 0 R 165710 W 0 c 18 w 2 I 48 O 40 L 10.64 10.33 10.42
@#@FSLOADPOST 2024:08:07:18:26:16 mri_label2label N 12 10.51 10.31 10.41
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.thresh.la
bel --trgsubject 0003 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi
lh --regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.thresh.la
bel
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./lh.perirhinal_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 450 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  450 nlabel points
Performing mapping from target back to the source label 136375
Number of reverse mapping hits = 43
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 493
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:16 mri_label2label N 12 e 3.07 S 0.25 U 2.81 P
99% M 556592 F 0 R 166570 W 0 c 39 w 87 I 48 O 40 L 10.51 10.31 10.41
@#@FSLOADPOST 2024:08:07:18:26:19 mri_label2label N 12 10.51 10.31 10.41
mris_label2annot --s 0003 --hemi lh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l
lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l
lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l
lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.
V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l
lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
Reading ctab /usr/local/freesurfer/average/colortable_BA.txt
Number of ctab entries 15
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/label
cmdline mris_label2annot --s 0003 --hemi lh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l
lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l
lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l
lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.
V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l
lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
subject 0003
hemi    lh
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
ColorTable /usr/local/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig
Index Offset 0
0 reading lh.BA1_exvivo.label
1 1530880 BA1_exvivo
1 reading lh.BA2_exvivo.label
2 16749699 BA2_exvivo
2 reading lh.BA3a_exvivo.label
3 16711680 BA3a_exvivo
3 reading lh.BA3b_exvivo.label
4 3368703 BA3b_exvivo
4 reading lh.BA4a_exvivo.label
5 1376196 BA4a_exvivo
5 reading lh.BA4p_exvivo.label
6 13382655 BA4p_exvivo
6 reading lh.BA6_exvivo.label
7 10036737 BA6_exvivo
7 reading lh.BA44_exvivo.label
8 2490521 BA44_exvivo
8 reading lh.BA45_exvivo.label
9 39283 BA45_exvivo
9 reading lh.V1_exvivo.label
10 3993 V1_exvivo
10 reading lh.V2_exvivo.label
11 8508928 V2_exvivo
11 reading lh.MT_exvivo.label
12 10027163 MT_exvivo
12 reading lh.perirhinal_exvivo.label
13 16422433 perirhinal_exvivo
13 reading lh.entorhinal_exvivo.label
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 90530 unhit vertices
Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/lh.BA_exvivo.annot
@#@FSTIME  2024:08:07:18:26:19 mris_label2annot N 38 e 0.47 S 0.05 U 0.41 P
99% M 158300 F 0 R 42933 W 0 c 3 w 7 I 8 O 2136 L 10.51 10.31 10.41
@#@FSLOADPOST 2024:08:07:18:26:19 mris_label2annot N 38 10.39 10.29 10.40
mris_label2annot --s 0003 --hemi lh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l
lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l
lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l
lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l
lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l
lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l
lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l
lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a
BA_exvivo.thresh --maxstatwinner --noverbose
Reading ctab /usr/local/freesurfer/average/colortable_BA.txt
Number of ctab entries 15
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/label
cmdline mris_label2annot --s 0003 --hemi lh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l
lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l
lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l
lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l
lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l
lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l
lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l
lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a
BA_exvivo.thresh --maxstatwinner --noverbose
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
subject 0003
hemi    lh
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
ColorTable /usr/local/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig
Index Offset 0
0 reading lh.BA1_exvivo.thresh.label
1 1530880 BA1_exvivo
1 reading lh.BA2_exvivo.thresh.label
2 16749699 BA2_exvivo
2 reading lh.BA3a_exvivo.thresh.label
3 16711680 BA3a_exvivo
3 reading lh.BA3b_exvivo.thresh.label
4 3368703 BA3b_exvivo
4 reading lh.BA4a_exvivo.thresh.label
5 1376196 BA4a_exvivo
5 reading lh.BA4p_exvivo.thresh.label
6 13382655 BA4p_exvivo
6 reading lh.BA6_exvivo.thresh.label
7 10036737 BA6_exvivo
7 reading lh.BA44_exvivo.thresh.label
8 2490521 BA44_exvivo
8 reading lh.BA45_exvivo.thresh.label
9 39283 BA45_exvivo
9 reading lh.V1_exvivo.thresh.label
10 3993 V1_exvivo
10 reading lh.V2_exvivo.thresh.label
11 8508928 V2_exvivo
11 reading lh.MT_exvivo.thresh.label
12 10027163 MT_exvivo
12 reading lh.perirhinal_exvivo.thresh.label
13 16422433 perirhinal_exvivo
13 reading lh.entorhinal_exvivo.thresh.label
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 109089 unhit vertices
Writing annot to
/home/chang/GBM_Data/VBG/0003/0003/label/lh.BA_exvivo.thresh.annot
@#@FSTIME  2024:08:07:18:26:19 mris_label2annot N 38 e 0.43 S 0.06 U 0.35 P
98% M 158432 F 0 R 42847 W 0 c 6 w 3 I 0 O 2136 L 10.39 10.29 10.40
@#@FSLOADPOST 2024:08:07:18:26:20 mris_label2annot N 38 10.39 10.29 10.40
mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a
./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 0003 lh white
computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 252503
Total vertex volume 252258 (mask=0)
Saving annotation colortable ./BA_exvivo.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
1219    712   2063  2.214 0.736     0.128     0.041       13     2.0
BA1_exvivo
5934   3970   7604  1.790 0.717     0.113     0.029       46     7.2
BA2_exvivo
1212    798   1139  1.886 0.602     0.123     0.030        9     1.4
BA3a_exvivo
2786   1856   4499  1.934 0.880     0.099     0.024       18     2.7
BA3b_exvivo
1912   1210   2756  2.045 0.702     0.116     0.034       14     3.0
BA4a_exvivo
1661   1078   1822  1.846 0.618     0.091     0.023        7     1.8
BA4p_exvivo
11737   7467  20672  2.472 0.869     0.120     0.036      102    18.1
BA6_exvivo
2041   1295   4534  2.984 0.825     0.095     0.025       11     1.7
BA44_exvivo
2851   1883   5563  2.221 0.888     0.111     0.030       25     3.3
BA45_exvivo
3305   2555   4984  1.926 0.739     0.142     0.043       34     6.4
V1_exvivo
8205   5769  14627  2.306 0.786     0.134     0.040       83    14.2
V2_exvivo
1741   1172   3785  2.492 0.817     0.126     0.030       16     2.4
MT_exvivo
676    503   2235  3.124 0.913     0.142     0.039        7     1.2
perirhinal_exvivo
565    407   1837  3.012 1.038     0.110     0.024        4     0.6
entorhinal_exvivo
@#@FSTIME  2024:08:07:18:26:20 mris_anatomical_stats N 12 e 2.66 S 0.16 U 2.
49 P 99% M 477632 F 0 R 137191 W 0 c 16 w 1 I 0 O 24 L 10.39 10.29 10.40
@#@FSLOADPOST 2024:08:07:18:26:23 mris_anatomical_stats N 12 10.39 10.29 10.
40
mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a
./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0003 lh white
computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 252503
Total vertex volume 252258 (mask=0)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
810    475   1209  2.056 0.573     0.136     0.044        9     1.5
BA1_exvivo
2334   1578   2772  1.649 0.594     0.123     0.033       20     3.3
BA2_exvivo
1014    661    876  1.768 0.475     0.125     0.031        8     1.2
BA3a_exvivo
1615   1057   1577  1.455 0.403     0.079     0.015        6     1.1
BA3b_exvivo
2090   1333   2707  1.932 0.685     0.117     0.034       14     3.5
BA4a_exvivo
1377    902   1508  1.903 0.609     0.101     0.027        7     1.8
BA4p_exvivo
6948   4386  10734  2.311 0.799     0.119     0.034       61    10.1
BA6_exvivo
1238    782   2940  2.940 0.928     0.096     0.026        7     1.1
BA44_exvivo
1186    812   3178  2.533 0.929     0.132     0.041       15     2.0
BA45_exvivo
3483   2694   5373  1.949 0.751     0.137     0.041       34     6.4
V1_exvivo
4106   2975   7313  2.236 0.783     0.145     0.047       49     8.6
V2_exvivo
402    282    838  2.450 0.841     0.144     0.037        5     0.6
MT_exvivo
309    215    832  2.915 0.865     0.106     0.024        2     0.3
perirhinal_exvivo
374    262   1001  2.887 1.087     0.106     0.021        2     0.4
entorhinal_exvivo
@#@FSTIME  2024:08:07:18:26:23 mris_anatomical_stats N 12 e 2.68 S 0.13 U 2.
55 P 100% M 478144 F 0 R 141227 W 0 c 8 w 1 I 0 O 24 L 10.39 10.29 10.40
@#@FSLOADPOST 2024:08:07:18:26:25 mris_anatomical_stats N 12 10.76 10.37 10.
43
#--------------------------------------------
#@# BA_exvivo Labels rh 公曆 20廿四年 八月 七日 週三 十八時廿六分廿五秒
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA1_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3962 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 192
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4154
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:25 mri_label2label N 12 e 2.82 S 0.17 U 2.64 P
99% M 549540 F 0 R 163447 W 0 c 11 w 7 I 16160 O 264 L 10.76 10.37 10.43
@#@FSLOADPOST 2024:08:07:18:26:28 mri_label2label N 12 10.76 10.37 10.43
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA2_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6687 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 333
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7020
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:28 mri_label2label N 12 e 2.99 S 0.20 U 2.79 P
99% M 550148 F 0 R 163497 W 0 c 11 w 5 I 520 O 448 L 10.76 10.37 10.43
@#@FSLOADPOST 2024:08:07:18:26:31 mri_label2label N 12 10.70 10.36 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA3a_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3980 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 41
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4021
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:31 mri_label2label N 12 e 2.91 S 0.19 U 2.71 P
99% M 550052 F 0 R 163447 W 0 c 12 w 3 I 312 O 224 L 10.70 10.36 10.42
@#@FSLOADPOST 2024:08:07:18:26:34 mri_label2label N 12 10.70 10.36 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA3b_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4522 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 129
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4651
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:34 mri_label2label N 12 e 3.01 S 0.19 U 2.81 P
99% M 549816 F 0 R 163455 W 0 c 19 w 4 I 352 O 272 L 10.70 10.36 10.42
@#@FSLOADPOST 2024:08:07:18:26:37 mri_label2label N 12 10.64 10.35 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA4a_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5747 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 378
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6125
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:37 mri_label2label N 12 e 2.97 S 0.20 U 2.77 P
100% M 550116 F 0 R 163481 W 0 c 9 w 3 I 440 O 392 L 10.64 10.35 10.42
@#@FSLOADPOST 2024:08:07:18:26:40 mri_label2label N 12 10.75 10.38 10.43
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA4p_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4473 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 80
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4553
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:40 mri_label2label N 12 e 2.70 S 0.19 U 2.51 P
99% M 549868 F 0 R 163456 W 0 c 15 w 3 I 344 O 256 L 10.75 10.38 10.43
@#@FSLOADPOST 2024:08:07:18:26:43 mri_label2label N 12 10.75 10.38 10.43
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA6_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  12256 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 1956
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14212
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:43 mri_label2label N 12 e 3.08 S 0.17 U 2.90 P
100% M 550436 F 0 R 163607 W 0 c 13 w 5 I 936 O 1048 L 10.75 10.38 10.43
@#@FSLOADPOST 2024:08:07:18:26:46 mri_label2label N 12 10.61 10.36 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA44_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6912 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 879
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7791
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:46 mri_label2label N 12 e 2.89 S 0.17 U 2.71 P
100% M 549408 F 0 R 163503 W 0 c 18 w 4 I 528 O 528 L 10.61 10.36 10.42
@#@FSLOADPOST 2024:08:07:18:26:49 mri_label2label N 12 10.61 10.36 10.42
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.label
--trgsubject 0003 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA45_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5355 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 381
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 5736
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:49 mri_label2label N 12 e 2.96 S 0.20 U 2.75 P
99% M 549388 F 0 R 163476 W 0 c 14 w 9 I 416 O 376 L 10.61 10.36 10.42
@#@FSLOADPOST 2024:08:07:18:26:52 mri_label2label N 12 10.64 10.37 10.43
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.label
--trgsubject 0003 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.V1_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4727 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 947
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 5674
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:52 mri_label2label N 12 e 3.43 S 0.23 U 3.19 P
99% M 549580 F 0 R 163518 W 0 c 14 w 53 I 376 O 432 L 10.64 10.37 10.43
@#@FSLOADPOST 2024:08:07:18:26:55 mri_label2label N 12 11.07 10.46 10.46
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.label
--trgsubject 0003 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.V2_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8016 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 2181
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10197
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:55 mri_label2label N 12 e 2.82 S 0.18 U 2.63 P
100% M 549940 F 0 R 163535 W 0 c 10 w 5 I 640 O 800 L 11.07 10.46 10.46
@#@FSLOADPOST 2024:08:07:18:26:58 mri_label2label N 12 11.07 10.46 10.46
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.label
--trgsubject 0003 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod
surface
srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.MT_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1932 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 265
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2197
mri_label2label: Done
@#@FSTIME  2024:08:07:18:26:58 mri_label2label N 12 e 2.07 S 0.14 U 1.92 P
99% M 549312 F 0 R 163410 W 0 c 20 w 3 I 160 O 176 L 11.07 10.46 10.46
@#@FSLOADPOST 2024:08:07:18:27:00 mri_label2label N 12 10.91 10.44 10.45
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.label
--trgsubject 0003 --trglabel ./rh.entorhinal_exvivo.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.entorhinal_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1038 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1038 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1068
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:00 mri_label2label N 12 e 2.62 S 0.17 U 2.44 P
99% M 548704 F 0 R 163393 W 0 c 23 w 3 I 96 O 72 L 10.91 10.44 10.45
@#@FSLOADPOST 2024:08:07:18:27:03 mri_label2label N 12 10.91 10.44 10.45
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.label
--trgsubject 0003 --trglabel ./rh.perirhinal_exvivo.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.perirhinal_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  752 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 25
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 777
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:03 mri_label2label N 12 e 2.84 S 0.18 U 2.65 P
100% M 548988 F 0 R 164163 W 0 c 10 w 2 I 72 O 56 L 10.91 10.44 10.45
@#@FSLOADPOST 2024:08:07:18:27:06 mri_label2label N 12 10.99 10.47 10.46
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG1.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.FG1.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 541 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  541 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 122
Checking for and removing duplicates
Writing label file ./rh.FG1.mpm.vpnl.label 663
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:06 mri_label2label N 12 e 2.67 S 0.17 U 2.49 P
99% M 549292 F 0 R 163380 W 0 c 9 w 4 I 56 O 56 L 10.99 10.47 10.46
@#@FSLOADPOST 2024:08:07:18:27:08 mri_label2label N 12 10.99 10.47 10.46
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG2.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.FG2.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 721 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  721 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 237
Checking for and removing duplicates
Writing label file ./rh.FG2.mpm.vpnl.label 958
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:08 mri_label2label N 12 e 2.53 S 0.18 U 2.34 P
100% M 549176 F 0 R 163381 W 0 c 12 w 2 I 72 O 88 L 10.99 10.47 10.46
@#@FSLOADPOST 2024:08:07:18:27:11 mri_label2label N 12 11.07 10.49 10.47
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG3.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG3.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.FG3.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1523 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1523 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 69
Checking for and removing duplicates
Writing label file ./rh.FG3.mpm.vpnl.label 1592
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:11 mri_label2label N 12 e 2.69 S 0.17 U 2.52 P
99% M 549144 F 0 R 163401 W 0 c 16 w 2 I 144 O 104 L 11.07 10.49 10.47
@#@FSLOADPOST 2024:08:07:18:27:14 mri_label2label N 12 11.07 10.49 10.47
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG4.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG4.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.FG4.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1586 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1586 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 119
Checking for and removing duplicates
Writing label file ./rh.FG4.mpm.vpnl.label 1705
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:14 mri_label2label N 12 e 2.81 S 0.17 U 2.63 P
99% M 549452 F 0 R 164172 W 0 c 10 w 3 I 152 O 120 L 11.07 10.49 10.47
@#@FSLOADPOST 2024:08:07:18:27:16 mri_label2label N 12 11.15 10.52 10.47
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc1.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.hOc1.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3667 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3667 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 640
Checking for and removing duplicates
Writing label file ./rh.hOc1.mpm.vpnl.label 4307
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:16 mri_label2label N 12 e 3.06 S 0.22 U 2.84 P
100% M 550044 F 0 R 163447 W 0 c 13 w 4 I 328 O 328 L 11.15 10.52 10.47
@#@FSLOADPOST 2024:08:07:18:27:19 mri_label2label N 12 11.30 10.56 10.49
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc2.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.hOc2.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2719 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2719 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 794
Checking for and removing duplicates
Writing label file ./rh.hOc2.mpm.vpnl.label 3513
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:20 mri_label2label N 12 e 2.96 S 0.22 U 2.74 P
99% M 549684 F 0 R 163429 W 0 c 24 w 3 I 248 O 288 L 11.30 10.56 10.49
@#@FSLOADPOST 2024:08:07:18:27:22 mri_label2label N 12 11.30 10.56 10.49
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc3v.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc3v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.hOc3v.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1228 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1228 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 480
Checking for and removing duplicates
Writing label file ./rh.hOc3v.mpm.vpnl.label 1708
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:22 mri_label2label N 12 e 2.55 S 0.17 U 2.37 P
99% M 549340 F 0 R 163397 W 0 c 13 w 4 I 112 O 152 L 11.30 10.56 10.49
@#@FSLOADPOST 2024:08:07:18:27:25 mri_label2label N 12 11.43 10.60 10.50
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc4v.mpm.vpnl.label
--trgsubject 0003 --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod
surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc4v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.hOc4v.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1025 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1025 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 408
Checking for and removing duplicates
Writing label file ./rh.hOc4v.mpm.vpnl.label 1433
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:25 mri_label2label N 12 e 2.54 S 0.17 U 2.37 P
99% M 549696 F 0 R 163431 W 0 c 9 w 39 I 96 O 128 L 11.43 10.60 10.50
@#@FSLOADPOST 2024:08:07:18:27:28 mri_label2label N 12 11.43 10.60 10.50
mris_label2annot --s 0003 --ctab
/usr/local/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl
--maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l
rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label
--l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.
label --l rh.hOc4v.mpm.vpnl.label
Reading ctab /usr/local/freesurfer/average/colortable_vpnl.txt
Number of ctab entries 9
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/label
cmdline mris_label2annot --s 0003 --ctab
/usr/local/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl
--maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l
rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label
--l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.
label --l rh.hOc4v.mpm.vpnl.label
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
subject 0003
hemi    rh
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
ColorTable /usr/local/freesurfer/average/colortable_vpnl.txt
AnnotName  mpm.vpnl
nlables 8
LabelThresh 0 0.000000
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig
Index Offset 0
0 reading rh.FG1.mpm.vpnl.label
1 1376057 FG1
1 reading rh.FG2.mpm.vpnl.label
2 16711935 FG2
2 reading rh.FG3.mpm.vpnl.label
3 16711680 FG3
3 reading rh.FG4.mpm.vpnl.label
4 1705837 FG4
4 reading rh.hOc1.mpm.vpnl.label
5 25600 hOc1
5 reading rh.hOc2.mpm.vpnl.label
6 255 hOc2
6 reading rh.hOc3v.mpm.vpnl.label
7 16776960 hOc3v
7 reading rh.hOc4v.mpm.vpnl.label
8 65535 hOc4v
Mapping unhit to unknown
Found 118945 unhit vertices
Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/rh.mpm.vpnl.annot
@#@FSTIME  2024:08:07:18:27:28 mris_label2annot N 26 e 0.53 S 0.06 U 0.47 P
99% M 154132 F 0 R 41590 W 0 c 2 w 7 I 0 O 2080 L 11.43 10.60 10.50
@#@FSLOADPOST 2024:08:07:18:27:28 mris_label2annot N 26 11.43 10.60 10.50
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA1_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  876 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 50
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 926
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:28 mri_label2label N 12 e 2.62 S 0.17 U 2.44 P
99% M 549404 F 0 R 163388 W 0 c 13 w 3 I 80 O 64 L 11.43 10.60 10.50
@#@FSLOADPOST 2024:08:07:18:27:31 mri_label2label N 12 11.32 10.59 10.50
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA2_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2688 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 125
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2813
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:31 mri_label2label N 12 e 2.68 S 0.17 U 2.50 P
99% M 549752 F 0 R 164188 W 0 c 9 w 2 I 240 O 184 L 11.32 10.59 10.50
@#@FSLOADPOST 2024:08:07:18:27:33 mri_label2label N 12 11.32 10.59 10.50
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA3a_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1698 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 10
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1708
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:34 mri_label2label N 12 e 2.59 S 0.19 U 2.40 P
99% M 549216 F 0 R 164171 W 0 c 12 w 3 I 152 O 96 L 11.32 10.59 10.50
@#@FSLOADPOST 2024:08:07:18:27:36 mri_label2label N 12 11.05 10.55 10.48
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA3b_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2183 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 45
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2228
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:36 mri_label2label N 12 e 2.98 S 0.20 U 2.78 P
99% M 549736 F 0 R 164183 W 0 c 15 w 4 I 192 O 144 L 11.05 10.55 10.48
@#@FSLOADPOST 2024:08:07:18:27:39 mri_label2label N 12 11.05 10.55 10.48
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA4a_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1388 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 41
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1429
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:39 mri_label2label N 12 e 2.63 S 0.19 U 2.43 P
100% M 549436 F 0 R 163397 W 0 c 10 w 2 I 120 O 88 L 11.05 10.55 10.48
@#@FSLOADPOST 2024:08:07:18:27:42 mri_label2label N 12 11.29 10.60 10.50
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA4p_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1489 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 21
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1510
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:42 mri_label2label N 12 e 2.38 S 0.20 U 2.17 P
99% M 548692 F 0 R 163396 W 0 c 20 w 3 I 136 O 96 L 11.29 10.60 10.50
@#@FSLOADPOST 2024:08:07:18:27:44 mri_label2label N 12 11.29 10.60 10.50
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA6_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6959 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 1207
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8166
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:44 mri_label2label N 12 e 2.53 S 0.16 U 2.37 P
100% M 549484 F 0 R 163508 W 0 c 20 w 3 I 592 O 608 L 11.29 10.60 10.50
@#@FSLOADPOST 2024:08:07:18:27:47 mri_label2label N 12 10.94 10.54 10.48
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA44_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1012 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1099
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:47 mri_label2label N 12 e 2.67 S 0.21 U 2.46 P
99% M 548920 F 0 R 163393 W 0 c 13 w 3 I 88 O 80 L 10.94 10.54 10.48
@#@FSLOADPOST 2024:08:07:18:27:49 mri_label2label N 12 11.27 10.62 10.51
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.BA45_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1178 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 51
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1229
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:49 mri_label2label N 12 e 3.21 S 0.21 U 3.00 P
99% M 549328 F 0 R 163392 W 0 c 19 w 3 I 104 O 80 L 11.27 10.62 10.51
@#@FSLOADPOST 2024:08:07:18:27:53 mri_label2label N 12 11.27 10.62 10.51
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.V1_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3232 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 561
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 3793
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:53 mri_label2label N 12 e 2.63 S 0.20 U 2.43 P
99% M 550028 F 0 R 164208 W 0 c 10 w 4 I 280 O 288 L 11.27 10.62 10.51
@#@FSLOADPOST 2024:08:07:18:27:55 mri_label2label N 12 10.93 10.56 10.49
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.V2_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3437 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 944
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4381
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:55 mri_label2label N 12 e 2.93 S 0.19 U 2.72 P
99% M 550036 F 0 R 163444 W 0 c 10 w 4 I 296 O 352 L 10.93 10.56 10.49
@#@FSLOADPOST 2024:08:07:18:27:58 mri_label2label N 12 10.93 10.56 10.49
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.thresh.label
--trgsubject 0003 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh
--regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.MT_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  268 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 47
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 315
mri_label2label: Done
@#@FSTIME  2024:08:07:18:27:58 mri_label2label N 12 e 2.68 S 0.21 U 2.47 P
99% M 549432 F 0 R 163379 W 0 c 12 w 3 I 24 O 32 L 10.93 10.56 10.49
@#@FSLOADPOST 2024:08:07:18:28:01 mri_label2label N 12 10.85 10.55 10.49
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.thresh.la
bel --trgsubject 0003 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi
rh --regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.thresh.la
bel
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.entorhinal_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 694 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  694 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 24
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 718
mri_label2label: Done
@#@FSTIME  2024:08:07:18:28:01 mri_label2label N 12 e 2.37 S 0.16 U 2.20 P
99% M 549260 F 0 R 163428 W 0 c 19 w 42 I 64 O 48 L 10.85 10.55 10.49
@#@FSLOADPOST 2024:08:07:18:28:03 mri_label2label N 12 10.85 10.55 10.49
mri_label2label --srcsubject fsaverage --srclabel
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.thresh.la
bel --trgsubject 0003 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi
rh --regmethod surface
srclabel =
/home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.thresh.la
bel
srcsubject = fsaverage
trgsubject = 0003
trglabel = ./rh.perirhinal_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR    /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 291 points in source label.
Starting surface-based mapping
Reading source registration
/home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white
Reading target registration
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  291 nlabel points
Performing mapping from target back to the source label 132793
Number of reverse mapping hits = 11
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 302
mri_label2label: Done
@#@FSTIME  2024:08:07:18:28:03 mri_label2label N 12 e 2.75 S 0.18 U 2.57 P
99% M 548840 F 0 R 163373 W 0 c 13 w 3 I 32 O 24 L 10.85 10.55 10.49
@#@FSLOADPOST 2024:08:07:18:28:06 mri_label2label N 12 10.95 10.57 10.50
mris_label2annot --s 0003 --hemi rh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l
rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l
rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l
rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.
V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l
rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
Reading ctab /usr/local/freesurfer/average/colortable_BA.txt
Number of ctab entries 15
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/label
cmdline mris_label2annot --s 0003 --hemi rh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l
rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l
rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l
rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.
V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l
rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
subject 0003
hemi    rh
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
ColorTable /usr/local/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig
Index Offset 0
0 reading rh.BA1_exvivo.label
1 1530880 BA1_exvivo
1 reading rh.BA2_exvivo.label
2 16749699 BA2_exvivo
2 reading rh.BA3a_exvivo.label
3 16711680 BA3a_exvivo
3 reading rh.BA3b_exvivo.label
4 3368703 BA3b_exvivo
4 reading rh.BA4a_exvivo.label
5 1376196 BA4a_exvivo
5 reading rh.BA4p_exvivo.label
6 13382655 BA4p_exvivo
6 reading rh.BA6_exvivo.label
7 10036737 BA6_exvivo
7 reading rh.BA44_exvivo.label
8 2490521 BA44_exvivo
8 reading rh.BA45_exvivo.label
9 39283 BA45_exvivo
9 reading rh.V1_exvivo.label
10 3993 V1_exvivo
10 reading rh.V2_exvivo.label
11 8508928 V2_exvivo
11 reading rh.MT_exvivo.label
12 10027163 MT_exvivo
12 reading rh.perirhinal_exvivo.label
13 16422433 perirhinal_exvivo
13 reading rh.entorhinal_exvivo.label
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 89838 unhit vertices
Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/rh.BA_exvivo.annot
@#@FSTIME  2024:08:07:18:28:06 mris_label2annot N 38 e 0.46 S 0.04 U 0.41 P
99% M 154456 F 0 R 41813 W 0 c 6 w 3 I 0 O 2080 L 10.95 10.57 10.50
@#@FSLOADPOST 2024:08:07:18:28:07 mris_label2annot N 38 10.95 10.57 10.50
mris_label2annot --s 0003 --hemi rh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l
rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l
rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l
rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l
rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l
rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l
rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l
rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a
BA_exvivo.thresh --maxstatwinner --noverbose
Reading ctab /usr/local/freesurfer/average/colortable_BA.txt
Number of ctab entries 15
7.4.1
cwd /home/chang/GBM_Data/VBG/0003/0003/label
cmdline mris_label2annot --s 0003 --hemi rh --ctab
/usr/local/freesurfer/average/colortable_BA.txt --l
rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l
rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l
rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l
rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l
rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l
rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l
rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a
BA_exvivo.thresh --maxstatwinner --noverbose
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
subject 0003
hemi    rh
SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
ColorTable /usr/local/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig
Index Offset 0
0 reading rh.BA1_exvivo.thresh.label
1 1530880 BA1_exvivo
1 reading rh.BA2_exvivo.thresh.label
2 16749699 BA2_exvivo
2 reading rh.BA3a_exvivo.thresh.label
3 16711680 BA3a_exvivo
3 reading rh.BA3b_exvivo.thresh.label
4 3368703 BA3b_exvivo
4 reading rh.BA4a_exvivo.thresh.label
5 1376196 BA4a_exvivo
5 reading rh.BA4p_exvivo.thresh.label
6 13382655 BA4p_exvivo
6 reading rh.BA6_exvivo.thresh.label
7 10036737 BA6_exvivo
7 reading rh.BA44_exvivo.thresh.label
8 2490521 BA44_exvivo
8 reading rh.BA45_exvivo.thresh.label
9 39283 BA45_exvivo
9 reading rh.V1_exvivo.thresh.label
10 3993 V1_exvivo
10 reading rh.V2_exvivo.thresh.label
11 8508928 V2_exvivo
11 reading rh.MT_exvivo.thresh.label
12 10027163 MT_exvivo
12 reading rh.perirhinal_exvivo.thresh.label
13 16422433 perirhinal_exvivo
13 reading rh.entorhinal_exvivo.thresh.label
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 108567 unhit vertices
Writing annot to
/home/chang/GBM_Data/VBG/0003/0003/label/rh.BA_exvivo.thresh.annot
@#@FSTIME  2024:08:07:18:28:07 mris_label2annot N 38 e 0.40 S 0.05 U 0.35 P
99% M 154388 F 0 R 41734 W 0 c 4 w 4 I 0 O 2080 L 10.95 10.57 10.50
@#@FSLOADPOST 2024:08:07:18:28:07 mris_label2annot N 38 10.95 10.57 10.50
mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a
./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 0003 rh white
computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 244738
Total vertex volume 244461 (mask=0)
Saving annotation colortable ./BA_exvivo.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
922    537   1782  2.449 0.818     0.128     0.037       12     1.2
BA1_exvivo
3661   2323   3927  1.726 0.653     0.095     0.021       23     3.2
BA2_exvivo
1067    680    946  1.729 0.564     0.124     0.028        9     1.2
BA3a_exvivo
1984   1269   2738  1.741 0.851     0.089     0.019       10     1.6
BA3b_exvivo
1508    974   1961  1.835 0.622     0.095     0.022        9     1.4
BA4a_exvivo
1259    817   1376  1.765 0.596     0.098     0.025        8     1.5
BA4p_exvivo
10950   7049  17297  2.235 0.778     0.124     0.034       96    15.4
BA6_exvivo
4137   2744   6951  2.316 0.782     0.118     0.032       40     5.5
BA44_exvivo
3473   2372   7014  2.230 0.983     0.122     0.031       33     4.5
BA45_exvivo
3396   2572   6040  2.119 0.736     0.145     0.047      134     7.9
V1_exvivo
7835   5913  14311  2.114 0.759     0.152     0.050      101    17.2
V2_exvivo
1909   1327   4358  2.784 0.823     0.124     0.035       16     2.7
MT_exvivo
316    231   1346  3.389 0.927     0.156     0.048        4     0.6
perirhinal_exvivo
538    428   1988  2.989 0.936     0.129     0.030        4     0.7
entorhinal_exvivo
@#@FSTIME  2024:08:07:18:28:07 mris_anatomical_stats N 12 e 2.90 S 0.13 U 2.
76 P 100% M 466212 F 0 R 133723 W 0 c 10 w 1 I 0 O 24 L 10.95 10.57 10.50
@#@FSLOADPOST 2024:08:07:18:28:10 mris_anatomical_stats N 12 11.11 10.61 10.
51
mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a
./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0003 rh white
computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz...
reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
reading input pial surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial...
reading input white surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 244738
Total vertex volume 244461 (mask=0)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1531637 mm^3    (det: 1.271911 )
625    356   1220  2.488 0.860     0.131     0.040        9     1.0
BA1_exvivo
2095   1340   2433  1.798 0.719     0.097     0.022       14     2.1
BA2_exvivo
973    609    730  1.715 0.481     0.127     0.027        9     1.0
BA3a_exvivo
1579   1022   1511  1.413 0.420     0.074     0.013        6     0.8
BA3b_exvivo
1014    626   1406  2.024 0.633     0.103     0.024        6     0.9
BA4a_exvivo
1039    687   1019  1.615 0.493     0.088     0.022        5     1.1
BA4p_exvivo
7056   4436  11131  2.268 0.782     0.120     0.034       62     9.8
BA6_exvivo
895    630   1925  2.430 0.795     0.121     0.031       10     1.1
BA44_exvivo
878    630   2281  2.524 0.986     0.138     0.042       11     1.6
BA45_exvivo
3265   2474   5407  2.062 0.693     0.146     0.047      133     7.7
V1_exvivo
3979   3043   7904  2.200 0.831     0.157     0.053       50     9.9
V2_exvivo
271    195    871  2.914 0.945     0.150     0.051        4     0.5
MT_exvivo
28     18     94  3.434 0.640     0.118     0.017        0     0.0
perirhinal_exvivo
529    410   1852  3.032 0.860     0.140     0.036        5     0.8
entorhinal_exvivo
@#@FSTIME  2024:08:07:18:28:10 mris_anatomical_stats N 12 e 2.68 S 0.15 U 2.
52 P 99% M 466004 F 0 R 133723 W 0 c 25 w 1 I 0 O 24 L 11.11 10.61 10.51
@#@FSLOADPOST 2024:08:07:18:28:13 mris_anatomical_stats N 12 11.11 10.61 10.
51
Started at 公曆 20廿四年 八月 七日 週三 十六時二分48秒
Ended   at 公曆 20廿四年 八月 七日 週三 十八時廿八分十三秒
#@#%# recon-all-run-time-hours 2.424
recon-all -s 0003 finished without error at 公曆 20廿四年 八月 七日 週三 十
八時廿八分十三秒
#New# invocation of recon-all
公曆 20廿四年 八月 七日 週三 十八時廿八分十三秒
cd /home/chang/GBM_Data/VBG/0003/0003
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
/usr/local/freesurfer/bin/recon-all -subjid 0003 -sd
/home/chang/GBM_Data/VBG/0003 -T2
/home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz -T2pial
subjid 0003
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 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  1048576
memorylocked 16453580 kbytes
maxproc      513872
maxlocks     unlimited
maxsignal    513872
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited
total        used        free      shared  buff/cache
available
Mem:           125Gi        16Gi       3.0Gi       2.4Gi       106Gi
105Gi
Swap:          2.0Gi       2.0Gi       1.0Mi
########################################
program versions used
7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460)
7.4.1
ProgramName: lta_convert  ProgramArguments: lta_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_compute_seg_overlap  ProgramArguments:
mri_compute_seg_overlap -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fuse_segmentations  ProgramArguments:
mri_fuse_segmentations -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion:
7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
chang  Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_relabel_hypointensities  ProgramArguments:
mri_relabel_hypointensities -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments:
mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_register  ProgramArguments: mri_robust_register
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_template  ProgramArguments: mri_robust_template
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_divide_parcellation  ProgramArguments:
mris_divide_parcellation -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_left_right_register  ProgramArguments:
mris_left_right_register -all-info  ProgramVersion: 7.4.1  TimeStamp:
2024/08/07-10:28:13-GMT  BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_register  ProgramArguments: mris_register -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT
BuildTime: Jun 14 2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
mri_motion_correct.fsl 7.4.1
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info
ProgramVersion: 7.4.1  TimeStamp: 2024/08/07-10:28:13-GMT  BuildTime: Jun 14
2023 03:45:01  BuildStamp:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: chang
Machine: chang-System-Product-Name  Platform: Linux  PlatformVersion:
6.5.0-44-generic  CompilerName: GCC  CompilerVersion: 8.4.0
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /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
#######################################
#--------------------------------------------
#@# T2/FLAIR Input 公曆 20廿四年 八月 七日 週三 十八時廿八分十三秒
/home/chang/GBM_Data/VBG/0003/0003
mri_convert --no_scale 1
/home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
mri_convert --no_scale 1
/home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
reading from /home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz...
@#@FSTIME  2024:08:07:18:28:13 mri_convert N 4 e 0.35 S 0.02 U 0.32 P 99% M
42240 F 0 R 9168 W 0 c 5 w 4 I 11280 O 10744 L 11.11 10.61 10.51
@#@FSLOADPOST 2024:08:07:18:28:13 mri_convert N 4 11.11 10.61 10.51
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR 公曆 20廿四年 八月 七日 週三 十八時廿八分
十三秒
bbregister --s 0003 --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.
mgz --lta /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta
--init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask
tmp /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180
Log file is /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.log
公曆 20廿四年 八月 七日 週三 十八時廿八分十三秒
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/scripts
/usr/local/freesurfer/bin/bbregister --s 0003 --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz --lta
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta
--init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask
bbregister 7.4.1
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii
mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii
reading from /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.
688180/template.nii...
mri_coreg --s 0003 --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii --regdat
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
init.dat --reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/mri_
coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01
--no-ref-mask
$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd /home/chang/GBM_Data/VBG/0003/0003/scripts
cmdline mri_coreg --s 0003 --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii --regdat
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
init.dat --reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/mri_
coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01
--no-ref-mask
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
dof    6
nsep    1
cras0    1
ftol    0.000100
linmintol    0.010000
bf       1
bflim    30.000000
bfnsamp    30
SmoothRef 0
SatPct    99.990000
MovOOB 0
optschema 1
Seed 53
Reading in mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii
Reading in ref /home/chang/GBM_Data/VBG/0003/0003/mri/brainmask.mgz
Setting cras translation parameters to align volume centers
Init matrix params  0.0000  1.0000 -1.0000  0.0000  0.0000  0.0000  1.0000
1.0000  1.0000  0.0000  0.0000  0.0000
Initial Matrix (RAS2RAS)
1.00000   0.00000   0.00000   0.00000;
0.00000   1.00000   0.00000  -1.00000;
0.00000   0.00000   1.00000   1.00000;
0.00000   0.00000   0.00000   1.00000;
Initial parameters to be opt  0.0000  1.0000 -1.0000  0.0000  0.0000  0.0000
Creating random numbers for coordinate dithering
Performing intensity dithering
Performing intensity dithering on mov with computed dither
Separation list (1):  4   min = 4
DoSmoothing 1
DoCoordDither 1
DoIntensityDither 1
nitersmax 4
ftol 1.000e-04
linmintol 1.000e-02
SatPct 99.990000
Hist FWHM 7.000000 7.000000
nthreads 1
movsat = 5.4220
mov gstd 1.8914 1.8914 1.8914
Smoothing mov
refsat = 123.0000
ref gstd 1.8914 1.8914 1.8914
Smoothing ref
COREGpreproc() done
Testing if mov and target overlap
Init cost   -1.0833937660
nhits = 137431 out of 16777216, Percent Overlap:  52.4
Initial  RefRAS-to-MovRAS
1.00000   0.00000   0.00000   0.00000;
0.00000   1.00000   0.00000   1.00000;
0.00000   0.00000   1.00000  -1.00000;
0.00000   0.00000   0.00000   1.00000;
Initial  RefVox-to-MovVox
1.00000   0.00000   0.00000  -8.00000;
0.00000   0.00000  -1.00000   247.00000;
0.00000  -1.00000   0.00000   204.50000;
0.00000   0.00000   0.00000   1.00000;
sep = 4 -----------------------------------
COREGoptBruteForce() 30 1 30
Turning on MovOOB for BruteForce Search
#BF# sep= 4 iter=0 lim=30.0 delta=2.00   0.00000   1.00000   1.00000
0.00000   0.00000   0.00000   -1.0597895
Turning  MovOOB back off after brute force search
---------------------------------
Init Powel Params dof = 6: 0.000000 1.000000 1.000000 0.000000 0.000000
0.000000
Starting OpenPowel2(), sep = 4
InitialCost        -1.0834896564
#@#  4  188  0.00000 1.00000 1.00000 0.00000 0.00000 0.00000   -1.0834897
fs_powell::minimize
nparams 6
maxfev 4
ftol   0.000100
linmin_xtol_   0.010000
powell nthiter 0: fret = -1.083490
#@#  4  194  0.38197 1.00000 1.00000 0.00000 0.00000 0.00000   -1.0836478
#@#  4  203  0.36268 0.38197 1.00000 0.00000 0.00000 0.00000   -1.0837729
#@#  4  205  0.36268 0.57609 1.00000 0.00000 0.00000 0.00000   -1.0838054
#@#  4  206  0.36268 0.56609 1.00000 0.00000 0.00000 0.00000   -1.0838056
#@#  4  207  0.36268 0.55609 1.00000 0.00000 0.00000 0.00000   -1.0838066
#@#  4  210  0.36268 0.52068 1.00000 0.00000 0.00000 0.00000   -1.0838077
#@#  4  214  0.36268 0.52068 -0.61803 0.00000 0.00000 0.00000   -1.0846199
#@#  4  215  0.36268 0.52068 -0.09597 0.00000 0.00000 0.00000   -1.0850186
#@#  4  219  0.36268 0.52068 -0.03848 0.00000 0.00000 0.00000   -1.0850224
#@#  4  220  0.36268 0.52068 -0.04848 0.00000 0.00000 0.00000   -1.0850245
#@#  4  237  0.36268 0.52068 -0.04848 0.00000 0.01488 0.00000   -1.0850266
powell nthiter 1: fret = -1.085027
#@#  4  254  0.37268 0.52068 -0.04848 0.00000 0.01488 0.00000   -1.0850269
#@#  4  262  0.37268 0.44233 -0.04848 0.00000 0.01488 0.00000   -1.0850277
#@#  4  263  0.37268 0.47741 -0.04848 0.00000 0.01488 0.00000   -1.0850282
#@#  4  264  0.37268 0.46741 -0.04848 0.00000 0.01488 0.00000   -1.0850288
#@#  4  272  0.37268 0.46741 -0.07814 0.00000 0.01488 0.00000   -1.0850306
#@#  4  289  0.37268 0.46741 -0.07814 0.00000 0.02488 0.00000   -1.0850319
#@#  4  298  0.37268 0.46741 -0.07814 0.00000 0.02488 0.01787   -1.0850326
Powell done niters total = 1
OptTimeSec  6.4 sec
OptTimeMin  0.11 min
nEvals 300
Final optimized parameters   0.37268403   0.46741304  -0.07813513
0.00000000   0.02487876   0.01787130
Final matrix parameters  0.3727  0.4674 -0.0781  0.0000  0.0249  0.0279
1.0000  1.0000  1.0000  0.0000  0.0000  0.0000
Final cost   -1.085032561910817
---------------------------------
Final  RefRAS-to-MovRAS
1.00000   0.00031   0.00043   0.37268;
-0.00031   1.00000   0.00000   0.46741;
-0.00043  -0.00000   1.00000  -0.07814;
0.00000   0.00000   0.00000   1.00000;
Final  RefVox-to-MovVox
1.00000   0.00043  -0.00031  -8.45911;
-0.00031   0.00000  -1.00000   247.53508;
0.00043  -1.00000  -0.00000   205.41837;
0.00000   0.00000   0.00000   1.00000;
Final matrix parameters  0.3727  0.4674 -0.0781  0.0000  0.0249  0.0179
0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
Final opt parameters  0.3727  0.4674 -0.0781  0.0000  0.0249  0.0179
nhits = 137429 out of 16777216, Percent Overlap:  52.4
mri_coreg RunTimeSec 38.5 sec
To check run:
tkregisterfv --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.
bbregister.688180/template.nii --targ
/home/chang/GBM_Data/VBG/0003/0003/mri/brainmask.mgz --reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/mri_
coreg.lta --s 0003 --surfs
mri_coreg done
mri_segreg --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii --init-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
init.dat --out-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr.
pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute
-4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5
7.4.1
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/scripts
mri_segreg --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii --init-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
init.dat --out-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr.
pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute
-4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
movvol
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii
regfile
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
init.dat
subject 0003
dof 6
outregfile /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.
688180/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjAbs 2.000000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1723607109
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
1.00000   0.00031   0.00043   0.44350;
-0.00043  -0.00000   1.00000  -0.02605;
-0.00031   1.00000  -0.00000   0.50484;
0.00000   0.00000   0.00000   1.00000;
Loading mov
ExcludeZeroVoxels 1
Reading in targ vol /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
Projecting LH Surfs
Loading lh.white surf
GM Proj: 0 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0  -25.0 -25.0 -25.0   0.946830
1  -25.0 -25.0  25.0   0.954694
2  -25.0  25.0 -25.0   1.000999
3  -25.0  25.0  25.0   0.982965
4   25.0 -25.0 -25.0   0.948758
5   25.0 -25.0  25.0   0.962045
6   25.0  25.0 -25.0   0.974763
7   25.0  25.0  25.0   0.974663
REL:  8  1.159603    7.745715  0.968214 rel = 1.19767
Initial costs ----------------
Number of surface hits 2512
WM  Intensity    -0.4722 +/-   0.6719
Ctx Intensity     0.1936 +/-   1.1155
Pct Contrast  -2293.4429 +/- 111257.5584
Cost   1.1596
RelCost   1.1977
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1
------------------------------------
Brute force preopt -4 4 4, n = 729
0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9548
0.9548  0.0
1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9240
0.9240  0.0
19  -4.0000  -4.0000  -4.0000   4.0000  -4.0000   0.0000      0.9239
0.9239  0.0
219  -4.0000   4.0000   4.0000  -4.0000   0.0000  -4.0000      0.9056
0.9056  0.0
Brute Force --------------------------
Min cost was 0.905642
Number of iterations   729
Search time 0.670579 sec
Parameters at best (transmm, rotdeg)
-4.000   4.000   4.000 -4.000  0.000 -4.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 -4
1 4
2 4
3 -4
4 0
5 -4
fs_powell::minimize
nparams 6
maxfev 36
ftol   0.000100
linmin_xtol_   0.001000
powell nthiter 0: fret = 0.905642
5 -4.618  4.000  4.000 -4.000  0.000 -4.000   0.9008647402
9 -4.531  4.000  4.000 -4.000  0.000 -4.000   0.8996386370
10 -4.520  4.000  4.000 -4.000  0.000 -4.000   0.8986073976
11 -4.470  4.000  4.000 -4.000  0.000 -4.000   0.8979427876
14 -4.458  4.000  4.000 -4.000  0.000 -4.000   0.8975149420
16 -4.460  4.000  4.000 -4.000  0.000 -4.000   0.8974104720
17 -4.464  4.000  4.000 -4.000  0.000 -4.000   0.8972284763
27 -4.464  3.948  4.000 -4.000  0.000 -4.000   0.8947837774
30 -4.464  3.944  4.000 -4.000  0.000 -4.000   0.8942695936
32 -4.464  3.930  4.000 -4.000  0.000 -4.000   0.8937001881
44 -4.464  3.930  4.027 -4.000  0.000 -4.000   0.8921445828
50 -4.464  3.930  4.026 -4.000  0.000 -4.000   0.8921406036
51 -4.464  3.930  4.025 -4.000  0.000 -4.000   0.8921390140
65 -4.464  3.930  4.025 -3.998  0.000 -4.000   0.8913596165
77 -4.464  3.930  4.025 -3.998  0.024 -4.000   0.8897987625
79 -4.464  3.930  4.025 -3.998  0.014 -4.000   0.8897798886
81 -4.464  3.930  4.025 -3.998  0.019 -4.000   0.8889510638
83 -4.464  3.930  4.025 -3.998  0.018 -4.000   0.8889485991
97 -4.464  3.930  4.025 -3.998  0.018 -4.003   0.8882235387
99 -4.464  3.930  4.025 -3.998  0.018 -4.002   0.8881980743
100 -4.464  3.930  4.025 -3.998  0.018 -4.001   0.8881790630
powell nthiter 1: fret = 0.888179
115 -4.463  3.930  4.025 -3.998  0.018 -4.001   0.8881564397
116 -4.462  3.930  4.025 -3.998  0.018 -4.001   0.8881510722
125 -4.462  3.931  4.025 -3.998  0.018 -4.001   0.8881343315
128 -4.462  3.932  4.025 -3.998  0.018 -4.001   0.8881201325
130 -4.462  3.934  4.025 -3.998  0.018 -4.001   0.8881012733
144 -4.462  3.934  4.024 -3.998  0.018 -4.001   0.8880386506
145 -4.462  3.934  4.023 -3.998  0.018 -4.001   0.8880083385
176 -4.462  3.934  4.023 -3.998  0.019 -4.001   0.8880010057
powell nthiter 2: fret = 0.888001
209 -4.461  3.934  4.023 -3.998  0.019 -4.001   0.8879996501
269 -4.461  3.934  4.023 -3.998  0.020 -4.001   0.8879948325
Powell done niters = 2
Computing relative cost
0  -25.0 -25.0 -25.0   1.024492
1  -25.0 -25.0  25.0   1.002858
2  -25.0  25.0 -25.0   0.972662
3  -25.0  25.0  25.0   0.951033
4   25.0 -25.0 -25.0   0.930944
5   25.0 -25.0  25.0   0.959659
6   25.0  25.0 -25.0   0.986401
7   25.0  25.0  25.0   0.958929
REL:  8  0.887995    7.786979  0.973372 rel = 0.912287
Number of iterations     2
Min cost was 0.887995
Number of FunctionCalls   288
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.199039 sec
Parameters at optimum (transmm) -4.46100  3.93356  4.02320
Parameters at optimum (rotdeg) -3.99810  0.01986 -4.00143
Final costs ----------------
Number of surface hits 2512
WM  Intensity    -0.1788 +/-   1.1407
Ctx Intensity    -0.2031 +/-   1.4149
Pct Contrast    454.6450 +/- 12168.3811
Cost   0.8880
RelCost   1.1977
Reg at min cost was
0.99753   0.00552   0.07002  -4.01776;
-0.07024   0.06951   0.99511   3.91180;
-0.00063   0.99757  -0.06972   4.52847;
0.00000   0.00000   0.00000   1.00000;
Writing optimal reg to
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr.
pass1.dat, type = 14
Original Reg
1.00000   0.00031   0.00043   0.44350;
-0.00043  -0.00000   1.00000  -0.02605;
-0.00031   1.00000  -0.00000   0.50484;
0.00000   0.00000   0.00000   1.00000;
Original Reg - Optimal Reg
0.00247  -0.00521  -0.06959   4.46126;
0.06980  -0.06951   0.00489  -3.93784;
0.00032   0.00243   0.06972  -4.02364;
0.00000   0.00000   0.00000   0.00000;
Computing change in lh position
LH rmsDiffMean 7.325218
Computing change in rh position
Surface-RMS-Diff-mm 6.808459 2.496179 12.116522
WARNING: initial G-W contrast was negative, but expected positive.
If the mov data has a T1 contrast, re-run with --T1
mri_segreg done
mri_segreg --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii --init-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr.
pass1.dat --out-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.
auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0
--mincost
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.mincost
--dof 6 --nmax 36 --param
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.param
--surf white --brute -0.1 0.1 0.1 --cur-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5
7.4.1
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
cd /home/chang/GBM_Data/VBG/0003/0003/scripts
mri_segreg --mov
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii --init-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr.
pass1.dat --out-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.
auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0
--mincost
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.mincost
--dof 6 --nmax 36 --param
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.param
--surf white --brute -0.1 0.1 0.1 --cur-reg
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg.
curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5
sysname  Linux
hostname chang-System-Product-Name
machine  x86_64
user     chang
movvol
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp
late.nii
regfile
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr.
pass1.dat
subject 0003
dof 6
outregfile /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjAbs 2.000000
WMProjAbs 1.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1723645545
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
0.99753   0.00552   0.07002  -4.01776;
-0.07024   0.06951   0.99511   3.91180;
-0.00063   0.99757  -0.06972   4.52847;
0.00000   0.00000   0.00000   1.00000;
Loading mov
ExcludeZeroVoxels 1
Reading in targ vol /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
Projecting LH Surfs
Loading lh.white surf
GM Proj: 0 0.500000 2.000000
WM Proj: 0 0.500000 1.000000
Projecting RH Surfs
Loading rh.white surf
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0  -25.0 -25.0 -25.0   0.983531
1  -25.0 -25.0  25.0   0.974198
2  -25.0  25.0 -25.0   0.986685
3  -25.0  25.0  25.0   0.979991
4   25.0 -25.0 -25.0   0.962851
5   25.0 -25.0  25.0   0.974900
6   25.0  25.0 -25.0   0.965208
7   25.0  25.0  25.0   0.957650
REL:  8  0.948762    7.785015  0.973127 rel = 0.974962
Initial costs ----------------
Number of surface hits 251486
WM  Intensity    -0.1886 +/-   1.1889
Ctx Intensity    -0.1968 +/-   1.3948
Pct Contrast    -67.6954 +/- 34550.7112
Cost   0.9488
RelCost   0.9750
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1
------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.9286
0.9286  0.0
5  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.1000      0.9240
0.9240  0.0
7  -0.1000  -0.1000  -0.1000  -0.1000   0.1000   0.0000      0.9206
0.9206  0.0
8  -0.1000  -0.1000  -0.1000  -0.1000   0.1000   0.1000      0.9133
0.9133  0.0
179  -0.1000   0.1000  -0.1000   0.0000   0.1000   0.1000      0.9120
0.9120  0.0
522   0.1000  -0.1000   0.0000   0.0000  -0.1000  -0.1000      0.9108
0.9108  0.0
650   0.1000   0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.9094
0.9094  0.0
653   0.1000   0.1000  -0.1000  -0.1000   0.0000   0.1000      0.9078
0.9078  0.0
661   0.1000   0.1000  -0.1000   0.0000   0.0000   0.0000      0.9067
0.9067  0.0
Brute Force --------------------------
Min cost was 0.906707
Number of iterations   729
Search time 0.510323 sec
Parameters at best (transmm, rotdeg)
0.100   0.100  -0.100  0.000  0.000  0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0.1
1 0.1
2 -0.1
3 0
4 0
5 0
fs_powell::minimize
nparams 6
maxfev 36
ftol   0.000000
linmin_xtol_   0.001000
powell nthiter 0: fret = 0.947728
3 -1.518  0.100 -0.100  0.000  0.000  0.000   0.9460698791
4 -0.893  0.100 -0.100  0.000  0.000  0.000   0.9447947841
6 -0.513  0.100 -0.100  0.000  0.000  0.000   0.9442331843
8 -0.590  0.100 -0.100  0.000  0.000  0.000   0.9439347554
16 -0.591  0.100 -0.100  0.000  0.000  0.000   0.9439090088
21 -0.591 -0.518 -0.100  0.000  0.000  0.000   0.9417197037
23 -0.591 -0.656 -0.100  0.000  0.000  0.000   0.9412219890
25 -0.591 -0.620 -0.100  0.000  0.000  0.000   0.9409964324
27 -0.591 -0.609 -0.100  0.000  0.000  0.000   0.9409446009
28 -0.591 -0.604 -0.100  0.000  0.000  0.000   0.9409383707
29 -0.591 -0.603 -0.100  0.000  0.000  0.000   0.9409307576
35 -0.591 -0.603 -1.718  0.000  0.000  0.000   0.9396632458
36 -0.591 -0.603 -1.011  0.000  0.000  0.000   0.9387022732
40 -0.591 -0.603 -0.994  0.000  0.000  0.000   0.9386344290
42 -0.591 -0.603 -0.957  0.000  0.000  0.000   0.9384991811
46 -0.591 -0.603 -0.959  0.000  0.000  0.000   0.9384968334
51 -0.591 -0.603 -0.959  1.000  0.000  0.000   0.9384050540
55 -0.591 -0.603 -0.959  0.618  0.000  0.000   0.9371076029
56 -0.591 -0.603 -0.959  0.382  0.000  0.000   0.9366999652
58 -0.591 -0.603 -0.959  0.383  0.000  0.000   0.9366292947
59 -0.591 -0.603 -0.959  0.473  0.000  0.000   0.9363311256
60 -0.591 -0.603 -0.959  0.430  0.000  0.000   0.9359123331
69 -0.591 -0.603 -0.959  0.430 -1.618  0.000   0.9111724936
76 -0.591 -0.603 -0.959  0.430 -2.539  0.000   0.9110926218
77 -0.591 -0.603 -0.959  0.430 -2.084  0.000   0.9105675952
78 -0.591 -0.603 -0.959  0.430 -2.095  0.000   0.9102657296
79 -0.591 -0.603 -0.959  0.430 -2.303  0.000   0.9102144494
80 -0.591 -0.603 -0.959  0.430 -2.393  0.000   0.9100245463
95 -0.591 -0.603 -0.959  0.430 -2.393  0.382   0.9079651798
97 -0.591 -0.603 -0.959  0.430 -2.393  0.409   0.9076807175
100 -0.591 -0.603 -0.959  0.430 -2.393  0.408   0.9076615681
101 -0.591 -0.603 -0.959  0.430 -2.393  0.398   0.9076461921
102 -0.591 -0.603 -0.959  0.430 -2.393  0.403   0.9076148761
103 -0.591 -0.603 -0.959  0.430 -2.393  0.402   0.9075915850
powell nthiter 1: fret = 0.907592
110 -1.209 -0.603 -0.959  0.430 -2.393  0.402   0.9074654142
112 -0.911 -0.603 -0.959  0.430 -2.393  0.402   0.9065864692
114 -1.050 -0.603 -0.959  0.430 -2.393  0.402   0.9063212523
116 -0.984 -0.603 -0.959  0.430 -2.393  0.402   0.9060953652
119 -0.975 -0.603 -0.959  0.430 -2.393  0.402   0.9060028945
120 -0.968 -0.603 -0.959  0.430 -2.393  0.402   0.9059992454
121 -0.971 -0.603 -0.959  0.430 -2.393  0.402   0.9059158367
122 -0.972 -0.603 -0.959  0.430 -2.393  0.402   0.9058846384
141 -0.972 -0.603 -1.577  0.430 -2.393  0.402   0.9039833344
143 -0.972 -0.603 -1.464  0.430 -2.393  0.402   0.9030349066
146 -0.972 -0.603 -1.494  0.430 -2.393  0.402   0.9027854120
152 -0.972 -0.603 -1.496  0.430 -2.393  0.402   0.9027495003
159 -0.972 -0.603 -1.496  0.812 -2.393  0.402   0.9016582789
161 -0.972 -0.603 -1.496  0.758 -2.393  0.402   0.9014010803
173 -0.972 -0.603 -1.496  0.758 -2.011  0.402   0.8998767388
175 -0.972 -0.603 -1.496  0.758 -2.135  0.402   0.8992842416
182 -0.972 -0.603 -1.496  0.758 -2.138  0.402   0.8992707754
191 -0.972 -0.603 -1.496  0.758 -2.138  0.300   0.8992569276
198 -0.972 -0.603 -1.496  0.758 -2.138  0.307   0.8991871153
199 -0.972 -0.603 -1.496  0.758 -2.138  0.311   0.8991616128
201 -0.972 -0.603 -1.496  0.758 -2.138  0.310   0.8991570772
202 -0.972 -0.603 -1.496  0.758 -2.138  0.309   0.8991434627
203 -1.353 -0.603 -2.032  1.085 -1.882  0.216   0.8979631489
powell nthiter 2: fret = 0.899143
227 -0.972 -0.818 -1.496  0.758 -2.138  0.309   0.8978256453
230 -0.972 -0.840 -1.496  0.758 -2.138  0.309   0.8978216686
231 -0.972 -0.829 -1.496  0.758 -2.138  0.309   0.8977918190
232 -0.972 -0.828 -1.496  0.758 -2.138  0.309   0.8977238065
245 -0.972 -0.828 -1.520  0.758 -2.138  0.309   0.8976367220
246 -0.972 -0.828 -1.516  0.758 -2.138  0.309   0.8976278778
247 -0.972 -0.828 -1.514  0.758 -2.138  0.309   0.8975725038
257 -0.972 -0.828 -1.514  0.878 -2.138  0.309   0.8973890101
262 -0.972 -0.828 -1.514  0.871 -2.138  0.309   0.8973410539
263 -0.972 -0.828 -1.514  0.872 -2.138  0.309   0.8973315240
264 -0.972 -0.828 -1.514  0.873 -2.138  0.309   0.8973196642
273 -0.972 -0.828 -1.514  0.873 -2.147  0.309   0.8971610146
274 -0.972 -0.828 -1.514  0.873 -2.157  0.309   0.8971265106
278 -0.972 -0.828 -1.514  0.873 -2.158  0.309   0.8971046587
287 -0.972 -0.828 -1.514  0.873 -2.158  0.319   0.8970466233
289 -0.972 -0.828 -1.514  0.873 -2.158  0.333   0.8970100905
290 -0.972 -0.828 -1.514  0.873 -2.158  0.334   0.8969714709
300 -0.972 -0.914 -1.521  0.917 -2.166  0.344   0.8963434071
302 -0.972 -0.903 -1.520  0.911 -2.165  0.343   0.8962190385
304 -0.972 -0.903 -1.520  0.912 -2.165  0.343   0.8961852573
305 -0.972 -0.908 -1.520  0.914 -2.165  0.343   0.8961830673
307 -0.972 -0.906 -1.520  0.913 -2.165  0.343   0.8961730429
310 -0.972 -0.906 -1.520  0.913 -2.165  0.343   0.8961720930
powell nthiter 3: fret = 0.896172
337 -0.972 -0.906 -1.520  0.913 -2.165  0.346   0.8961067251
383 -0.972 -0.906 -1.520  0.913 -2.164  0.346   0.8960750602
powell nthiter 4: fret = 0.896075
Powell done niters = 4
Computing relative cost
0  -25.0 -25.0 -25.0   0.975964
1  -25.0 -25.0  25.0   0.967428
2  -25.0  25.0 -25.0   0.981661
3  -25.0  25.0  25.0   0.990489
4   25.0 -25.0 -25.0   0.953759
5   25.0 -25.0  25.0   0.968768
6   25.0  25.0 -25.0   0.976922
7   25.0  25.0  25.0   0.968822
REL:  8  0.896075    7.783812  0.972977 rel = 0.920963
Number of iterations     4
Min cost was 0.896075
Number of FunctionCalls   483
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 13.680996 sec
Parameters at optimum (transmm) -0.97176 -0.90599 -1.52009
Parameters at optimum (rotdeg)  0.91314 -2.16414  0.34635
Final costs ----------------
Number of surface hits 251486
WM  Intensity    -0.2146 +/-   1.0957
Ctx Intensity    -0.1295 +/-   1.4043
Pct Contrast    110.8027 +/- 25392.8264
Cost   0.8961
RelCost   0.9750
Reg at min cost was
0.99729  -0.03251   0.06598  -5.18313;
-0.06419   0.05341   0.99651   2.90775;
0.03592   0.99804  -0.05117   2.91515;
0.00000   0.00000   0.00000   1.00000;
Writing optimal reg to
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat, type = 14
Original Reg
0.99753   0.00552   0.07002  -4.01776;
-0.07024   0.06951   0.99511   3.91180;
-0.00063   0.99757  -0.06972   4.52847;
0.00000   0.00000   0.00000   1.00000;
Original Reg - Optimal Reg
0.00024   0.03803   0.00404   1.16536;
-0.00605   0.01610  -0.00140   1.00404;
-0.03655  -0.00048  -0.01855   1.61332;
0.00000   0.00000   0.00000   0.00000;
Computing change in lh position
LH rmsDiffMean 3.004314
Computing change in rh position
Surface-RMS-Diff-mm 2.334677 1.059853 4.406749
WARNING: initial G-W contrast was negative, but expected positive.
If the mov data has a T1 contrast, re-run with --T1
mri_segreg done
MinCost: 0.896075 -0.214632 -0.129454 110.802654
tkregister2_cmdl --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
--reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat
--noedit --ltaout
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
reg file       /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.
dat
LoadVol        0
ZeroCRAS       0
7.4.1
Diagnostic Level -1
---- Input registration matrix --------
0.99729  -0.03251   0.06598  -5.18313;
-0.06419   0.05341   0.99651   2.90775;
0.03592   0.99804  -0.05117   2.91515;
0.00000   0.00000   0.00000   1.00000;
float2int = 0
---------------------------------------
INFO: loading target /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
Ttarg: --------------------
-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;
INFO: loading movable /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
Tmov: --------------------
-1.00000   0.00000   0.00000   120.00000;
0.00000   0.00000   1.00000  -77.50000;
0.00000  -1.00000   0.00000   120.00000;
0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
0.99729  -0.03251   0.06598  -5.18313;
-0.06419   0.05341   0.99651   2.90775;
0.03592   0.99804  -0.05117   2.91515;
0.00000   0.00000   0.00000   1.00000;
Determinant -1
subject = 0003
RegMat ---------------------------
0.99729  -0.03251   0.06598  -5.18313;
-0.06419   0.05341   0.99651   2.90775;
0.03592   0.99804  -0.05117   2.91515;
0.00000   0.00000   0.00000   1.00000;
Cleaning up
Started at 公曆 20廿四年 八月 七日 週三 十八時廿八分十三秒
Ended   at 公曆 20廿四年 八月 七日 週三 十八時廿九分十二秒
BBR-Run-Time-Sec 59
bbregister Done
To check results, run:
tkregisterfv --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
--reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta
--surfs  --sd /home/chang/GBM_Data/VBG/0003
@#@FSTIME  2024:08:07:18:28:13 bbregister N 13 e 59.04 S 1.71 U 57.30 P 99%
M 706656 F 12 R 2218542 W 0 c 213 w 1068 I 1536 O 70784 L 11.11 10.61 10.51
@#@FSLOADPOST 2024:08:07:18:29:12 bbregister N 13 10.89 10.65 10.53
cp /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta
@#@FSTIME  2024:08:07:18:29:12 cp N 2 e 0.00 S 0.00 U 0.00 P 100% M 2304 F 0
R 189 W 0 c 0 w 1 I 0 O 8 L 10.89 10.65 10.53
@#@FSLOADPOST 2024:08:07:18:29:12 cp N 2 10.89 10.65 10.53
mri_convert -odt float -at
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta -rl
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz
reading from /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
INFO: Reading transformation from file
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading template info from volume
/home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz...
INFO: Applying transformation from file
/home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
0.99729   0.03592  -0.06419   5.62565;
-0.03251   0.99804   0.05341  -11.04095;
0.06598  -0.05117   0.99651   11.87163;
0.00000   0.00000   0.00000   1.00000;
---------------------------------
Applying LTAtransformInterp (resample_type 1)
writing to /home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz...
@#@FSTIME  2024:08:07:18:29:12 mri_convert N 8 e 1.08 S 0.02 U 1.06 P 99% M
108032 F 0 R 25681 W 0 c 12 w 1 I 0 O 11560 L 10.89 10.65 10.53
@#@FSLOADPOST 2024:08:07:18:29:14 mri_convert N 8 10.89 10.65 10.53
mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg
/home/chang/GBM_Data/VBG/0003/0003/mri/aseg.presurf.mgz -surface
/home/chang/GBM_Data/VBG/0003/0003/surf/lh.white identity.nofile -surface
/home/chang/GBM_Data/VBG/0003/0003/surf/rh.white identity.nofile
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.norm.mgz
setting seed for random number genererator to 1234
using Gaussian smoothing of bias field, sigma=0.500
disabling nonmaximum suppression
retaining  points that are at least 1.000mm from the boundary
using segmentation for initial intensity normalization
reading mri_src from
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz...
Copying mri_dst from mri_src
computing distance transform
computing distance transform
min_dist = 1
Erasing Border planes 4
aseg read with width 256 (src width 256)
resampling aseg...
Removing non-wm voxels
78821 non wm control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
smoothing bias field with sigma=0.500
MRIapplyBiasCorrectionSameGeometry()
NaN found at voxel (0, 0, 0, 0)
error: Numerical argument out of domain
error: WARNING: 16777216 NaNs found in volume
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz...
\00
writing normalized volume to /home/chang/GBM_Data/VBG/0003/0003/mri/T2.norm.
mgz
#VMPC# mri_normalize VmPeak  877864
mri_normalize done
@#@FSTIME  2024:08:07:18:29:14 mri_normalize N 18 e 13.40 S 0.45 U 12.95 P
100% M 745184 F 3 R 487208 W 0 c 49 w 2 I 32 O 136 L 10.89 10.65 10.53
@#@FSLOADPOST 2024:08:07:18:29:27 mri_normalize N 18 11.28 10.75 10.57
mri_mask -transfer 255 -keep_mask_deletion_edits
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.norm.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/brain.finalsurfs.mgz
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.mgz
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
DoAbs = 0
maskval=255, outval=255
Writing masked volume to
/home/chang/GBM_Data/VBG/0003/0003/mri/T2.mgz...done.
@#@FSTIME  2024:08:07:18:29:27 mri_mask N 6 e 1.07 S 0.05 U 1.02 P 99% M
238076 F 0 R 58376 W 0 c 5 w 2 I 0 O 136 L 11.28 10.75 10.57
@#@FSLOADPOST 2024:08:07:18:29:28 mri_mask N 6 11.28 10.75 10.57
#--------------------------------------------
#@# MMPialSurf lh 公曆 20廿四年 八月 七日 週三 十八時廿九分廿八秒
cd /home/chang/GBM_Data/VBG/0003/0003/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label
../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label
--white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf
../surf/lh.white --mmvol T2.mgz T2
7.4.1
7.4.1
cd /home/chang/GBM_Data/VBG/0003/0003/mri
setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg
aseg.presurf.mgz --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh
--i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label
../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label
--white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf
../surf/lh.white --mmvol T2.mgz T2
Reading in input surface ../surf/lh.pial.T1
Not smoothing input surface
Area    272746  0.44422  0.37554 0.000119   7.1834
Corner  818238 60.00000 30.10735 0.040969 179.8384
Edge    409119  1.06184  0.52459 0.002581   8.1249
Hinge   409119 18.15251 25.58024 0.000094 179.9970
Reading white surface coordinates from ../surf/lh.white
Reading repulsion surface coordinates from ../surf/lh.white
Reading in aparc ../label/lh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110
MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 60.756
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex+hipamyg.label
MRISripNotLabel() ripped 7099/136375 vertices (129276 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
Reading in multimodal volume T2.mgz
using multi modal weights
vertex 68188: xyz = (-30.7907,-17.9909,34.3246) oxyz =
(-28.7963,-16.4263,32.6041) wxzy = (-28.7963,-16.4263,32.6041) pxyz =
(-30.7907,-17.9909,34.3246)
CBVO Creating mask 136375
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Computing pial target locations using multimodal (1)
starting MRIScomputePialTargetLocationsMultiModal()
max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7
T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside
300
inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5
wm_weight = 3, nlabels=0, contrast_type=1
Changed 500997 aseg cortex voxels to 0
Creating lowres distance volumes t=0.0159976
Creating white distance volumes t=0.153809
(box.dx, box.dy, box.dz) = (136, 234, 316)
(region->dx, region->dy, region->dz) = (136, 234, 316)
(region->dx, region->dy, region->dz) = (136, 234, 316)
Creating pial distance volumes t=0.471721
(box.dx, box.dy, box.dz) = (146, 250, 328)
(region->dx, region->dy, region->dz) = (146, 250, 328)
(region->dx, region->dy, region->dz) = (146, 250, 328)
locating cortical regions not in interior range [110.0 --> 300.0], and not
in exterior range [130.0 --> 300.0]
t = 0.849581
Starting loop over 136375 vertices
vno = 0, t = 0.849581
error: Numerical argument out of domain
error: MRIhistogramLabelRegion: constant image\00
error: Numerical argument out of domain
error: MRIhistogramLabelRegion: constant image\00
Command terminated by signal 11
@#@FSTIME  2024:08:07:18:29:28 mris_place_surface N 31 e 56.54 S 1.26 U
55.14 P 99% M 1937256 F 2 R 1106903 W 0 c 234 w 542 I 272 O 0 L 11.28 10.75
10.57
@#@FSLOADPOST 2024:08:07:18:30:25 mris_place_surface N 31 10.93 10.78 10.59
Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 0003 exited with ERRORS at 公曆 20廿四年 八月 七日 週三 十八時
卅分廿五秒
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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[Freesurfer] recon-all.error using T2 data to improve pial surfaces