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_305_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: 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: 2024/08/07-08:02:48-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: 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: 2024/08/07-08:02:48-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_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: 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: 2024/08/07-08:02:48-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)