Freesurfer August 2024

freesurfer@nmr.mgh.harvard.edu

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58 discussions

recon-all.error using T2 data to improve pial surfaces
by r04458005＠ntu.edu.tw 07 Aug '24

07 Aug '24

External Email - Use Caution Dear Freesurfer Expert, I am encountering errors when attempting to run recon-all with T2 images. It appears there are issues specifically related to the processing of the T2 files. Could you kindly advise on the appropriate steps to resolve this issue? Please find the recon-all.error and recon-all.log files attached for your reference. Thank you for your assistance. Best regards, -Edward ------------------------------ SUBJECT 0003 DATE 公曆 20廿四年八月七日週三十八時卅分廿五秒 USER chang HOST chang-System-Product-Name PROCESSOR x86_64 OS Linux Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460) /usr/local/freesurfer/bin/recon-all PWD /home/chang/GBM_Data/VBG/0003/0003/mri CMD mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 公曆 20廿四年八月七日週三十一時35分37秒 cd /home/chang/GBM_Data/VBG/0003/0003 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 /usr/local/freesurfer/bin/recon-all -autorecon1 -i /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz -subjid 0003 -sd /home/chang/GBM_Data/VBG/0003 subjid 0003 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 16453580 kbytes maxproc 513872 maxlocks unlimited maxsignal 513872 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 16Gi 3.4Gi 2.5Gi 105Gi 104Gi Swap: 2.0Gi 2.0Gi 0.0Ki ######################################## program versions used 7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-03:35:37-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/chang/GBM_Data/VBG/0003/0003 mri_convert /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz mri_convert /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz reading from /home/chang/GBM_Data/VBG/0003/0003_T1_VBG_supered.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz... @#@FSTIME 2024:08:07:11:35:38 mri_convert N 2 e 0.97 S 0.03 U 0.93 P 99% M 42240 F 0 R 9169 W 0 c 13 w 3 I 46584 O 46368 L 10.40 10.73 10.73 @#@FSLOADPOST 2024:08:07:11:35:38 mri_convert N 2 10.40 10.73 10.73 #-------------------------------------------- #@# MotionCor 公曆 20廿四年八月七日週三十一時35分39秒 Found 1 runs /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /home/chang/GBM_Data/VBG/0003/0003/mri/orig/001.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz mri_info /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz type: MGH dimensions: 240 x 240 x 155 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 240.000 dof: 1 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -77.5, zend: 77.5 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -120. 0000 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 119. 0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 77. 5000 talairach xfm : Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 0.0000 0.0000 -1.0000 0.0000 239.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: -1.0000 0.0000 0.0000 0.0000 0.0000 -1.0000 0.0000 239.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 /home/chang/GBM_Data/VBG/0003/0003 mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz --conform mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz --conform reading from /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram -46.4572 182.552 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz... @#@FSTIME 2024:08:07:11:35:42 mri_convert N 3 e 1.09 S 0.03 U 1.05 P 99% M 50688 F 0 R 19668 W 0 c 13 w 1 I 0 O 5872 L 10.12 10.66 10.71 @#@FSLOADPOST 2024:08:07:11:35:44 mri_convert N 3 10.12 10.66 10.71 mri_add_xform_to_header -c /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach.xfm /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2024:08:07:11:35:44 mri_add_xform_to_header N 4 e 0.32 S 0.00 U 0.31 P 100% M 23552 F 0 R 4597 W 0 c 7 w 1 I 0 O 5872 L 10.12 10.66 10.71 @#@FSLOADPOST 2024:08:07:11:35:44 mri_add_xform_to_header N 4 10.12 10.66 10.71 mri_info /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz orig.mgz ======================================== Volume information for /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -120. 0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 119. 0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 77. 5000 talairach xfm : /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach. xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 8.0000 0.0000 0.0000 1.0000 -9.0000 0.0000 -1.0000 0.0000 205.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 8.0000 -0.0000 -0.0000 -1.0000 205.5000 -0.0000 1.0000 -0.0000 9.0000 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach 公曆 20廿四年八月七日週三十一時35分44秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /home/chang/GBM_Data/VBG/0003/0003/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.4.1 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 公曆 20廿四年八月七日週三十一時35分44秒 tmpdir is ./tmp.mri_nu_correct.mni.602679 cd /home/chang/GBM_Data/VBG/0003/0003/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.602679/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.602679/nu0.mgz orig_nu.mgz --like orig. mgz --conform mri_convert ./tmp.mri_nu_correct.mni.602679/nu0.mgz orig_nu.mgz --like orig. mgz --conform reading from ./tmp.mri_nu_correct.mni.602679/nu0.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... 公曆 20廿四年八月七日週三十一時36分58秒 mri_nu_correct.mni done @#@FSTIME 2024:08:07:11:35:44 mri_nu_correct.mni N 12 e 73.84 S 0.15 U 73.69 P 100% M 505444 F 0 R 147801 W 0 c 362 w 101 I 0 O 10776 L 10.12 10.66 10.71 @#@FSLOADPOST 2024:08:07:11:36:58 mri_nu_correct.mni N 12 10.52 10.64 10.69 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /home/chang/GBM_Data/VBG/0003/0003/mri/talsrcimg_to_711-2C_as_mni_average_30 5_t4_vox2vox.txt /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talsrcimg_to_711-2C_as_mni _average_305_t4_vox2vox.txt Started at 公曆 20廿四年八月七日週三十一時36分58秒 Ended at 公曆 20廿四年八月七日週三十一時37分十一秒 talairach_avi done @#@FSTIME 2024:08:07:11:36:58 talairach_avi N 4 e 12.96 S 0.80 U 6.15 P 53% M 254976 F 0 R 401480 W 0 c 52 w 593 I 0 O 295368 L 10.52 10.64 10.69 @#@FSLOADPOST 2024:08:07:11:37:11 talairach_avi N 4 11.01 10.74 10.73 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.4.1 --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.08931 0.00911 -0.03807 131.53241; -0.00637 0.90387 0.49920 -147.69925; 0.04987 -0.48152 1.02395 -18.16597; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection 公曆 20廿四年八月七日週三十一時37分十三秒 /home/chang/GBM_Data/VBG/0003/0003/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4547, pval=0.1049 >= threshold=0.0050) @#@FSTIME 2024:08:07:11:37:13 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 5888 F 0 R 253 W 0 c 0 w 1 I 0 O 0 L 11.01 10.74 10.73 @#@FSLOADPOST 2024:08:07:11:37:13 talairach_afd N 4 11.01 10.74 10.73 awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach_avi.log tal_QC_AZS /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach_avi.log TalAviQA: 0.98085 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction 公曆 20廿四年八月七日週三十一時37分十三秒 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /home/chang/GBM_Data/VBG/0003/0003/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.4.1 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 公曆 20廿四年八月七日週三十一時37分十三秒 tmpdir is ./tmp.mri_nu_correct.mni.603046 cd /home/chang/GBM_Data/VBG/0003/0003/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.603046/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --min -1 --o ./tmp. mri_nu_correct.mni.603046/ones.mgz 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.603046/ones.mgz sysname Linux hostname chang-System-Product-Name machine x86_64 user chang input ./tmp.mri_nu_correct.mni.603046/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.603046/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.603046/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz --i orig. mgz --sum ./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603046/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603046/input.mean.dat sysname Linux hostname chang-System-Product-Name machine x86_64 user chang whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.603046/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.603046/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz --i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --sum ./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603046/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603046/ones.mgz --i ./tmp.mri_nu_correct.mni.603046/nu0.mgz --sum ./tmp.mri_nu_correct.mni.603046/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603046/output.mean.dat sysname Linux hostname chang-System-Product-Name machine x86_64 user chang whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.603046/ones.mgz Loading ./tmp.mri_nu_correct.mni.603046/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.603046/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.603046/nu0.mgz ./tmp.mri_nu_correct.mni.603046/nu0.mgz mul 1.57903263683775183189 Saving result to './tmp.mri_nu_correct.mni.603046/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.603046/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.603046/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.603046/nu0.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 2 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 23, i2 = 80 #mri_make_uchar# mapping 55 190 to 3 110 : b -40.807 m 0.794143 : thresh 51.385 maxsat 372.486 : nzero 10396308 nsat 0 公曆 20廿四年八月七日週三十一時38分39秒 mri_nu_correct.mni done @#@FSTIME 2024:08:07:11:37:13 mri_nu_correct.mni N 9 e 85.82 S 0.53 U 85.30 P 100% M 614144 F 0 R 518305 W 0 c 354 w 171 I 0 O 26960 L 11.01 10.74 10.73 @#@FSLOADPOST 2024:08:07:11:38:39 mri_nu_correct.mni N 9 11.39 10.97 10.81 mri_add_xform_to_header -c /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2024:08:07:11:38:39 mri_add_xform_to_header N 4 e 0.47 S 0.01 U 0.45 P 99% M 23552 F 0 R 4598 W 0 c 2 w 1 I 0 O 5240 L 11.39 10.97 10.81 @#@FSLOADPOST 2024:08:07:11:38:39 mri_add_xform_to_header N 4 11.39 10.97 10.81 #-------------------------------------------- #@# Intensity Normalization 公曆 20廿四年八月七日週三十一時38分39秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.08931 0.00911 -0.03807 131.53241; -0.00637 0.90387 0.49920 -147.69925; 0.04987 -0.48152 1.02395 -18.16597; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 67 (67), valley at 40 (40) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 66 (66), valley at 40 (40) csf peak at 10, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 0 minutes and 36 seconds. @#@FSTIME 2024:08:07:11:38:39 mri_normalize N 7 e 36.80 S 0.25 U 36.55 P 99% M 583648 F 0 R 263304 W 0 c 139 w 15 I 0 O 5512 L 11.39 10.97 10.81 @#@FSLOADPOST 2024:08:07:11:39:16 mri_normalize N 7 11.59 11.06 10.85 #-------------------------------------------- #@# Skull Stripping 公曆 20廿四年八月七日週三十一時39分十六秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (50, 54, 18) --> (203, 206, 197) finding center of left hemi white matter using (101, 105, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (82,86,86) --> (119, 123,130) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 108 +- 4.0 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.374 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.377367 @ (0.000, 0.000, 0.000) max log p = -4.320559 @ (-5.263, -5.263, -15.789) max log p = -4.259204 @ (2.632, -2.632, 7.895) max log p = -4.215544 @ (1.316, -1.316, 1.316) max log p = -4.215544 @ (0.000, 0.000, 0.000) max log p = -4.210229 @ (0.329, 0.987, -1.645) max log p = -4.210229 @ (0.000, 0.000, 0.000) max log p = -4.210229 @ (0.000, 0.000, 0.000) Found translation: (-1.0, -8.2, -8.2): log p = -4.210 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.795, old_max_log_p =-4.210 (thresh=-4.2) 1.07500 0.00000 0.00000 -10.44355; 0.00000 1.13162 0.49132 -79.17023; 0.00000 -0.36573 0.93367 54.67687; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 57 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.795, old_max_log_p =-3.795 (thresh=-3.8) 1.07500 0.00000 0.00000 -10.44355; 0.00000 1.13162 0.49132 -79.17023; 0.00000 -0.36573 0.93367 54.67687; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 55 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.743, old_max_log_p =-3.795 (thresh=-3.8) 1.09516 0.00000 0.00000 -12.98503; 0.00000 1.06935 0.57067 -79.45934; 0.00000 -0.49134 0.91473 73.19285; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 40 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.743, old_max_log_p =-3.743 (thresh=-3.7) 1.09516 0.00000 0.00000 -12.98503; 0.00000 1.06935 0.57067 -79.45934; 0.00000 -0.49134 0.91473 73.19285; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 40 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.728, old_max_log_p =-3.743 (thresh=-3.7) 1.09127 0.00359 -0.00736 -11.66309; 0.00000 1.08237 0.53905 -78.51374; 0.00863 -0.45433 0.92968 65.93478; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 28 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.727, old_max_log_p =-3.728 (thresh=-3.7) 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.727 (old=-4.374) transform before final EM align: 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.09244 0.01734 0.00925 -15.29819; -0.01769 1.07340 0.55346 -76.69473; -0.00029 -0.47254 0.92184 70.62347; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 787448 FSRUNTIME@ mri_em_register 0.0787 hours 1 threads registration took 4 minutes and 43 seconds. @#@FSTIME 2024:08:07:11:39:16 mri_em_register N 4 e 283.19 S 0.32 U 282.83 P 99% M 628268 F 0 R 166964 W 0 c 871 w 336 I 0 O 32 L 11.59 11.06 10.85 @#@FSLOADPOST 2024:08:07:11:43:59 mri_em_register N 4 10.31 10.67 10.75 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=126 y=124 z=106 r=79 first estimation of the main basin volume: 2102595 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=107, y=120, z=69, Imax=255 CSF=14, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=1800067864817858 voxels, voxel volume =1.000 = 1800067864817858 mmm3 = 1800067904176.128 cm3 done. PostAnalyze...Basin Prior 7 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=132, z=111, r=136104 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=5, CSF_intensity=23, CSF_MAX=41 , nb = 42066 RIGHT_CER CSF_MIN=6, CSF_intensity=16, CSF_MAX=54 , nb = 2340 LEFT_CER CSF_MIN=5, CSF_intensity=13, CSF_MAX=76 , nb = 2628 RIGHT_BRAIN CSF_MIN=6, CSF_intensity=23, CSF_MAX=40 , nb = 17100 LEFT_BRAIN CSF_MIN=6, CSF_intensity=23, CSF_MAX=39 , nb = 18864 OTHER CSF_MIN=5, CSF_intensity=10, CSF_MAX=19 , nb = 1134 Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 41, 37, 31, 64 after analyzing : 33, 37, 37, 43 RIGHT_CER before analyzing : 54, 47, 42, 70 after analyzing : 39, 47, 47, 52 LEFT_CER before analyzing : 76, 58, 54, 68 after analyzing : 46, 58, 58, 60 RIGHT_BRAIN before analyzing : 40, 36, 32, 60 after analyzing : 32, 36, 36, 42 LEFT_BRAIN before analyzing : 39, 36, 33, 63 after analyzing : 32, 36, 36, 42 OTHER before analyzing : 19, 13, 0, 23 after analyzing : 13, 21, 25, 22 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...71 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.593, std = 7.859 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 7.07, sigma = 18.44 after rotation: sse = 7.07, sigma = 18.44 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 8.68, its var is 21.07 before Erosion-Dilatation 6.68% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...36 iterations mri_strip_skull: done peeling brain Brain Size = 1598794 voxels, voxel volume = 1.000 mm3 = 1598794 mmm3 = 1598.794 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done @#@FSTIME 2024:08:07:11:43:59 mri_watershed N 6 e 7.90 S 0.23 U 7.66 P 99% M 817432 F 0 R 207178 W 0 c 23 w 18 I 0 O 2512 L 10.31 10.67 10.75 @#@FSLOADPOST 2024:08:07:11:44:07 mri_watershed N 6 10.58 10.71 10.76 cp brainmask.auto.mgz brainmask.mgz Started at 公曆 20廿四年八月七日週三十一時35分37秒 Ended at 公曆 20廿四年八月七日週三十一時44分八秒 #@#%# recon-all-run-time-hours 0.142 recon-all -s 0003 finished without error at 公曆 20廿四年八月七日週三十一時44分八秒 #New# invocation of recon-all 公曆 20廿四年八月七日週三十六時二分48秒 cd /home/chang/GBM_Data/VBG/0003/0003 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 /usr/local/freesurfer/bin/recon-all -autorecon2 -autorecon3 -subjid 0003 -sd /home/chang/GBM_Data/VBG/0003 subjid 0003 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 16453580 kbytes maxproc 513872 maxlocks unlimited maxsignal 513872 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 16Gi 2.1Gi 2.4Gi 106Gi 105Gi Swap: 2.0Gi 2.0Gi 9.0Mi ######################################## program versions used 7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-08:02:48-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 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) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1403 voxels, peak = 79), gca=79.0 gca peak = 0.08618 (78) mri peak = 0.10561 (81) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1640 voxels, overlap=0.877) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1640 voxels, peak = 79), gca=79.2 gca peak = 0.08005 (78) mri peak = 0.09765 (86) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11171 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11171 voxels, peak = 83), gca=83.1 gca peak = 0.12854 (88) mri peak = 0.08520 (95) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1008 voxels, overlap=0.782) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1008 voxels, peak = 94), gca=93.7 gca peak = 0.15703 (87) mri peak = 0.07869 (93) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1072 voxels, overlap=0.781) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1072 voxels, peak = 93), gca=92.7 gca peak = 0.17522 (25) mri peak = 0.10934 (11) Third_Ventricle (14): linear fit = 0.40 x + 0.0 (172 voxels, overlap=0.118) Third_Ventricle (14): linear fit = 0.40 x + 0.0 (172 voxels, peak = 10), gca=9.9 gca peak = 0.17113 (14) mri peak = 0.15791 ( 7) Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (180 voxels, overlap=0.087) Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (180 voxels, peak = 6), gca=6.0 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.58 x + 0.0 Right_Pallidum too bright - rescaling by 0.982 (from 1.065) to 100.4 (was 102.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21508 (11) mri peak = 0.14123 ( 9) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (8168 voxels, overlap=0.913) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (8168 voxels, peak = 11), gca=11.5 gca peak = 0.25554 ( 7) mri peak = 0.20590 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (7768 voxels, overlap=0.801) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (7768 voxels, peak = 7), gca=6.6 gca peak = 0.21127 (97) mri peak = 0.15139 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (720 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (720 voxels, peak = 97), gca=97.5 gca peak = 0.18013 (92) mri peak = 0.11044 (90) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (499 voxels, overlap=0.857) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (499 voxels, peak = 93), gca=93.4 gca peak = 0.30247 (57) mri peak = 0.10739 (57) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1209 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1209 voxels, peak = 57), gca=57.0 gca peak = 0.33035 (58) mri peak = 0.10453 (60) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1146 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1146 voxels, peak = 57), gca=57.1 gca peak = 0.08114 (103) mri peak = 0.23320 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40003 voxels, overlap=0.568) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40003 voxels, peak = 102), gca=102.5 gca peak = 0.08124 (104) mri peak = 0.17446 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33779 voxels, overlap=0.597) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33779 voxels, peak = 103), gca=103.5 gca peak = 0.08546 (69) mri peak = 0.04919 (69) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (33492 voxels, overlap=0.913) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (33492 voxels, peak = 68), gca=68.0 gca peak = 0.10313 (64) mri peak = 0.04487 (65) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (29706 voxels, overlap=0.956) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (29706 voxels, peak = 66), gca=65.6 gca peak = 0.22760 (73) mri peak = 0.08893 (72) Right_Caudate (50): linear fit = 1.03 x + 0.0 (1095 voxels, overlap=0.796) Right_Caudate (50): linear fit = 1.03 x + 0.0 (1095 voxels, peak = 76), gca=75.6 gca peak = 0.12384 (71) mri peak = 0.07841 (73) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1024 voxels, overlap=0.842) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1024 voxels, peak = 71), gca=71.0 gca peak = 0.13024 (60) mri peak = 0.09727 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30241 voxels, overlap=0.915) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30241 voxels, peak = 62), gca=61.5 gca peak = 0.14380 (59) mri peak = 0.11156 (60) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29541 voxels, overlap=0.937) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29541 voxels, peak = 60), gca=60.5 gca peak = 0.15848 (86) mri peak = 0.17077 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4606 voxels, overlap=0.884) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4606 voxels, peak = 86), gca=85.6 gca peak = 0.15314 (86) mri peak = 0.18225 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4821 voxels, overlap=0.758) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4821 voxels, peak = 86), gca=85.6 gca peak = 0.23055 (63) mri peak = 0.17276 (64) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (411 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (411 voxels, peak = 64), gca=63.9 gca peak = 0.32741 (61) mri peak = 0.17013 (63) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (529 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (529 voxels, peak = 62), gca=61.9 gca peak = 0.12181 (86) mri peak = 0.08271 (82) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3762 voxels, overlap=0.967) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3762 voxels, peak = 86), gca=85.6 gca peak = 0.10629 (86) mri peak = 0.06745 (86) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (2955 voxels, overlap=0.919) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (2955 voxels, peak = 86), gca=85.6 gca peak = 0.08843 (77) mri peak = 0.11198 (77) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1403 voxels, overlap=0.847) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1403 voxels, peak = 77), gca=77.0 gca peak = 0.08736 (77) mri peak = 0.10561 (81) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1640 voxels, overlap=0.944) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1640 voxels, peak = 77), gca=77.0 gca peak = 0.07578 (86) mri peak = 0.09765 (86) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11171 voxels, overlap=0.699) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11171 voxels, peak = 85), gca=84.7 gca peak = 0.12327 (95) mri peak = 0.08520 (95) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1008 voxels, overlap=0.860) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1008 voxels, peak = 96), gca=96.4 gca peak = 0.14047 (91) mri peak = 0.07869 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1072 voxels, overlap=0.907) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1072 voxels, peak = 91), gca=91.0 gca peak = 0.30661 (15) mri peak = 0.10934 (11) Third_Ventricle (14): linear fit = 0.69 x + 0.0 (172 voxels, overlap=1.028) Third_Ventricle (14): linear fit = 0.69 x + 0.0 (172 voxels, peak = 10), gca=10.3 gca peak = 0.29372 ( 9) mri peak = 0.15791 ( 7) Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (180 voxels, overlap=0.850) Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (180 voxels, peak = 7), gca=6.7 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.21552 (29) gca peak CSF = 0.33827 (21) gca peak Left_Accumbens_area = 0.51915 (65) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.27120 (24) gca peak Right_Accumbens_area = 0.29187 (71) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.73434 (19) gca peak WM_hypointensities = 0.12365 (76) gca peak non_WM_hypointensities = 0.08214 (41) gca peak Optic_Chiasm = 0.51663 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 37799 voxels changed in iteration 0 of unlikely voxel relabeling 247 voxels changed in iteration 1 of unlikely voxel relabeling 144 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 35863 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 377 hippocampal voxels changed. 1 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 59580 changed. image ll: -2.100, PF=0.500 pass 2: 13570 changed. image ll: -2.100, PF=0.500 pass 3: 4116 changed. 29172 voxels changed in iteration 0 of unlikely voxel relabeling 254 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6910 voxels changed in iteration 0 of unlikely voxel relabeling 65 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6614 voxels changed in iteration 0 of unlikely voxel relabeling 62 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6156 voxels changed in iteration 0 of unlikely voxel relabeling 39 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 1 with volume 22600 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 327 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 280 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 281 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 21080 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 917 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 986.315517 mri_ca_label stimesec 1.031911 mri_ca_label ru_maxrss 2095812 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1025163 mri_ca_label ru_majflt 13 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2088 mri_ca_label ru_oublock 712 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 177 mri_ca_label ru_nivcsw 2964 mri_ca_label took 16 minutes and 27 seconds. mri_ca_label done @#@FSTIME 2024:08:07:17:03:06 mri_ca_label N 10 e 987.51 S 1.10 U 986.31 P 99% M 2095812 F 13 R 1025168 W 0 c 2965 w 178 I 2088 O 712 L 11.78 10.80 10. 55 @#@FSLOADPOST 2024:08:07:17:19:34 mri_ca_label N 10 10.07 10.34 10.44 #-------------------------------------- #@# CC Seg 公曆 20廿四年八月七日週三十七時十九分34秒 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/cc_up.lta 0003 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/cc_up.lta reading aseg from /home/chang/GBM_Data/VBG/0003/0003/mri/aseg.auto_noCCseg.mgz reading norm from /home/chang/GBM_Data/VBG/0003/0003/mri/norm.mgz 18173 voxels in left wm, 21786 in right wm, xrange [123, 129] searching rotation angles z=[-6 8], y=[-8 6] searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 global minimum found at slice 125.4, rotations (-0.63, 0.68) final transformation (x=125.4, yr=-0.629, zr=0.683): 0.99987 -0.01192 -0.01098 4.93699; 0.01192 0.99993 -0.00013 12.52455; 0.01098 -0.00000 0.99994 41.62889; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 137 min_x_fornix = 137 min_x_fornix = 137 min_x_fornix = 137 min_x_fornix = 137 cc center is found at 128 114 85 eigenvectors: 0.00079 0.00244 1.00000; -0.23427 -0.97217 0.00256; 0.97217 -0.23427 -0.00020; error in mid anterior detected - correcting... writing aseg with callosum to /home/chang/GBM_Data/VBG/0003/0003/mri/aseg.auto.mgz... corpus callosum segmentation took 0.2 minutes #VMPC# mri_cc VmPeak 436900 mri_cc done @#@FSTIME 2024:08:07:17:19:34 mri_cc N 7 e 12.01 S 0.22 U 11.78 P 99% M 343560 F 8 R 277682 W 0 c 50 w 8 I 1336 O 696 L 10.07 10.34 10.44 @#@FSLOADPOST 2024:08:07:17:19:46 mri_cc N 7 9.97 10.31 10.43 #-------------------------------------- #@# Merge ASeg 公曆 20廿四年八月七日週三十七時十九分46秒 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 公曆 20廿四年八月七日週三十七時十九分46秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 256 (src width 256) ************** resampling aseg to account for mismatch with source image *************** normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 379 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 69 (69), valley at 37 (37) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 71 (71), valley at 38 (38) csf peak at 36, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 0 minutes and 59 seconds. @#@FSTIME 2024:08:07:17:19:46 mri_normalize N 9 e 61.80 S 0.67 U 61.12 P 99% M 1200992 F 0 R 665514 W 0 c 202 w 14 I 8 O 2520 L 9.97 10.31 10.43 @#@FSLOADPOST 2024:08:07:17:20:47 mri_normalize N 9 9.05 9.95 10.30 #-------------------------------------------- #@# Mask BFS 公曆 20廿四年八月七日週三十七時廿分47秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1588968 voxels in mask (pct= 9.47) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:08:07:17:20:47 mri_mask N 5 e 0.61 S 0.01 U 0.59 P 99% M 74240 F 6 R 17283 W 0 c 4 w 7 I 1056 O 2512 L 9.05 9.95 10.30 @#@FSLOADPOST 2024:08:07:17:20:48 mri_mask N 5 9.05 9.95 10.30 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation 公曆 20廿四年八月七日週三十七時廿分48秒 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:08:07:17:20:48 AntsDenoiseImageFs N 4 e 14.63 S 0.09 U 14.53 P 99% M 350720 F 23 R 86513 W 0 c 88 w 23 I 4928 O 2560 L 9.05 9.95 10.30 @#@FSLOADPOST 2024:08:07:17:21:03 AntsDenoiseImageFs N 4 9.28 9.95 10.29 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 373563, nonwhite = 16121213, ambig = 282440, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (104.0): 103.7 +- 5.7 [79.0 --> 125.0] CCS GM (71.0) : 69.8 +- 11.3 [30.0 --> 95.0] white_mean 103.715 white_sigma 5.70945 gray_mean 69.7889 gray_sigma 11.2917 setting bottom of white matter range wm_low to 81.1 setting top of gray matter range gray_hi to 92.4 wm_low 81.0806 wm_hi 125 gray_low 30 gray_hi 92.3723 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=81.0806, wm_hi=125, gray_hi=92.3723 white = 457273, nonwhite = 16173821, ambig = 146122, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 81.0806 wm_hi 125 gray_low 30 gray_hi 92.3723 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 92.3723, wm_low = 81.0806 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=92.3723, wmlow=81.0806 135314 voxels processed (0.81%) 64383 voxels white (0.38%) 70931 voxels non-white (0.42%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=76.0806, gray_hi=92.3723, wsize=13 237738 voxels tested (1.42%) 45308 voxels changed (0.27%) 50480 multi-scale searches (0.30%) Recovering bright white MRIrecoverBrightWhite() wm_low 81.0806 wm_hi 125 slack 5.70945 pct_thresh 0.33 intensity_thresh 130.709 nvox_thresh 8.58 368 voxels tested (0.00%) 325 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=76.0806, hithr=92.3723 smoothing input volume with sigma = 0.250 93133 voxels tested (0.56%) 18543 voxels changed (0.11%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1044 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1070 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 2194 filled MRIfindBrightNonWM(): 889 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 0.5 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:08:07:17:21:03 mri_segment N 5 e 29.43 S 0.20 U 29.22 P 99% M 143024 F 7 R 295539 W 0 c 110 w 7 I 1056 O 816 L 9.28 9.95 10.29 @#@FSLOADPOST 2024:08:07:17:21:32 mri_segment N 5 9.34 9.91 10.27 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.22 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 5212 additional wm voxels added 0 additional wm voxels added SEG EDIT: 93917 voxels turned on, 31197 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:08:07:17:21:32 mri_edit_wm_with_aseg N 5 e 13.50 S 0.23 U 13.27 P 99% M 463900 F 5 R 315082 W 0 c 42 w 6 I 960 O 760 L 9.34 9.91 10.27 @#@FSLOADPOST 2024:08:07:17:21:46 mri_edit_wm_with_aseg N 5 9.81 10.00 10.29 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 20 found - 20 modified | TOTAL: 20 pass 2 (xy+): 0 found - 20 modified | TOTAL: 20 pass 1 (xy-): 9 found - 9 modified | TOTAL: 29 pass 2 (xy-): 0 found - 9 modified | TOTAL: 29 pass 1 (yz+): 14 found - 14 modified | TOTAL: 43 pass 2 (yz+): 0 found - 14 modified | TOTAL: 43 pass 1 (yz-): 19 found - 19 modified | TOTAL: 62 pass 2 (yz-): 0 found - 19 modified | TOTAL: 62 pass 1 (xz+): 15 found - 15 modified | TOTAL: 77 pass 2 (xz+): 0 found - 15 modified | TOTAL: 77 pass 1 (xz-): 12 found - 12 modified | TOTAL: 89 pass 2 (xz-): 0 found - 12 modified | TOTAL: 89 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 6 found - 6 modified | TOTAL: 14 pass 2 (+++): 0 found - 6 modified | TOTAL: 14 Iteration Number : 1 pass 1 (++): 24 found - 24 modified | TOTAL: 24 pass 2 (++): 0 found - 24 modified | TOTAL: 24 pass 1 (+-): 14 found - 14 modified | TOTAL: 38 pass 2 (+-): 0 found - 14 modified | TOTAL: 38 pass 1 (--): 17 found - 17 modified | TOTAL: 55 pass 2 (--): 0 found - 17 modified | TOTAL: 55 pass 1 (-+): 9 found - 9 modified | TOTAL: 64 pass 2 (-+): 0 found - 9 modified | TOTAL: 64 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 174 (out of 573424: 0.030344) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:08:07:17:21:46 mri_pretess N 4 e 1.49 S 0.01 U 1.47 P 99% M 56832 F 19 R 12964 W 0 c 6 w 18 I 4128 O 760 L 9.81 10.00 10.29 @#@FSLOADPOST 2024:08:07:17:21:47 mri_pretess N 4 10.07 10.05 10.31 #-------------------------------------------- #@# Fill 公曆 20廿四年八月七日週三十七時廿一分47秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... done. searching for cutting planes...voxel to talairach voxel transform 1.02154 -0.01478 0.00988 -2.50282; 0.00536 1.04188 0.48781 -67.20425; -0.01686 -0.43513 0.90963 68.71252; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.02154 -0.01478 0.00988 -2.50282; 0.00536 1.04188 0.48781 -67.20425; -0.01686 -0.43513 0.90963 68.71252; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1581 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) need search nearby using seed (125, 109, 88), TAL = (3.0, -40.0, 19.0) talairach voxel to voxel transform 0.97863 0.00772 -0.01477 3.98269; -0.01106 0.78408 -0.42036 81.55042; 0.01285 0.37522 0.89799 -36.45474; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 109, 88) --> (3.0, -40.0, 19.0) done. filling took 0.6 minutes talairach cc position changed to (3.00, -40.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -40.00, 19.00) SRC: (108.24, 128.84, 84.84) search lh wm seed point around talairach space (-15.00, -40.00, 19.00), SRC: (143.47, 128.44, 85.31) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2024:08:07:17:21:47 mri_fill N 10 e 34.39 S 0.55 U 33.84 P 99% M 967712 F 8 R 512484 W 0 c 158 w 8 I 1440 O 264 L 10.07 10.05 10.31 @#@FSLOADPOST 2024:08:07:17:22:22 mri_fill N 10 10.68 10.21 10.35 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh 公曆 20廿四年八月七日週三十七時廿二分廿二秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 5 found - 5 modified | TOTAL: 7 pass 2 (yz+): 0 found - 5 modified | TOTAL: 7 pass 1 (yz-): 6 found - 6 modified | TOTAL: 13 pass 2 (yz-): 0 found - 6 modified | TOTAL: 13 pass 1 (xz+): 2 found - 2 modified | TOTAL: 15 pass 2 (xz+): 0 found - 2 modified | TOTAL: 15 pass 1 (xz-): 1 found - 1 modified | TOTAL: 16 pass 2 (xz-): 0 found - 1 modified | TOTAL: 16 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 19 (out of 280395: 0.006776) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:08:07:17:22:22 mri_pretess N 4 e 0.85 S 0.00 U 0.84 P 99% M 40448 F 0 R 8833 W 0 c 4 w 0 I 0 O 256 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:22 mri_pretess N 4 10.68 10.21 10.35 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.4.1 7.4.1 slice 40: 3157 vertices, 3372 faces slice 50: 11715 vertices, 12071 faces slice 60: 23505 vertices, 23965 faces slice 70: 36140 vertices, 36564 faces slice 80: 47809 vertices, 48236 faces slice 90: 59176 vertices, 59577 faces slice 100: 70387 vertices, 70817 faces slice 110: 81044 vertices, 81462 faces slice 120: 91301 vertices, 91727 faces slice 130: 101530 vertices, 101931 faces slice 140: 110558 vertices, 110932 faces slice 150: 118275 vertices, 118586 faces slice 160: 124610 vertices, 124867 faces slice 170: 130090 vertices, 130299 faces slice 180: 133577 vertices, 133707 faces slice 190: 134332 vertices, 134394 faces slice 200: 134332 vertices, 134394 faces slice 210: 134332 vertices, 134394 faces slice 220: 134332 vertices, 134394 faces slice 230: 134332 vertices, 134394 faces slice 240: 134332 vertices, 134394 faces slice 250: 134332 vertices, 134394 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:08:07:17:22:23 mri_tessellate N 3 e 0.68 S 0.02 U 0.65 P 99% M 37632 F 7 R 8374 W 0 c 7 w 16 I 1024 O 6304 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:23 mri_tessellate N 3 10.68 10.21 10.35 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 134332 voxel in cpt #1: X=-62 [v=134332,e=403182,f=268788] located at (-25.795513, -29.102404, 6.299958) For the whole surface: X=-62 [v=134332,e=403182,f=268788] One single component has been found nothing to do done @#@FSTIME 2024:08:07:17:22:23 mris_extract_main_component N 2 e 0.64 S 0.09 U 0.54 P 99% M 267080 F 18 R 70699 W 0 c 4 w 26 I 3440 O 9456 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:24 mris_extract_main_component N 2 10.68 10.21 10.35 #-------------------------------------------- #@# Tessellate rh 公曆 20廿四年八月七日週三十七時廿二分廿四秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 6 found - 6 modified | TOTAL: 6 pass 2 (yz+): 0 found - 6 modified | TOTAL: 6 pass 1 (yz-): 4 found - 4 modified | TOTAL: 10 pass 2 (yz-): 0 found - 4 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 1 found - 1 modified | TOTAL: 12 pass 2 (xz-): 0 found - 1 modified | TOTAL: 12 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 16 (out of 274986: 0.005818) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:08:07:17:22:24 mri_pretess N 4 e 0.86 S 0.01 U 0.84 P 99% M 40448 F 0 R 8834 W 0 c 2 w 1 I 0 O 256 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:25 mri_pretess N 4 10.68 10.21 10.35 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.4.1 7.4.1 slice 40: 2057 vertices, 2235 faces slice 50: 9673 vertices, 10005 faces slice 60: 19918 vertices, 20259 faces slice 70: 30458 vertices, 30824 faces slice 80: 41510 vertices, 41884 faces slice 90: 52067 vertices, 52440 faces slice 100: 63281 vertices, 63707 faces slice 110: 73931 vertices, 74369 faces slice 120: 84531 vertices, 84951 faces slice 130: 94606 vertices, 95060 faces slice 140: 104034 vertices, 104391 faces slice 150: 112205 vertices, 112525 faces slice 160: 119186 vertices, 119427 faces slice 170: 124431 vertices, 124673 faces slice 180: 128752 vertices, 128902 faces slice 190: 129764 vertices, 129826 faces slice 200: 129764 vertices, 129826 faces slice 210: 129764 vertices, 129826 faces slice 220: 129764 vertices, 129826 faces slice 230: 129764 vertices, 129826 faces slice 240: 129764 vertices, 129826 faces slice 250: 129764 vertices, 129826 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:08:07:17:22:25 mri_tessellate N 3 e 0.77 S 0.01 U 0.75 P 99% M 36608 F 0 R 8275 W 0 c 6 w 1 I 0 O 6088 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:26 mri_tessellate N 3 10.68 10.21 10.35 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 129764 voxel in cpt #1: X=-62 [v=129764,e=389478,f=259652] located at (29.572609, -25.736021, 5.940870) For the whole surface: X=-62 [v=129764,e=389478,f=259652] One single component has been found nothing to do done @#@FSTIME 2024:08:07:17:22:26 mris_extract_main_component N 2 e 0.55 S 0.10 U 0.44 P 99% M 258860 F 0 R 68280 W 0 c 5 w 4 I 8 O 9128 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:26 mris_extract_main_component N 2 10.68 10.21 10.35 #-------------------------------------------- #@# Smooth1 lh 公曆 20廿四年八月七日週三十七時廿二分廿六秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2024:08:07:17:22:26 mris_smooth N 5 e 1.46 S 0.06 U 1.39 P 99% M 213016 F 7 R 63984 W 0 c 6 w 12 I 632 O 9456 L 10.68 10.21 10.35 @#@FSLOADPOST 2024:08:07:17:22:28 mris_smooth N 5 10.47 10.17 10.34 #-------------------------------------------- #@# Smooth1 rh 公曆 20廿四年八月七日週三十七時廿二分廿八秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2024:08:07:17:22:28 mris_smooth N 5 e 1.32 S 0.05 U 1.26 P 99% M 206232 F 0 R 61191 W 0 c 4 w 5 I 0 O 9136 L 10.47 10.17 10.34 @#@FSLOADPOST 2024:08:07:17:22:29 mris_smooth N 5 10.47 10.17 10.34 #-------------------------------------------- #@# Inflation1 lh 公曆 20廿四年八月七日週三十七時廿二分廿九秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.8 mm, total surface area = 73822 mm^2 step 000: RMS=0.145 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.038 (target=0.015) writing inflated surface to ../surf/lh. inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 10.421465 mris_inflate stimesec 0.643843 mris_inflate ru_maxrss 213704 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 562020 mris_inflate ru_majflt 22 mris_inflate ru_nswap 0 mris_inflate ru_inblock 4016 mris_inflate ru_oublock 9456 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 24 mris_inflate ru_nivcsw 39 @#@FSTIME 2024:08:07:17:22:29 mris_inflate N 3 e 11.07 S 0.65 U 10.42 P 99% M 213704 F 22 R 562027 W 0 c 39 w 25 I 4016 O 9456 L 10.47 10.17 10.34 @#@FSLOADPOST 2024:08:07:17:22:40 mris_inflate N 3 10.85 10.27 10.37 #-------------------------------------------- #@# Inflation1 rh 公曆 20廿四年八月七日週三十七時廿二分40秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.1 mm, total surface area = 70773 mm^2 step 000: RMS=0.148 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.038 (target=0.015) writing inflated surface to ../surf/rh. inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 10.002528 mris_inflate stimesec 0.499926 mris_inflate ru_maxrss 206656 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 550105 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9136 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2 mris_inflate ru_nivcsw 29 @#@FSTIME 2024:08:07:17:22:40 mris_inflate N 3 e 10.51 S 0.50 U 10.00 P 99% M 206656 F 0 R 550111 W 0 c 29 w 3 I 0 O 9136 L 10.85 10.27 10.37 @#@FSLOADPOST 2024:08:07:17:22:51 mris_inflate N 3 11.02 10.32 10.39 #-------------------------------------------- #@# QSphere lh 公曆 20廿四年八月七日週三十七時廿二分51秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 scaling brain by 0.331... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.59 (0.00-->6.09) (max @ vno 57993 --> 59004) face area 0.03 +- 0.04 (-0.15-->0.63) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.378, avgs=0 005/300: dt: 0.9000, rms radial error=174.125, avgs=0 010/300: dt: 0.9000, rms radial error=173.582, avgs=0 015/300: dt: 0.9000, rms radial error=172.870, avgs=0 020/300: dt: 0.9000, rms radial error=172.059, avgs=0 025/300: dt: 0.9000, rms radial error=171.189, avgs=0 030/300: dt: 0.9000, rms radial error=170.288, avgs=0 035/300: dt: 0.9000, rms radial error=169.369, avgs=0 040/300: dt: 0.9000, rms radial error=168.442, avgs=0 045/300: dt: 0.9000, rms radial error=167.512, avgs=0 050/300: dt: 0.9000, rms radial error=166.583, avgs=0 055/300: dt: 0.9000, rms radial error=165.654, avgs=0 060/300: dt: 0.9000, rms radial error=164.728, avgs=0 065/300: dt: 0.9000, rms radial error=163.805, avgs=0 070/300: dt: 0.9000, rms radial error=162.889, avgs=0 075/300: dt: 0.9000, rms radial error=161.977, avgs=0 080/300: dt: 0.9000, rms radial error=161.070, avgs=0 085/300: dt: 0.9000, rms radial error=160.167, avgs=0 090/300: dt: 0.9000, rms radial error=159.269, avgs=0 095/300: dt: 0.9000, rms radial error=158.377, avgs=0 100/300: dt: 0.9000, rms radial error=157.490, avgs=0 105/300: dt: 0.9000, rms radial error=156.607, avgs=0 110/300: dt: 0.9000, rms radial error=155.728, avgs=0 115/300: dt: 0.9000, rms radial error=154.855, avgs=0 120/300: dt: 0.9000, rms radial error=153.986, avgs=0 125/300: dt: 0.9000, rms radial error=153.121, avgs=0 130/300: dt: 0.9000, rms radial error=152.261, avgs=0 135/300: dt: 0.9000, rms radial error=151.406, avgs=0 140/300: dt: 0.9000, rms radial error=150.555, avgs=0 145/300: dt: 0.9000, rms radial error=149.709, avgs=0 150/300: dt: 0.9000, rms radial error=148.867, avgs=0 155/300: dt: 0.9000, rms radial error=148.030, avgs=0 160/300: dt: 0.9000, rms radial error=147.197, avgs=0 165/300: dt: 0.9000, rms radial error=146.369, avgs=0 170/300: dt: 0.9000, rms radial error=145.546, avgs=0 175/300: dt: 0.9000, rms radial error=144.726, avgs=0 180/300: dt: 0.9000, rms radial error=143.912, avgs=0 185/300: dt: 0.9000, rms radial error=143.102, avgs=0 190/300: dt: 0.9000, rms radial error=142.296, avgs=0 195/300: dt: 0.9000, rms radial error=141.495, avgs=0 200/300: dt: 0.9000, rms radial error=140.698, avgs=0 205/300: dt: 0.9000, rms radial error=139.906, avgs=0 210/300: dt: 0.9000, rms radial error=139.118, avgs=0 215/300: dt: 0.9000, rms radial error=138.335, avgs=0 220/300: dt: 0.9000, rms radial error=137.556, avgs=0 225/300: dt: 0.9000, rms radial error=136.781, avgs=0 230/300: dt: 0.9000, rms radial error=136.011, avgs=0 235/300: dt: 0.9000, rms radial error=135.244, avgs=0 240/300: dt: 0.9000, rms radial error=134.483, avgs=0 245/300: dt: 0.9000, rms radial error=133.725, avgs=0 250/300: dt: 0.9000, rms radial error=132.971, avgs=0 255/300: dt: 0.9000, rms radial error=132.222, avgs=0 260/300: dt: 0.9000, rms radial error=131.477, avgs=0 265/300: dt: 0.9000, rms radial error=130.736, avgs=0 270/300: dt: 0.9000, rms radial error=129.999, avgs=0 275/300: dt: 0.9000, rms radial error=129.266, avgs=0 280/300: dt: 0.9000, rms radial error=128.538, avgs=0 285/300: dt: 0.9000, rms radial error=127.813, avgs=0 290/300: dt: 0.9000, rms radial error=127.093, avgs=0 295/300: dt: 0.9000, rms radial error=126.376, avgs=0 300/300: dt: 0.9000, rms radial error=125.664, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15322.79 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00044 epoch 2 (K=40.0), pass 1, starting sse = 2434.48 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00062 epoch 3 (K=160.0), pass 1, starting sse = 241.35 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/16 = 0.00964 epoch 4 (K=640.0), pass 1, starting sse = 17.17 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/22 = 0.00711 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0205 hours FSRUNTIME@ mris_sphere 0.0205 hours 1 threads #VMPC# mris_sphere VmPeak 476096 mris_sphere done @#@FSTIME 2024:08:07:17:22:51 mris_sphere N 9 e 73.91 S 3.49 U 70.41 P 99% M 217528 F 12 R 3507278 W 0 c 355 w 13 I 1600 O 9456 L 11.02 10.32 10.39 @#@FSLOADPOST 2024:08:07:17:24:05 mris_sphere N 9 10.55 10.40 10.41 #-------------------------------------------- #@# QSphere rh 公曆 20廿四年八月七日週三十七時廿四分五秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 scaling brain by 0.337... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.60 (0.00-->6.70) (max @ vno 59826 --> 60976) face area 0.03 +- 0.04 (-0.07-->0.62) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.539, avgs=0 005/300: dt: 0.9000, rms radial error=174.286, avgs=0 010/300: dt: 0.9000, rms radial error=173.742, avgs=0 015/300: dt: 0.9000, rms radial error=173.026, avgs=0 020/300: dt: 0.9000, rms radial error=172.209, avgs=0 025/300: dt: 0.9000, rms radial error=171.334, avgs=0 030/300: dt: 0.9000, rms radial error=170.426, avgs=0 035/300: dt: 0.9000, rms radial error=169.501, avgs=0 040/300: dt: 0.9000, rms radial error=168.567, avgs=0 045/300: dt: 0.9000, rms radial error=167.632, avgs=0 050/300: dt: 0.9000, rms radial error=166.697, avgs=0 055/300: dt: 0.9000, rms radial error=165.765, avgs=0 060/300: dt: 0.9000, rms radial error=164.836, avgs=0 065/300: dt: 0.9000, rms radial error=163.913, avgs=0 070/300: dt: 0.9000, rms radial error=162.997, avgs=0 075/300: dt: 0.9000, rms radial error=162.085, avgs=0 080/300: dt: 0.9000, rms radial error=161.178, avgs=0 085/300: dt: 0.9000, rms radial error=160.276, avgs=0 090/300: dt: 0.9000, rms radial error=159.378, avgs=0 095/300: dt: 0.9000, rms radial error=158.485, avgs=0 100/300: dt: 0.9000, rms radial error=157.597, avgs=0 105/300: dt: 0.9000, rms radial error=156.714, avgs=0 110/300: dt: 0.9000, rms radial error=155.835, avgs=0 115/300: dt: 0.9000, rms radial error=154.961, avgs=0 120/300: dt: 0.9000, rms radial error=154.092, avgs=0 125/300: dt: 0.9000, rms radial error=153.227, avgs=0 130/300: dt: 0.9000, rms radial error=152.367, avgs=0 135/300: dt: 0.9000, rms radial error=151.511, avgs=0 140/300: dt: 0.9000, rms radial error=150.661, avgs=0 145/300: dt: 0.9000, rms radial error=149.815, avgs=0 150/300: dt: 0.9000, rms radial error=148.974, avgs=0 155/300: dt: 0.9000, rms radial error=148.138, avgs=0 160/300: dt: 0.9000, rms radial error=147.307, avgs=0 165/300: dt: 0.9000, rms radial error=146.480, avgs=0 170/300: dt: 0.9000, rms radial error=145.658, avgs=0 175/300: dt: 0.9000, rms radial error=144.840, avgs=0 180/300: dt: 0.9000, rms radial error=144.027, avgs=0 185/300: dt: 0.9000, rms radial error=143.218, avgs=0 190/300: dt: 0.9000, rms radial error=142.413, avgs=0 195/300: dt: 0.9000, rms radial error=141.613, avgs=0 200/300: dt: 0.9000, rms radial error=140.817, avgs=0 205/300: dt: 0.9000, rms radial error=140.026, avgs=0 210/300: dt: 0.9000, rms radial error=139.239, avgs=0 215/300: dt: 0.9000, rms radial error=138.456, avgs=0 220/300: dt: 0.9000, rms radial error=137.677, avgs=0 225/300: dt: 0.9000, rms radial error=136.903, avgs=0 230/300: dt: 0.9000, rms radial error=136.133, avgs=0 235/300: dt: 0.9000, rms radial error=135.367, avgs=0 240/300: dt: 0.9000, rms radial error=134.606, avgs=0 245/300: dt: 0.9000, rms radial error=133.848, avgs=0 250/300: dt: 0.9000, rms radial error=133.095, avgs=0 255/300: dt: 0.9000, rms radial error=132.346, avgs=0 260/300: dt: 0.9000, rms radial error=131.601, avgs=0 265/300: dt: 0.9000, rms radial error=130.861, avgs=0 270/300: dt: 0.9000, rms radial error=130.124, avgs=0 275/300: dt: 0.9000, rms radial error=129.391, avgs=0 280/300: dt: 0.9000, rms radial error=128.663, avgs=0 285/300: dt: 0.9000, rms radial error=127.938, avgs=0 290/300: dt: 0.9000, rms radial error=127.218, avgs=0 295/300: dt: 0.9000, rms radial error=126.502, avgs=0 300/300: dt: 0.9000, rms radial error=125.789, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14716.43 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00050 epoch 2 (K=40.0), pass 1, starting sse = 2287.75 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00043 epoch 3 (K=160.0), pass 1, starting sse = 224.77 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/18 = 0.01101 epoch 4 (K=640.0), pass 1, starting sse = 13.78 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.25/26 = 0.00969 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0214 hours FSRUNTIME@ mris_sphere 0.0214 hours 1 threads #VMPC# mris_sphere VmPeak 468692 mris_sphere done @#@FSTIME 2024:08:07:17:24:05 mris_sphere N 9 e 77.02 S 3.80 U 73.20 P 99% M 210544 F 0 R 3626328 W 0 c 307 w 25 I 0 O 9136 L 10.55 10.40 10.41 @#@FSLOADPOST 2024:08:07:17:25:22 mris_sphere N 9 11.28 10.66 10.50 #@# Fix Topology lh 公曆 20廿四年八月七日週三十七時廿五分廿二秒 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 0003 lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.4.1 7.4.1 before topology correction, eno=-62 (nv=134332, nf=268788, ne=403182, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 8322 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.5572 (-4.7786) -vertex loglikelihood: -6.7775 (-3.3887) -normal dot loglikelihood: -3.6675 (-3.6675) -quad curv loglikelihood: -5.7838 (-2.8919) Total Loglikelihood : -25.7860 CORRECTING DEFECT 0 (vertices=122, convex hull=169, v0=519) After retessellation of defect 0 (v0=519), euler #=-21 (129392,386375,256962) : difference with theory (-23) = -2 CORRECTING DEFECT 1 (vertices=1504, convex hull=796, v0=989) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev iew After retessellation of defect 1 (v0=989), euler #=-21 (129765,387922,258136) : difference with theory (-22) = -1 CORRECTING DEFECT 2 (vertices=902, convex hull=305, v0=7739) After retessellation of defect 2 (v0=7739), euler #=-21 (129853,388351,258477) : difference with theory (-21) = 0 CORRECTING DEFECT 3 (vertices=110, convex hull=73, v0=9937) After retessellation of defect 3 (v0=9937), euler #=-20 (129879,388458,258559) : difference with theory (-20) = 0 CORRECTING DEFECT 4 (vertices=77, convex hull=99, v0=10732) After retessellation of defect 4 (v0=10732), euler #=-19 (129906,388583,258658) : difference with theory (-19) = 0 CORRECTING DEFECT 5 (vertices=31, convex hull=65, v0=14128) After retessellation of defect 5 (v0=14128), euler #=-18 (129922,388658,258718) : difference with theory (-18) = 0 CORRECTING DEFECT 6 (vertices=49, convex hull=89, v0=19640) After retessellation of defect 6 (v0=19640), euler #=-17 (129952,388788,258819) : difference with theory (-17) = 0 CORRECTING DEFECT 7 (vertices=197, convex hull=174, v0=22045) After retessellation of defect 7 (v0=22045), euler #=-16 (130035,389121,259070) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=169, convex hull=126, v0=26189) After retessellation of defect 8 (v0=26189), euler #=-15 (130071,389289,259203) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=91, convex hull=142, v0=26866) After retessellation of defect 9 (v0=26866), euler #=-14 (130117,389494,259363) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=151, convex hull=195, v0=32544) After retessellation of defect 10 (v0=32544), euler #=-13 (130179,389769,259577) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=102, convex hull=138, v0=36049) After retessellation of defect 11 (v0=36049), euler #=-12 (130232,389992,259748) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=275, convex hull=257, v0=37633) After retessellation of defect 12 (v0=37633), euler #=-11 (130359,390499,260129) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=83, convex hull=137, v0=44132) After retessellation of defect 13 (v0=44132), euler #=-10 (130397,390672,260265) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=279, convex hull=235, v0=46527) After retessellation of defect 14 (v0=46527), euler #=-9 (130540,391219,260670) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=23, convex hull=56, v0=60200) After retessellation of defect 15 (v0=60200), euler #=-8 (130552,391279,260719) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=6, convex hull=12, v0=61082) After retessellation of defect 16 (v0=61082), euler #=-7 (130554,391289,260728) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=8, convex hull=25, v0=61123) After retessellation of defect 17 (v0=61123), euler #=-6 (130557,391305,260742) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=6, convex hull=26, v0=67901) After retessellation of defect 18 (v0=67901), euler #=-5 (130559,391319,260755) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=84, convex hull=122, v0=78033) After retessellation of defect 19 (v0=78033), euler #=-4 (130609,391518,260905) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=109, convex hull=143, v0=88396) After retessellation of defect 20 (v0=88396), euler #=-3 (130667,391760,261090) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=54, convex hull=28, v0=99495) After retessellation of defect 21 (v0=99495), euler #=-2 (130675,391793,261116) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=50, convex hull=72, v0=106668) After retessellation of defect 22 (v0=106668), euler #=-1 (130703,391905,261201) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=180, convex hull=215, v0=114064) After retessellation of defect 23 (v0=114064), euler #=0 (130794,392281,261487) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=250, convex hull=94, v0=114280) After retessellation of defect 24 (v0=114280), euler #=1 (130809,392367,261559) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=90, convex hull=119, v0=127382) After retessellation of defect 25 (v0=127382), euler #=2 (130852,392550,261700) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.02-->13.95) (max @ vno 13606 --> 15813) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.02-->13.95) (max @ vno 13606 --> 15813) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 69 mutations (35.6%), 125 crossovers (64.4%), 321 vertices were eliminated building final representation... 3480 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=130852, nf=261700, ne=392550, g=0) writing corrected surface to /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 350 intersecting 001: 37 intersecting 002: 5 intersecting terminating search with 0 intersecting topology fixing took 2.7 minutes FSRUNTIME@ mris_fix_topology lh 0.0455 hours 1 threads #VMPC# mris_fix_topology VmPeak 755536 @#@FSTIME 2024:08:07:17:25:22 mris_fix_topology N 14 e 163.65 S 0.23 U 163. 40 P 99% M 735944 F 18 R 219862 W 0 c 503 w 44 I 2112 O 12376 L 11.28 10.66 10.50 @#@FSLOADPOST 2024:08:07:17:28:05 mris_fix_topology N 14 10.48 10.58 10.50 #@# Fix Topology rh 公曆 20廿四年八月七日週三十七時廿八分五秒 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 0003 rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.4.1 7.4.1 before topology correction, eno=-62 (nv=129764, nf=259652, ne=389478, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 5716 ambiguous faces found in tessellation segmenting defects... 31 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 12 30 defects to be corrected 0 vertices coincident reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.4820 (-4.7410) -vertex loglikelihood: -6.8165 (-3.4082) -normal dot loglikelihood: -3.6692 (-3.6692) -quad curv loglikelihood: -5.8688 (-2.9344) Total Loglikelihood : -25.8364 CORRECTING DEFECT 0 (vertices=222, convex hull=187, v0=62) After retessellation of defect 0 (v0=62), euler #=-28 (126273,377339,251038) : difference with theory (-27) = 1 CORRECTING DEFECT 1 (vertices=308, convex hull=186, v0=943) After retessellation of defect 1 (v0=943), euler #=-27 (126359,377686,251300) : difference with theory (-26) = 1 CORRECTING DEFECT 2 (vertices=299, convex hull=243, v0=1269) After retessellation of defect 2 (v0=1269), euler #=-26 (126426,378001,251549) : difference with theory (-25) = 1 CORRECTING DEFECT 3 (vertices=27, convex hull=28, v0=7643) After retessellation of defect 3 (v0=7643), euler #=-25 (126429,378024,251570) : difference with theory (-24) = 1 CORRECTING DEFECT 4 (vertices=85, convex hull=111, v0=9239) After retessellation of defect 4 (v0=9239), euler #=-24 (126483,378235,251728) : difference with theory (-23) = 1 CORRECTING DEFECT 5 (vertices=320, convex hull=267, v0=10439) After retessellation of defect 5 (v0=10439), euler #=-23 (126632,378816,252161) : difference with theory (-22) = 1 CORRECTING DEFECT 6 (vertices=56, convex hull=63, v0=20922) After retessellation of defect 6 (v0=20922), euler #=-22 (126653,378904,252229) : difference with theory (-21) = 1 CORRECTING DEFECT 7 (vertices=229, convex hull=221, v0=29223) After retessellation of defect 7 (v0=29223), euler #=-21 (126726,379234,252487) : difference with theory (-20) = 1 CORRECTING DEFECT 8 (vertices=237, convex hull=197, v0=29276) After retessellation of defect 8 (v0=29276), euler #=-20 (126839,379674,252815) : difference with theory (-19) = 1 CORRECTING DEFECT 9 (vertices=193, convex hull=189, v0=35208) normal vector of length zero at vertex 127986 with 3 faces normal vector of length zero at vertex 127986 with 3 faces normal vector of length zero at vertex 127990 with 3 faces normal vector of length zero at vertex 127998 with 4 faces normal vector of length zero at vertex 127998 with 4 faces normal vector of length zero at vertex 127998 with 4 faces After retessellation of defect 9 (v0=35208), euler #=-19 (126909,379974,253046) : difference with theory (-18) = 1 CORRECTING DEFECT 10 (vertices=6, convex hull=21, v0=40311) After retessellation of defect 10 (v0=40311), euler #=-18 (126910,379983,253055) : difference with theory (-17) = 1 CORRECTING DEFECT 11 (vertices=21, convex hull=30, v0=40553) After retessellation of defect 11 (v0=40553), euler #=-17 (126916,380010,253077) : difference with theory (-16) = 1 CORRECTING DEFECT 12 (vertices=460, convex hull=360, v0=52977) After retessellation of defect 12 (v0=52977), euler #=-15 (127091,380724,253618) : difference with theory (-15) = 0 CORRECTING DEFECT 13 (vertices=17, convex hull=27, v0=53691) After retessellation of defect 13 (v0=53691), euler #=-14 (127094,380743,253635) : difference with theory (-14) = 0 CORRECTING DEFECT 14 (vertices=110, convex hull=125, v0=62704) After retessellation of defect 14 (v0=62704), euler #=-13 (127147,380963,253803) : difference with theory (-13) = 0 CORRECTING DEFECT 15 (vertices=32, convex hull=59, v0=64095) After retessellation of defect 15 (v0=64095), euler #=-12 (127165,381042,253865) : difference with theory (-12) = 0 CORRECTING DEFECT 16 (vertices=154, convex hull=163, v0=66535) After retessellation of defect 16 (v0=66535), euler #=-11 (127249,381374,254114) : difference with theory (-11) = 0 CORRECTING DEFECT 17 (vertices=5, convex hull=16, v0=72365) After retessellation of defect 17 (v0=72365), euler #=-10 (127250,381380,254120) : difference with theory (-10) = 0 CORRECTING DEFECT 18 (vertices=6, convex hull=22, v0=74779) After retessellation of defect 18 (v0=74779), euler #=-9 (127253,381394,254132) : difference with theory (-9) = 0 CORRECTING DEFECT 19 (vertices=18, convex hull=46, v0=81334) After retessellation of defect 19 (v0=81334), euler #=-8 (127262,381437,254167) : difference with theory (-8) = 0 CORRECTING DEFECT 20 (vertices=29, convex hull=70, v0=85891) After retessellation of defect 20 (v0=85891), euler #=-7 (127277,381509,254225) : difference with theory (-7) = 0 CORRECTING DEFECT 21 (vertices=58, convex hull=80, v0=90055) After retessellation of defect 21 (v0=90055), euler #=-6 (127308,381638,254324) : difference with theory (-6) = 0 CORRECTING DEFECT 22 (vertices=61, convex hull=43, v0=94515) After retessellation of defect 22 (v0=94515), euler #=-5 (127321,381692,254366) : difference with theory (-5) = 0 CORRECTING DEFECT 23 (vertices=9, convex hull=28, v0=97415) After retessellation of defect 23 (v0=97415), euler #=-4 (127323,381706,254379) : difference with theory (-4) = 0 CORRECTING DEFECT 24 (vertices=135, convex hull=42, v0=98383) After retessellation of defect 24 (v0=98383), euler #=-3 (127332,381750,254415) : difference with theory (-3) = 0 CORRECTING DEFECT 25 (vertices=165, convex hull=197, v0=112537) After retessellation of defect 25 (v0=112537), euler #=-2 (127401,382058,254655) : difference with theory (-2) = 0 CORRECTING DEFECT 26 (vertices=188, convex hull=159, v0=121916) After retessellation of defect 26 (v0=121916), euler #=-1 (127481,382367,254885) : difference with theory (-1) = 0 CORRECTING DEFECT 27 (vertices=15, convex hull=23, v0=124765) After retessellation of defect 27 (v0=124765), euler #=0 (127483,382379,254896) : difference with theory (0) = 0 CORRECTING DEFECT 28 (vertices=82, convex hull=99, v0=125754) After retessellation of defect 28 (v0=125754), euler #=1 (127522,382539,255018) : difference with theory (1) = 0 CORRECTING DEFECT 29 (vertices=27, convex hull=57, v0=129230) After retessellation of defect 29 (v0=129230), euler #=2 (127536,382602,255068) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.02-->9.09) (max @ vno 15793 --> 21757) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.02-->9.09) (max @ vno 15793 --> 21757) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 90 mutations (34.9%), 168 crossovers (65.1%), 78 vertices were eliminated building final representation... 2228 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=127536, nf=255068, ne=382602, g=0) writing corrected surface to /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 412 intersecting 001: 27 intersecting terminating search with 0 intersecting topology fixing took 2.4 minutes FSRUNTIME@ mris_fix_topology rh 0.0394 hours 1 threads #VMPC# mris_fix_topology VmPeak 750508 @#@FSTIME 2024:08:07:17:28:05 mris_fix_topology N 14 e 141.83 S 0.29 U 141. 53 P 99% M 732304 F 0 R 217954 W 0 c 370 w 20 I 0 O 12024 L 10.48 10.58 10.50 @#@FSLOADPOST 2024:08:07:17:30:27 mris_fix_topology N 14 10.19 10.49 10.48 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 130852 - 392550 + 261700 = 2 --> 0 holes F =2V-4: 261700 = 261704-4 (0) 2E=3F: 785100 = 785100 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 127536 - 382602 + 255068 = 2 --> 0 holes F =2V-4: 255068 = 255072-4 (0) 2E=3F: 765204 = 765204 (0) total defect index = 0 公曆 20廿四年八月七日週三十七時卅分廿八秒 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 cd /home/chang/GBM_Data/VBG/0003/0003/scripts /usr/local/freesurfer/bin/defect2seg --s 0003 --cortex freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 defect2seg 7.4.1 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux pid 678883 mri_label2label --label-cortex /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix /home/chang/GBM_Data/VBG/0003/0003/mri/aseg.presurf.mgz 0 /home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 6 non-cortical segments detected only using segment with 7612 vertices erasing segment 1 (vno[0] = 102116) erasing segment 2 (vno[0] = 102166) erasing segment 3 (vno[0] = 102199) erasing segment 4 (vno[0] = 103023) erasing segment 5 (vno[0] = 106757) mri_label2vol --defects /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix /home/chang/GBM_Data/VBG/0003/0003/surf/lh.defect_labels /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz 1000 0 /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz /home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz mris_defects_pointset -s /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix -d /home/chang/GBM_Data/VBG/0003/0003/surf/lh.defect_labels -o /home/chang/GBM_Data/VBG/0003/0003/surf/lh.defects.pointset --label /home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label Reading in surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.nofix Reading in defect segmentation /home/chang/GBM_Data/VBG/0003/0003/surf/lh.defect_labels Reading in label /home/chang/GBM_Data/VBG/0003/0003/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 177600 mris_defects_pointset done mri_label2label --label-cortex /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix /home/chang/GBM_Data/VBG/0003/0003/mri/aseg.presurf.mgz 0 /home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 19 non-cortical segments detected only using segment with 7828 vertices erasing segment 0 (vno[0] = 29124) erasing segment 1 (vno[0] = 29136) erasing segment 2 (vno[0] = 30107) erasing segment 3 (vno[0] = 30189) erasing segment 4 (vno[0] = 31165) erasing segment 5 (vno[0] = 33343) erasing segment 7 (vno[0] = 58089) erasing segment 8 (vno[0] = 60517) erasing segment 9 (vno[0] = 86191) erasing segment 10 (vno[0] = 89279) erasing segment 11 (vno[0] = 96444) erasing segment 12 (vno[0] = 97210) erasing segment 13 (vno[0] = 97362) erasing segment 14 (vno[0] = 98209) erasing segment 15 (vno[0] = 98249) erasing segment 16 (vno[0] = 99207) erasing segment 17 (vno[0] = 114165) erasing segment 18 (vno[0] = 116301) mri_label2vol --defects /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix /home/chang/GBM_Data/VBG/0003/0003/surf/rh.defect_labels /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz 2000 1 /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz /home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /home/chang/GBM_Data/VBG/0003/0003/mri/surface.defects.mgz mris_defects_pointset -s /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix -d /home/chang/GBM_Data/VBG/0003/0003/surf/rh.defect_labels -o /home/chang/GBM_Data/VBG/0003/0003/surf/rh.defects.pointset --label /home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label Reading in surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.nofix Reading in defect segmentation /home/chang/GBM_Data/VBG/0003/0003/surf/rh.defect_labels Reading in label /home/chang/GBM_Data/VBG/0003/0003/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 172060 mris_defects_pointset done Started at 公曆 20廿四年八月七日週三十七時卅分廿八秒 Ended at 公曆 20廿四年八月七日週三十七時卅分44秒 Defect2seg-Run-Time-Sec 16 Defect2seg-Run-Time-Min 0.32 Defect2seg-Run-Time-Hours 0.00 tkmeditfv 0003 brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:08:07:17:30:28 defect2seg N 3 e 16.56 S 0.44 U 16.12 P 100% M 379692 F 56 R 439303 W 0 c 79 w 256 I 13280 O 21904 L 10.19 10.49 10.48 @#@FSLOADPOST 2024:08:07:17:30:44 defect2seg N 3 10.15 10.47 10.48 mris_remesh --remesh --iters 3 --input /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig.premesh --output /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.715263 remeshing to edge length 0.715263 with 3 iterations avg qual before : 0.888071 after: 0.97149 Removing intersections Remeshed surface quality stats nv0 = 130852 nv = 136375 1.04221 Area 272746 0.30605 0.03364 0.091724 0.4745 Corner 818238 60.00000 8.74347 16.982359 144.8765 Edge 409119 0.84866 0.08239 0.453496 1.2830 Hinge 409119 9.13168 9.22303 0.000000 164.8331 mris_remesh done @#@FSTIME 2024:08:07:17:30:44 mris_remesh N 7 e 22.07 S 0.25 U 21.78 P 99% M 732392 F 22 R 277722 W 0 c 71 w 250 I 3656 O 9592 L 10.15 10.47 10.48 @#@FSLOADPOST 2024:08:07:17:31:06 mris_remesh N 7 10.38 10.52 10.49 mris_remesh --remesh --iters 3 --input /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig.premesh --output /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.713047 remeshing to edge length 0.713047 with 3 iterations avg qual before : 0.88755 after: 0.971537 Removing intersections Remeshed surface quality stats nv0 = 127536 nv = 132793 1.04122 Area 265582 0.30442 0.03356 0.080014 0.5220 Corner 796746 60.00000 8.74022 15.729575 147.2339 Edge 398373 0.84637 0.08211 0.473788 1.2690 Hinge 398373 9.28281 9.32584 0.000009 132.5121 mris_remesh done @#@FSTIME 2024:08:07:17:31:06 mris_remesh N 7 e 19.82 S 0.27 U 19.53 P 99% M 711844 F 0 R 263256 W 0 c 56 w 183 I 0 O 9344 L 10.38 10.52 10.49 @#@FSLOADPOST 2024:08:07:17:31:26 mris_remesh N 7 10.77 10.60 10.52 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/lh.orig @#@FSTIME 2024:08:07:17:31:26 mris_remove_intersection N 2 e 2.82 S 0.09 U 2.73 P 99% M 330452 F 21 R 94642 W 0 c 10 w 26 I 3952 O 9592 L 10.77 10.60 10.52 @#@FSLOADPOST 2024:08:07:17:31:29 mris_remove_intersection N 2 10.71 10.59 10.52 rm -f ../surf/lh.inflated /home/chang/GBM_Data/VBG/0003/0003/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/rh.orig @#@FSTIME 2024:08:07:17:31:29 mris_remove_intersection N 2 e 2.52 S 0.12 U 2.39 P 99% M 322292 F 0 R 92542 W 0 c 12 w 8 I 0 O 9344 L 10.71 10.59 10.52 @#@FSLOADPOST 2024:08:07:17:31:32 mris_remove_intersection N 2 10.71 10.59 10.52 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh 公曆 20廿四年八月七日週三十七時卅一分32秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 249897 voxels (1.49%) border gray 269695 voxels (1.61%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.0 +- 8.4 [70.0 --> 110.0] CCS GM (73.0) : 70.7 +- 12.7 [30.0 --> 110.0] white_mean = 98.9893 +/- 8.36131, gray_mean = 70.7223 +/- 12.7089 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=168 nbins=169 intensity peaks found at WM=104+-5.2, GM=64+-15.7 white_mode = 104, gray_mode = 64 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 51.3 (was 70.000000) setting MAX_BORDER_WHITE to 112.4 (was 105.000000) setting MIN_BORDER_WHITE to 64.0 (was 85.000000) setting MAX_CSF to 38.6 (was 40.000000) setting MAX_GRAY to 95.6 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 51.3 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 25.9 (was 40.000000) When placing the white surface white_border_hi = 112.361; white_border_low = 64; white_outside_low = 51.2911; white_inside_hi = 120; white_outside_hi = 112.361; When placing the pial surface pial_border_hi = 51.2911; pial_border_low = 25.8734; pial_outside_low = 10; pial_inside_hi = 95.6387; pial_outside_hi = 44.9367; #VMPC# mris_autodet_gwstats VmPeak 254600 mris_autodet_gwstats done @#@FSTIME 2024:08:07:17:31:32 mris_autodet_gwstats N 8 e 2.03 S 0.07 U 1.95 P 99% M 235796 F 24 R 65987 W 0 c 8 w 20 I 4576 O 8 L 10.81 10.61 10.53 @#@FSLOADPOST 2024:08:07:17:31:34 mris_autodet_gwstats N 8 10.81 10.61 10.53 #-------------------------------------------- #@# AutoDetGWStats rh 公曆 20廿四年八月七日週三十七時卅一分34秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 249897 voxels (1.49%) border gray 269695 voxels (1.61%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.0 +- 8.4 [70.0 --> 110.0] CCS GM (73.0) : 70.7 +- 12.7 [30.0 --> 110.0] white_mean = 98.9893 +/- 8.36131, gray_mean = 70.7223 +/- 12.7089 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=168 nbins=169 intensity peaks found at WM=104+-6.1, GM=62+-18.3 white_mode = 104, gray_mode = 62 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70.000000) setting MAX_BORDER_WHITE to 112.4 (was 105.000000) setting MIN_BORDER_WHITE to 62.0 (was 85.000000) setting MAX_CSF to 36.6 (was 40.000000) setting MAX_GRAY to 95.6 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 23.9 (was 40.000000) When placing the white surface white_border_hi = 112.361; white_border_low = 62; white_outside_low = 49.2911; white_inside_hi = 120; white_outside_hi = 112.361; When placing the pial surface pial_border_hi = 49.2911; pial_border_low = 23.8734; pial_outside_low = 10; pial_inside_hi = 95.6387; pial_outside_hi = 42.9367; #VMPC# mris_autodet_gwstats VmPeak 249900 mris_autodet_gwstats done @#@FSTIME 2024:08:07:17:31:34 mris_autodet_gwstats N 8 e 1.93 S 0.04 U 1.88 P 100% M 230612 F 0 R 64725 W 0 c 13 w 1 I 0 O 8 L 10.81 10.61 10.53 @#@FSLOADPOST 2024:08:07:17:31:36 mris_autodet_gwstats N 8 10.81 10.61 10.53 #-------------------------------------------- #@# WhitePreAparc lh 公曆 20廿四年八月七日週三十七時卅一分36秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations Area 272746 0.27449 0.06222 0.002558 0.5929 Corner 818238 60.00000 8.91476 8.209122 160.4169 Edge 409119 0.79945 0.11110 0.053273 1.3467 Hinge 409119 6.15827 5.96714 0.000031 133.2966 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=6971, nmarked2=0, nripped=6971 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68188: xyz = (-28.9837,-16.6139,32.7592) oxyz = (-28.9837,-16.6139,32.7592) wxzy = (-28.9837,-16.6139,32.7592) pxyz = (0,0,0) CBVO Creating mask 136375 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6971 #FML# MRISripMidline(): nmarked=6971, nmarked2=0, nripped=6971 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=2 had to be increased for 174 vertices, nripped=6971 mean border=79.9, 283 (283) missing vertices, mean dist 0.3 [0.5 (%37.7)->0. 9 (%62.3))] %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1092 min Finding expansion regions mean absolute distance = 0.74 +- 0.98 5336 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=3510442.2, rms=11.405 001: dt: 0.5000, sse=1837154.5, rms=8.085 (29.107%) 002: dt: 0.5000, sse=1161537.2, rms=6.264 (22.530%) 003: dt: 0.5000, sse=836888.6, rms=5.163 (17.571%) 004: dt: 0.5000, sse=670005.9, rms=4.490 (13.044%) 005: dt: 0.5000, sse=581758.4, rms=4.083 (9.061%) 006: dt: 0.5000, sse=537952.8, rms=3.854 (5.609%) 007: dt: 0.5000, sse=512957.6, rms=3.719 (3.488%) 008: dt: 0.5000, sse=501343.3, rms=3.645 (2.004%) rms = 3.6070/3.6449, sse=494225.2/501343.4, time step reduction 1 of 3 to 0. 250 0 0 1 009: dt: 0.5000, sse=494225.2, rms=3.607 (1.041%) 010: dt: 0.2500, sse=254779.7, rms=1.899 (47.362%) 011: dt: 0.2500, sse=212998.3, rms=1.433 (24.544%) 012: dt: 0.2500, sse=202290.4, rms=1.270 (11.376%) 013: dt: 0.2500, sse=196069.9, rms=1.183 (6.831%) rms = 1.1461/1.1829, sse=196967.0/196069.9, time step reduction 2 of 3 to 0. 125 0 1 1 014: dt: 0.2500, sse=196967.0, rms=1.146 (3.112%) 015: dt: 0.1250, sse=191625.9, rms=1.051 (8.311%) rms = 1.0389/1.0509, sse=187967.0/191625.9, time step reduction 3 of 3 to 0. 062 0 0 1 016: dt: 0.1250, sse=187967.0, rms=1.039 (1.140%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6971 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7123, nmarked2=0, nripped=7123 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=1 had to be increased for 87 vertices, nripped=7123 mean border=82.2, 184 (107) missing vertices, mean dist -0.3 [0.5 (%65.6)->0.2 (%34.4))] %64 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0759 min Finding expansion regions mean absolute distance = 0.41 +- 0.84 5487 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=695346.3, rms=4.334 017: dt: 0.5000, sse=476271.4, rms=3.183 (26.556%) rms = 3.3847/3.1829, sse=511297.8/476271.4, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=365999.0, rms=2.412 (24.217%) 019: dt: 0.2500, sse=300724.7, rms=1.843 (23.590%) 020: dt: 0.2500, sse=271759.8, rms=1.534 (16.773%) 021: dt: 0.2500, sse=257332.0, rms=1.349 (12.079%) 022: dt: 0.2500, sse=248794.5, rms=1.220 (9.505%) 023: dt: 0.2500, sse=245329.3, rms=1.129 (7.480%) 024: dt: 0.2500, sse=242380.4, rms=1.067 (5.464%) rms = 1.0192/1.0675, sse=253121.2/242380.4, time step reduction 2 of 3 to 0. 125 0 1 1 025: dt: 0.2500, sse=253121.2, rms=1.019 (4.520%) rms = 0.9751/1.0192, sse=264779.5/253121.2, time step reduction 3 of 3 to 0. 062 0 1 1 026: dt: 0.1250, sse=264779.5, rms=0.975 (4.328%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7123 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7124, nmarked2=0, nripped=7124 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 115 vertices, nripped=7124 mean border=84.0, 181 (94) missing vertices, mean dist -0.2 [0.4 (%64.7)->0. 2 (%35.3))] %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0422 min Finding expansion regions mean absolute distance = 0.35 +- 0.66 5037 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=479384.2, rms=3.083 027: dt: 0.5000, sse=369465.4, rms=2.480 (19.559%) rms = 2.8765/2.4801, sse=420014.1/369465.4, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=282188.3, rms=1.702 (31.387%) 029: dt: 0.2500, sse=249428.6, rms=1.223 (28.135%) 030: dt: 0.2500, sse=236799.2, rms=1.029 (15.888%) 031: dt: 0.2500, sse=234373.3, rms=0.946 (8.019%) rms = 0.9138/0.9461, sse=231459.3/234373.3, time step reduction 2 of 3 to 0. 125 0 0 1 032: dt: 0.2500, sse=231459.3, rms=0.914 (3.420%) 033: dt: 0.1250, sse=227292.4, rms=0.860 (5.877%) rms = 0.8519/0.8601, sse=227134.7/227292.4, time step reduction 3 of 3 to 0. 062 0 0 1 034: dt: 0.1250, sse=227134.7, rms=0.852 (0.950%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7124 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7132, nmarked2=0, nripped=7132 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 126 vertices, nripped=7132 mean border=84.9, 183 (88) missing vertices, mean dist -0.1 [0.4 (%56.2)->0. 2 (%43.8))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0268 min Finding expansion regions mean absolute distance = 0.31 +- 0.55 4538 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=293603.2, rms=1.868 rms = 1.6913/1.8683, sse=294285.6/293603.2, time step reduction 1 of 3 to 0. 250 0 1 0 035: dt: 0.5000, sse=294285.7, rms=1.691 (9.477%) 036: dt: 0.2500, sse=235204.7, rms=1.038 (38.651%) 037: dt: 0.2500, sse=224320.8, rms=0.852 (17.888%) rms = 0.8649/0.8520, sse=231503.8/224320.8, time step reduction 2 of 3 to 0. 125 0 1 1 RMS increased, rejecting step 038: dt: 0.1250, sse=221693.5, rms=0.791 (7.141%) rms = 0.7015/0.7911, sse=223918.3/221693.5, time step reduction 3 of 3 to 0. 062 0 1 0 039: dt: 0.1250, sse=223918.3, rms=0.702 (11.324%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.61 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2181584 mris_place_surface done @#@FSTIME 2024:08:07:17:31:36 mris_place_surface N 18 e 161.10 S 0.56 U 160.51 P 99% M 1923004 F 13 R 504279 W 0 c 522 w 100 I 1976 O 9592 L 10.81 10.61 10.53 @#@FSLOADPOST 2024:08:07:17:34:17 mris_place_surface N 18 10.60 10.65 10.56 #-------------------------------------------- #@# WhitePreAparc rh 公曆 20廿四年八月七日週三十七時34分十七秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations Area 265582 0.27191 0.06213 0.009507 0.6410 Corner 796746 60.00000 8.91331 15.619468 143.3381 Edge 398373 0.79557 0.11136 0.127784 1.3356 Hinge 398373 6.33360 6.08459 0.000015 129.9691 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=7243, nmarked2=15, nripped=7243 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 66397: xyz = (50.0673,-13.5794,19.2827) oxyz = (50.0673,-13.5794,19.2827) wxzy = (50.0673,-13.5794,19.2827) pxyz = (0,0,0) CBVO Creating mask 132793 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7243 #FML# MRISripMidline(): nmarked=7243, nmarked2=15, nripped=7243 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=2 had to be increased for 197 vertices, nripped=7243 mean border=79.5, 85 (85) missing vertices, mean dist 0.3 [0.6 (%38.1)->0.9 (%61.9))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1083 min Finding expansion regions mean absolute distance = 0.79 +- 1.07 5662 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=3562774.8, rms=11.669 001: dt: 0.5000, sse=1944082.5, rms=8.473 (27.394%) 002: dt: 0.5000, sse=1271436.0, rms=6.709 (20.819%) 003: dt: 0.5000, sse=917817.3, rms=5.558 (17.157%) 004: dt: 0.5000, sse=729986.0, rms=4.832 (13.052%) 005: dt: 0.5000, sse=615465.8, rms=4.328 (10.429%) 006: dt: 0.5000, sse=561660.8, rms=4.062 (6.152%) 007: dt: 0.5000, sse=527542.3, rms=3.862 (4.927%) 008: dt: 0.5000, sse=512620.0, rms=3.787 (1.944%) 009: dt: 0.5000, sse=501858.6, rms=3.704 (2.200%) rms = 3.6931/3.7036, sse=495481.9/501858.6, time step reduction 1 of 3 to 0. 250 0 0 1 010: dt: 0.5000, sse=495481.9, rms=3.693 (0.285%) 011: dt: 0.2500, sse=252359.9, rms=1.967 (46.751%) 012: dt: 0.2500, sse=211218.6, rms=1.514 (23.007%) 013: dt: 0.2500, sse=200146.5, rms=1.355 (10.506%) 014: dt: 0.2500, sse=194912.3, rms=1.268 (6.444%) rms = 1.2262/1.2677, sse=193616.4/194912.3, time step reduction 2 of 3 to 0. 125 0 0 1 015: dt: 0.2500, sse=193616.4, rms=1.226 (3.273%) 016: dt: 0.1250, sse=185492.3, rms=1.111 (9.361%) rms = 1.0956/1.1114, sse=185089.9/185492.3, time step reduction 3 of 3 to 0. 062 0 0 1 017: dt: 0.1250, sse=185089.9, rms=1.096 (1.429%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7243 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7358, nmarked2=28, nripped=7358 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=1 had to be increased for 83 vertices, nripped=7358 mean border=81.5, 155 (23) missing vertices, mean dist -0.2 [0.5 (%64.0)->0. 3 (%36.0))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0780 min Finding expansion regions mean absolute distance = 0.42 +- 0.86 5520 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=683148.7, rms=4.353 018: dt: 0.5000, sse=480223.1, rms=3.298 (24.239%) rms = 3.5460/3.2979, sse=530335.2/480223.1, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=361994.4, rms=2.483 (24.705%) 020: dt: 0.2500, sse=298075.1, rms=1.889 (23.916%) 021: dt: 0.2500, sse=271548.9, rms=1.561 (17.400%) 022: dt: 0.2500, sse=262395.0, rms=1.366 (12.446%) 023: dt: 0.2500, sse=248962.8, rms=1.243 (9.040%) 024: dt: 0.2500, sse=248095.7, rms=1.154 (7.143%) rms = 1.0976/1.1540, sse=249059.1/248095.7, time step reduction 2 of 3 to 0. 125 0 1 0 025: dt: 0.2500, sse=249059.1, rms=1.098 (4.890%) rms = 1.0283/1.0976, sse=249164.9/249059.1, time step reduction 3 of 3 to 0. 062 0 1 0 026: dt: 0.1250, sse=249164.9, rms=1.028 (6.315%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7358 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7381, nmarked2=28, nripped=7381 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 118 vertices, nripped=7381 mean border=83.3, 137 (17) missing vertices, mean dist -0.2 [0.4 (%64.0)->0. 2 (%36.0))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0408 min Finding expansion regions mean absolute distance = 0.35 +- 0.66 5015 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=435865.3, rms=2.958 027: dt: 0.5000, sse=369905.2, rms=2.518 (14.873%) rms = 3.0289/2.5179, sse=436262.3/369905.1, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=286725.1, rms=1.710 (32.099%) 029: dt: 0.2500, sse=253819.9, rms=1.259 (26.366%) 030: dt: 0.2500, sse=235221.5, rms=1.070 (15.022%) 031: dt: 0.2500, sse=230755.0, rms=0.992 (7.259%) rms = 0.9640/0.9921, sse=230331.3/230755.0, time step reduction 2 of 3 to 0. 125 0 0 1 032: dt: 0.2500, sse=230331.3, rms=0.964 (2.836%) 033: dt: 0.1250, sse=223829.9, rms=0.896 (7.104%) rms = 0.8850/0.8955, sse=223368.9/223829.9, time step reduction 3 of 3 to 0. 062 0 0 1 034: dt: 0.1250, sse=223368.9, rms=0.885 (1.173%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7381 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7400, nmarked2=28, nripped=7400 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 113 vertices, nripped=7400 mean border=84.1, 144 (9) missing vertices, mean dist -0.1 [0.4 (%56.1)->0.3 (%43.9))] %76 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0291 min Finding expansion regions mean absolute distance = 0.32 +- 0.55 4705 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=287258.4, rms=1.879 035: dt: 0.5000, sse=284827.0, rms=1.780 (5.265%) rms = 2.4401/1.7800, sse=351464.8/284827.0, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=232336.6, rms=1.083 (39.157%) 037: dt: 0.2500, sse=220988.4, rms=0.857 (20.860%) 038: dt: 0.2500, sse=219423.3, rms=0.784 (8.470%) rms = 0.7927/0.7845, sse=223985.8/219423.3, time step reduction 2 of 3 to 0. 125 0 1 1 RMS increased, rejecting step rms = 0.7570/0.7845, sse=218440.6/219423.3, time step reduction 3 of 3 to 0. 062 0 0 1 039: dt: 0.1250, sse=218440.7, rms=0.757 (3.506%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.58 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2156700 mris_place_surface done @#@FSTIME 2024:08:07:17:34:17 mris_place_surface N 18 e 158.93 S 0.58 U 158.34 P 99% M 1897548 F 0 R 497418 W 0 c 553 w 14 I 0 O 9344 L 10.60 10.65 10.56 @#@FSLOADPOST 2024:08:07:17:36:56 mris_place_surface N 18 11.07 10.78 10.62 #-------------------------------------------- #@# CortexLabel lh 公曆 20廿四年八月七日週三十七時36分56秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 4 non-cortical segments detected only using segment with 8548 vertices erasing segment 1 (vno[0] = 85124) erasing segment 2 (vno[0] = 116733) erasing segment 3 (vno[0] = 126247) @#@FSTIME 2024:08:07:17:36:56 mri_label2label N 5 e 8.38 S 0.11 U 8.27 P 100% M 315248 F 0 R 93972 W 0 c 30 w 4 I 0 O 11160 L 11.07 10.78 10.62 @#@FSLOADPOST 2024:08:07:17:37:05 mri_label2label N 5 11.67 10.92 10.67 #-------------------------------------------- #@# CortexLabel+HipAmyg lh 公曆 20廿四年八月七日週三十七時37分五秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 4 non-cortical segments detected only using segment with 6801 vertices erasing segment 1 (vno[0] = 85124) erasing segment 2 (vno[0] = 116733) erasing segment 3 (vno[0] = 126247) @#@FSTIME 2024:08:07:17:37:05 mri_label2label N 5 e 8.30 S 0.11 U 8.19 P 99% M 315056 F 0 R 93994 W 0 c 22 w 2 I 0 O 11312 L 11.67 10.92 10.67 @#@FSLOADPOST 2024:08:07:17:37:13 mri_label2label N 5 11.34 10.87 10.65 #-------------------------------------------- #@# CortexLabel rh 公曆 20廿四年八月七日週三十七時37分十三秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 7 non-cortical segments detected only using segment with 8549 vertices erasing segment 0 (vno[0] = 23127) erasing segment 1 (vno[0] = 25756) erasing segment 3 (vno[0] = 33919) erasing segment 4 (vno[0] = 82304) erasing segment 5 (vno[0] = 83828) erasing segment 6 (vno[0] = 86921) @#@FSTIME 2024:08:07:17:37:13 mri_label2label N 5 e 7.94 S 0.08 U 7.85 P 99% M 324336 F 0 R 98121 W 0 c 25 w 5 I 0 O 10616 L 11.34 10.87 10.65 @#@FSLOADPOST 2024:08:07:17:37:21 mri_label2label N 5 11.39 10.89 10.66 #-------------------------------------------- #@# CortexLabel+HipAmyg rh 公曆 20廿四年八月七日週三十七時37分廿一秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 8 non-cortical segments detected only using segment with 6937 vertices erasing segment 0 (vno[0] = 23127) erasing segment 1 (vno[0] = 25756) erasing segment 3 (vno[0] = 33919) erasing segment 4 (vno[0] = 52453) erasing segment 5 (vno[0] = 82304) erasing segment 6 (vno[0] = 83828) erasing segment 7 (vno[0] = 86921) @#@FSTIME 2024:08:07:17:37:22 mri_label2label N 5 e 7.61 S 0.09 U 7.51 P 99% M 329168 F 0 R 100494 W 0 c 20 w 2 I 0 O 10736 L 11.39 10.89 10.66 @#@FSLOADPOST 2024:08:07:17:37:29 mri_label2label N 5 11.33 10.90 10.66 #-------------------------------------------- #@# Smooth2 lh 公曆 20廿四年八月七日週三十七時37分廿九秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2024:08:07:17:37:29 mris_smooth N 7 e 1.42 S 0.08 U 1.33 P 99% M 208772 F 0 R 62525 W 0 c 13 w 7 I 0 O 9592 L 11.33 10.90 10.66 @#@FSLOADPOST 2024:08:07:17:37:31 mris_smooth N 7 11.33 10.90 10.66 #-------------------------------------------- #@# Smooth2 rh 公曆 20廿四年八月七日週三十七時37分卅一秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2024:08:07:17:37:31 mris_smooth N 7 e 1.64 S 0.06 U 1.57 P 99% M 203340 F 0 R 60884 W 0 c 20 w 10 I 0 O 9344 L 11.33 10.90 10.66 @#@FSLOADPOST 2024:08:07:17:37:32 mris_smooth N 7 11.30 10.90 10.67 #-------------------------------------------- #@# Inflation2 lh 公曆 20廿四年八月七日週三十七時37分32秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.6 mm, total surface area = 84453 mm^2 step 000: RMS=0.161 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (target=0.015) writing inflated surface to ../surf/lh. inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 11.422791 mris_inflate stimesec 0.439953 mris_inflate ru_maxrss 209792 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 449848 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 184 mris_inflate ru_oublock 10672 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 32 @#@FSTIME 2024:08:07:17:37:32 mris_inflate N 2 e 11.87 S 0.44 U 11.42 P 99% M 209792 F 1 R 449855 W 0 c 32 w 6 I 184 O 10672 L 11.30 10.90 10.67 @#@FSLOADPOST 2024:08:07:17:37:44 mris_inflate N 2 11.33 10.92 10.68 #-------------------------------------------- #@# Inflation2 rh 公曆 20廿四年八月七日週三十七時37分44秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.0 mm, total surface area = 82720 mm^2 step 000: RMS=0.165 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (target=0.015) writing inflated surface to ../surf/rh. inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 11.928528 mris_inflate stimesec 0.588026 mris_inflate ru_maxrss 204564 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 522193 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10384 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 44 @#@FSTIME 2024:08:07:17:37:44 mris_inflate N 2 e 12.52 S 0.59 U 11.92 P 99% M 204564 F 0 R 522199 W 0 c 44 w 6 I 0 O 10384 L 11.33 10.92 10.68 @#@FSLOADPOST 2024:08:07:17:37:57 mris_inflate N 2 11.44 10.96 10.69 #-------------------------------------------- #@# Curv .H and .K lh 公曆 20廿四年八月七日週三十七時37分57秒 /home/chang/GBM_Data/VBG/0003/0003/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 20.595*4pi (258.800) --> -20 handles ICI = 176.0, FI = 1137.6, variation=20146.676 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. @#@FSTIME 2024:08:07:17:37:57 mris_curvature N 4 e 0.89 S 0.04 U 0.85 P 99% M 155496 F 9 R 42029 W 0 c 6 w 8 I 968 O 2144 L 11.44 10.96 10.69 @#@FSLOADPOST 2024:08:07:17:37:58 mris_curvature N 4 11.32 10.94 10.69 rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 164 vertices thresholded to be in k1 ~ [-0.68 0.38], k2 ~ [-0.13 0.08] total integrated curvature = 0.373*4pi (4.688) --> 1 handles ICI = 1.4, FI = 8.6, variation=150.433 127 vertices thresholded to be in [-0.02 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 119 vertices thresholded to be in [-0.23 0.18] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. @#@FSTIME 2024:08:07:17:37:58 mris_curvature N 12 e 28.37 S 0.12 U 28.24 P 99% M 368956 F 0 R 95437 W 0 c 92 w 3 I 0 O 2144 L 11.32 10.94 10.69 @#@FSLOADPOST 2024:08:07:17:38:26 mris_curvature N 12 10.70 10.82 10.65 #-------------------------------------------- #@# Curv .H and .K rh 公曆 20廿四年八月七日週三十七時38分廿六秒 /home/chang/GBM_Data/VBG/0003/0003/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 21.584*4pi (271.234) --> -21 handles ICI = 185.4, FI = 1230.1, variation=21625.765 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. @#@FSTIME 2024:08:07:17:38:26 mris_curvature N 4 e 0.94 S 0.05 U 0.89 P 99% M 152308 F 0 R 40933 W 0 c 8 w 2 I 0 O 2080 L 10.70 10.82 10.65 @#@FSLOADPOST 2024:08:07:17:38:27 mris_curvature N 4 10.70 10.82 10.65 rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 217 vertices thresholded to be in k1 ~ [-0.25 0.43], k2 ~ [-0.12 0.05] total integrated curvature = 0.360*4pi (4.523) --> 1 handles ICI = 1.4, FI = 8.6, variation=149.486 131 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 154 vertices thresholded to be in [-0.15 0.21] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. @#@FSTIME 2024:08:07:17:38:27 mris_curvature N 12 e 27.74 S 0.13 U 27.61 P 99% M 358716 F 0 R 92949 W 0 c 112 w 2 I 0 O 2080 L 10.70 10.82 10.65 @#@FSLOADPOST 2024:08:07:17:38:55 mris_curvature N 12 10.78 10.83 10.66 #-------------------------------------------- #@# Sphere lh 公曆 20廿四年八月七日週三十七時38分55秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.307... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.42 pass 1: epoch 2 of 3 starting distance error %21.37 unfolding complete - removing small folds... starting distance error %21.31 removing remaining folds... final distance error %21.36 MRISunfold() return, current seed 1234 -01: dt=0.0000, 3 negative triangles VmPeak 537716 154: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0728 hours FSRUNTIME@ mris_sphere 0.0728 hours 1 threads #VMPC# mris_sphere VmPeak 537716 mris_sphere done @#@FSTIME 2024:08:07:17:38:55 mris_sphere N 4 e 262.21 S 12.08 U 250.10 P 99% M 279856 F 0 R 11513000 W 0 c 1162 w 92 I 0 O 9600 L 10.78 10.83 10.66 @#@FSLOADPOST 2024:08:07:17:43:17 mris_sphere N 4 11.21 11.01 10.77 #-------------------------------------------- #@# Sphere rh 公曆 20廿四年八月七日週三十七時43分十七秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.310... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %44.01 pass 1: epoch 2 of 3 starting distance error %22.08 unfolding complete - removing small folds... starting distance error %21.95 removing remaining folds... final distance error %21.99 MRISunfold() return, current seed 1234 -01: dt=0.0000, 2 negative triangles VmPeak 530576 149: dt=0.9900, 2 negative triangles 150: dt=0.9405, 2 negative triangles 151: dt=0.9405, 1 negative triangles 152: dt=0.9405, 1 negative triangles 153: dt=0.9405, 3 negative triangles 154: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0617 hours FSRUNTIME@ mris_sphere 0.0617 hours 1 threads #VMPC# mris_sphere VmPeak 530576 mris_sphere done @#@FSTIME 2024:08:07:17:43:17 mris_sphere N 4 e 222.18 S 11.35 U 210.79 P 99% M 272708 F 0 R 10911357 W 0 c 911 w 249 I 0 O 9344 L 11.21 11.01 10.77 @#@FSLOADPOST 2024:08:07:17:46:59 mris_sphere N 4 9.94 10.60 10.68 #-------------------------------------------- #@# Surf Reg lh 公曆 20廿四年八月七日週三十七時46分59秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/chang/GBM_Data/VBG/0003/0003/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=chang, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.720 curvature mean = 0.046, std = 0.815 curvature mean = 0.004, std = 0.858 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (5.00, -6.00, -12.50) sse = 212802.5, elapsed since starting=0.2022 min MRISrigidBodyAlignGlobal() done 0.20 min curvature mean = 0.029, std = 0.839 curvature mean = 0.000, std = 0.944 curvature mean = 0.027, std = 0.850 curvature mean = -0.000, std = 0.976 curvature mean = 0.027, std = 0.854 curvature mean = -0.000, std = 0.989 2 Reading smoothwm curvature mean = -0.017, std = 0.226 curvature mean = 0.045, std = 0.247 curvature mean = 0.028, std = 0.445 curvature mean = 0.044, std = 0.302 curvature mean = 0.021, std = 0.657 curvature mean = 0.044, std = 0.328 curvature mean = 0.010, std = 0.800 curvature mean = 0.043, std = 0.340 curvature mean = 0.003, std = 0.890 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 519808 registration took 0.06 hours #VMPC# mris_register VmPeak 519808 FSRUNTIME@ mris_register 0.0581 hours 1 threads @#@FSTIME 2024:08:07:17:46:59 mris_register N 4 e 209.08 S 7.61 U 201.43 P 99% M 261452 F 18 R 7515214 W 0 c 768 w 200 I 8128 O 9600 L 9.94 10.60 10.68 @#@FSLOADPOST 2024:08:07:17:50:28 mris_register N 4 10.44 10.62 10.68 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh 公曆 20廿四年八月七日週三十七時50分廿八秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/chang/GBM_Data/VBG/0003/0003/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chang, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=chang, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.658 curvature mean = 0.050, std = 0.822 curvature mean = -0.000, std = 0.858 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (6.50, -3.50, -4.50) sse = 224771.5, elapsed since starting=0.1902 min MRISrigidBodyAlignGlobal() done 0.19 min curvature mean = 0.029, std = 0.830 curvature mean = -0.001, std = 0.948 curvature mean = 0.025, std = 0.839 curvature mean = -0.000, std = 0.979 curvature mean = 0.023, std = 0.840 curvature mean = -0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.015, std = 0.232 curvature mean = 0.039, std = 0.237 curvature mean = 0.023, std = 0.438 curvature mean = 0.039, std = 0.293 curvature mean = 0.019, std = 0.651 curvature mean = 0.038, std = 0.319 curvature mean = 0.009, std = 0.796 curvature mean = 0.038, std = 0.330 curvature mean = 0.002, std = 0.887 MRISregister() return, current seed 0 -01: dt=0.0000, 1 negative triangles VmPeak 515992 112: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.06 hours #VMPC# mris_register VmPeak 515992 FSRUNTIME@ mris_register 0.0626 hours 1 threads @#@FSTIME 2024:08:07:17:50:28 mris_register N 4 e 225.33 S 7.68 U 217.61 P 99% M 257012 F 0 R 7460050 W 0 c 780 w 301 I 5584 O 9344 L 10.44 10.62 10.68 @#@FSLOADPOST 2024:08:07:17:54:14 mris_register N 4 11.27 10.78 10.72 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh 公曆 20廿四年八月七日週三十七時54分十四秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2024:08:07:17:54:14 mris_jacobian N 3 e 0.63 S 0.08 U 0.54 P 99% M 209104 F 5 R 62485 W 0 c 2 w 8 I 648 O 1072 L 11.27 10.78 10.72 @#@FSLOADPOST 2024:08:07:17:54:14 mris_jacobian N 3 11.27 10.78 10.72 #-------------------------------------------- #@# Jacobian white rh 公曆 20廿四年八月七日週三十七時54分十四秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2024:08:07:17:54:14 mris_jacobian N 3 e 0.50 S 0.06 U 0.43 P 99% M 203228 F 0 R 60864 W 0 c 8 w 3 I 0 O 1040 L 11.27 10.78 10.72 @#@FSLOADPOST 2024:08:07:17:54:15 mris_jacobian N 3 11.27 10.78 10.72 #-------------------------------------------- #@# AvgCurv lh 公曆 20廿四年八月七日週三十七時54分十五秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2024:08:07:17:54:15 mrisp_paint N 5 e 0.42 S 0.05 U 0.37 P 99% M 160452 F 8 R 43295 W 0 c 5 w 9 I 1104 O 1072 L 11.27 10.78 10.72 @#@FSLOADPOST 2024:08:07:17:54:15 mrisp_paint N 5 11.27 10.78 10.72 #-------------------------------------------- #@# AvgCurv rh 公曆 20廿四年八月七日週三十七時54分十五秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02 .tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2024:08:07:17:54:15 mrisp_paint N 5 e 0.42 S 0.05 U 0.36 P 99% M 156920 F 0 R 42211 W 0 c 5 w 3 I 0 O 1040 L 11.27 10.78 10.72 @#@FSLOADPOST 2024:08:07:17:54:16 mrisp_paint N 5 11.27 10.78 10.72 #----------------------------------------- #@# Cortical Parc lh 公曆 20廿四年八月七日週三十七時54分十六秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0003 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1105 labels changed using aseg relabeling using gibbs priors... 000: 2968 changed, 136375 examined... 001: 660 changed, 12596 examined... 002: 145 changed, 3813 examined... 003: 44 changed, 903 examined... 004: 8 changed, 278 examined... 005: 1 changed, 56 examined... 006: 0 changed, 8 examined... 278 labels changed using aseg 000: 97 total segments, 56 labels (143 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1793 vertices marked for relabeling... 1793 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 6 seconds. @#@FSTIME 2024:08:07:17:54:16 mris_ca_label N 11 e 5.66 S 0.36 U 5.28 P 99% M 1136268 F 10 R 411388 W 0 c 25 w 98 I 64856 O 2136 L 11.27 10.78 10.72 @#@FSLOADPOST 2024:08:07:17:54:21 mris_ca_label N 11 11.01 10.73 10.70 #----------------------------------------- #@# Cortical Parc rh 公曆 20廿四年八月七日週三十七時54分廿一秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0003 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 987 labels changed using aseg relabeling using gibbs priors... 000: 2616 changed, 132793 examined... 001: 586 changed, 11348 examined... 002: 124 changed, 3422 examined... 003: 45 changed, 773 examined... 004: 21 changed, 256 examined... 005: 8 changed, 133 examined... 006: 4 changed, 44 examined... 007: 2 changed, 20 examined... 008: 1 changed, 12 examined... 009: 1 changed, 7 examined... 010: 1 changed, 6 examined... 011: 0 changed, 8 examined... 231 labels changed using aseg 000: 101 total segments, 56 labels (168 vertices) changed 001: 45 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1340 vertices marked for relabeling... 1340 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 5 seconds. @#@FSTIME 2024:08:07:17:54:21 mris_ca_label N 11 e 5.41 S 0.33 U 5.07 P 99% M 1136480 F 0 R 365822 W 0 c 20 w 4 I 36352 O 2080 L 11.01 10.73 10.70 @#@FSLOADPOST 2024:08:07:17:54:27 mris_ca_label N 11 10.93 10.72 10.70 #-------------------------------------------- #@# WhiteSurfs lh 公曆 20廿四年八月七日週三十七時54分廿七秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 272746 0.33816 0.11534 0.002272 3.1832 Corner 818238 60.00000 13.02321 0.283077 178.2590 Edge 409119 0.89362 0.18737 0.015059 4.0252 Hinge 409119 9.49847 10.03758 0.000001 179.8258 Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 8790/136375 vertices (127585 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 389 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68188: xyz = (-28.8076,-16.4404,32.5965) oxyz = (-28.8076,-16.4404,32.5965) wxzy = (-28.8076,-16.4404,32.5965) pxyz = (0,0,0) CBVO Creating mask 136375 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=2 had to be increased for 128 vertices, nripped=9179 mean border=79.5, 181 (181) missing vertices, mean dist 0.3 [0.7 (%20.4)->0. 6 (%79.6))] %57 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1043 min Finding expansion regions mean absolute distance = 0.61 +- 1.01 5103 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1649126.6, rms=7.539 001: dt: 0.5000, sse=930038.9, rms=5.374 (28.715%) 002: dt: 0.5000, sse=704554.6, rms=4.482 (16.595%) 003: dt: 0.5000, sse=627665.1, rms=4.094 (8.657%) 004: dt: 0.5000, sse=553975.8, rms=3.737 (8.725%) 005: dt: 0.5000, sse=540183.3, rms=3.683 (1.435%) 006: dt: 0.5000, sse=507197.3, rms=3.490 (5.250%) rms = 3.5568/3.4899, sse=522696.2/507197.3, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=329416.6, rms=2.271 (34.932%) 008: dt: 0.2500, sse=270572.3, rms=1.634 (28.047%) 009: dt: 0.2500, sse=249053.9, rms=1.407 (13.920%) 010: dt: 0.2500, sse=243521.0, rms=1.325 (5.806%) 011: dt: 0.2500, sse=242632.4, rms=1.274 (3.832%) rms = 1.2477/1.2741, sse=242299.1/242632.4, time step reduction 2 of 3 to 0. 125 0 0 1 012: dt: 0.2500, sse=242299.1, rms=1.248 (2.068%) rms = 1.2019/1.2477, sse=238906.3/242299.1, time step reduction 3 of 3 to 0. 062 0 0 1 013: dt: 0.1250, sse=238906.3, rms=1.202 (3.670%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=1 had to be increased for 101 vertices, nripped=9179 mean border=82.1, 221 (115) missing vertices, mean dist -0.3 [0.6 (%65.7)->0.2 (%34.3))] %63 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0755 min Finding expansion regions mean absolute distance = 0.45 +- 0.90 5611 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=723190.6, rms=4.437 014: dt: 0.5000, sse=495846.8, rms=3.280 (26.068%) rms = 3.4005/3.2805, sse=516489.5/495846.8, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 015: dt: 0.2500, sse=391216.1, rms=2.587 (21.138%) 016: dt: 0.2500, sse=331558.1, rms=2.024 (21.748%) 017: dt: 0.2500, sse=298149.3, rms=1.698 (16.144%) 018: dt: 0.2500, sse=286515.8, rms=1.484 (12.598%) 019: dt: 0.2500, sse=272789.6, rms=1.333 (10.131%) 020: dt: 0.2500, sse=262646.3, rms=1.226 (8.070%) 021: dt: 0.2500, sse=262408.5, rms=1.153 (5.928%) 022: dt: 0.2500, sse=258558.3, rms=1.096 (4.969%) rms = 1.0590/1.0959, sse=256231.2/258558.3, time step reduction 2 of 3 to 0. 125 0 0 1 023: dt: 0.2500, sse=256231.2, rms=1.059 (3.365%) rms = 1.0145/1.0590, sse=252701.9/256231.2, time step reduction 3 of 3 to 0. 062 0 0 1 024: dt: 0.1250, sse=252701.9, rms=1.014 (4.205%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 175 vertices, nripped=9179 mean border=84.1, 225 (102) missing vertices, mean dist -0.2 [0.4 (%65.3)->0.2 (%34.7))] %71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0432 min Finding expansion regions mean absolute distance = 0.37 +- 0.69 5492 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=470661.5, rms=3.164 025: dt: 0.5000, sse=381812.5, rms=2.526 (20.171%) rms = 2.8871/2.5262, sse=432543.7/381812.5, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=295975.0, rms=1.762 (30.263%) 027: dt: 0.2500, sse=261866.4, rms=1.279 (27.405%) rms = 1.0708/1.2789, sse=263346.2/261866.4, time step reduction 2 of 3 to 0. 125 0 1 0 028: dt: 0.2500, sse=263346.2, rms=1.071 (16.270%) 029: dt: 0.1250, sse=243083.3, rms=0.980 (8.482%) rms = 0.9448/0.9800, sse=242664.1/243083.3, time step reduction 3 of 3 to 0. 062 0 0 1 030: dt: 0.1250, sse=242664.1, rms=0.945 (3.588%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 64.0000000; outside_low = 51.2911300; outside_hi = 112.3613130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 113 vertices, nripped=9179 mean border=84.9, 252 (98) missing vertices, mean dist -0.1 [0.4 (%56.7)->0. 3 (%43.3))] %75 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0286 min Finding expansion regions mean absolute distance = 0.33 +- 0.56 4436 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=309507.7, rms=1.932 031: dt: 0.5000, sse=302431.8, rms=1.724 (10.756%) rms = 2.2850/1.7245, sse=349086.6/302431.8, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=245943.4, rms=1.091 (36.716%) 033: dt: 0.2500, sse=236383.9, rms=0.850 (22.068%) 034: dt: 0.2500, sse=232593.1, rms=0.773 (9.144%) rms = 0.7675/0.7727, sse=234206.4/232593.1, time step reduction 2 of 3 to 0. 125 0 1 1 035: dt: 0.2500, sse=234206.4, rms=0.767 (0.681%) 036: dt: 0.1250, sse=228430.4, rms=0.716 (6.663%) rms = 0.7074/0.7163, sse=225214.3/228430.4, time step reduction 3 of 3 to 0. 062 0 0 1 037: dt: 0.1250, sse=225214.3, rms=0.707 (1.250%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.51 minutes Writing output to ../surf/lh.white #VMPC# mris_place_surfaces VmPeak 2164264 mris_place_surface done @#@FSTIME 2024:08:07:17:54:27 mris_place_surface N 25 e 155.65 S 0.59 U 155.05 P 99% M 1905528 F 0 R 538708 W 0 c 546 w 42 I 0 O 9592 L 10.93 10.72 10.70 @#@FSLOADPOST 2024:08:07:17:57:03 mris_place_surface N 25 10.39 10.47 10.61 #-------------------------------------------- #@# WhiteSurfs rh 公曆 20廿四年八月七日週三十七時57分三秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 265582 0.34259 0.12168 0.002037 2.5951 Corner 796746 60.00000 13.24604 0.376281 176.7460 Edge 398373 0.89985 0.19702 0.016821 3.4749 Hinge 398373 9.84040 10.71187 0.000003 179.8247 Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 8892/132793 vertices (123901 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 409 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 66397: xyz = (50.1364,-13.7269,19.1954) oxyz = (50.1364,-13.7269,19.1954) wxzy = (50.1364,-13.7269,19.1954) pxyz = (0,0,0) CBVO Creating mask 132793 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=2 had to be increased for 184 vertices, nripped=9301 mean border=78.9, 179 (179) missing vertices, mean dist 0.3 [0.7 (%22.0)->0. 6 (%78.0))] %59 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1039 min Finding expansion regions mean absolute distance = 0.63 +- 1.07 4567 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chang, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1608454.8, rms=7.559 001: dt: 0.5000, sse=959092.6, rms=5.574 (26.270%) 002: dt: 0.5000, sse=758160.2, rms=4.740 (14.953%) 003: dt: 0.5000, sse=665441.2, rms=4.365 (7.906%) 004: dt: 0.5000, sse=594201.2, rms=3.979 (8.844%) 005: dt: 0.5000, sse=582043.4, rms=3.919 (1.513%) 006: dt: 0.5000, sse=531500.7, rms=3.683 (6.015%) rms = 3.7380/3.6834, sse=542452.8/531500.7, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=352007.8, rms=2.502 (32.080%) 008: dt: 0.2500, sse=287511.7, rms=1.897 (24.172%) 009: dt: 0.2500, sse=266896.0, rms=1.654 (12.798%) 010: dt: 0.2500, sse=263011.6, rms=1.548 (6.444%) 011: dt: 0.2500, sse=256604.5, rms=1.471 (4.967%) rms = 1.4230/1.4708, sse=249419.5/256604.5, time step reduction 2 of 3 to 0. 125 0 0 1 012: dt: 0.2500, sse=249419.5, rms=1.423 (3.249%) 013: dt: 0.1250, sse=248150.6, rms=1.365 (4.091%) rms = 1.3476/1.3648, sse=249619.6/248150.6, time step reduction 3 of 3 to 0. 062 0 1 1 014: dt: 0.1250, sse=249619.6, rms=1.348 (1.261%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=1 had to be increased for 138 vertices, nripped=9301 mean border=81.3, 205 (96) missing vertices, mean dist -0.3 [0.6 (%64.7)->0. 3 (%35.3))] %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0756 min Finding expansion regions mean absolute distance = 0.46 +- 0.93 5906 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chang, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=735868.4, rms=4.545 015: dt: 0.5000, sse=518800.8, rms=3.441 (24.293%) rms = 3.5340/3.4405, sse=532536.9/518800.7, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 016: dt: 0.2500, sse=407538.5, rms=2.712 (21.181%) 017: dt: 0.2500, sse=337413.7, rms=2.108 (22.255%) 018: dt: 0.2500, sse=299869.5, rms=1.757 (16.681%) 019: dt: 0.2500, sse=289669.3, rms=1.534 (12.693%) 020: dt: 0.2500, sse=272518.7, rms=1.383 (9.804%) 021: dt: 0.2500, sse=267529.3, rms=1.271 (8.087%) 022: dt: 0.2500, sse=264880.4, rms=1.198 (5.740%) rms = 1.1380/1.1984, sse=265182.1/264880.4, time step reduction 2 of 3 to 0. 125 0 1 0 023: dt: 0.2500, sse=265182.2, rms=1.138 (5.040%) 024: dt: 0.1250, sse=262272.7, rms=1.084 (4.758%) rms = 1.0650/1.0839, sse=264757.5/262272.7, time step reduction 3 of 3 to 0. 062 0 1 1 025: dt: 0.1250, sse=264757.5, rms=1.065 (1.744%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 186 vertices, nripped=9301 mean border=83.2, 188 (80) missing vertices, mean dist -0.2 [0.5 (%64.9)->0. 3 (%35.1))] %71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0397 min Finding expansion regions mean absolute distance = 0.38 +- 0.70 5070 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chang, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=461516.9, rms=3.088 026: dt: 0.5000, sse=395712.1, rms=2.600 (15.801%) rms = 3.0407/2.5998, sse=469765.1/395712.1, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=314416.0, rms=1.806 (30.516%) 028: dt: 0.2500, sse=276677.0, rms=1.348 (25.371%) 029: dt: 0.2500, sse=256800.5, rms=1.143 (15.193%) 030: dt: 0.2500, sse=249938.3, rms=1.052 (8.025%) rms = 1.0139/1.0516, sse=242593.3/249938.3, time step reduction 2 of 3 to 0. 125 0 0 1 031: dt: 0.2500, sse=242593.2, rms=1.014 (3.586%) 032: dt: 0.1250, sse=237817.3, rms=0.951 (6.155%) rms = 0.9405/0.9515, sse=238283.0/237817.3, time step reduction 3 of 3 to 0. 062 0 1 1 033: dt: 0.1250, sse=238283.0, rms=0.940 (1.154%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 112.3613130; border_low = 62.0000000; outside_low = 49.2911300; outside_hi = 112.3613130; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 127 vertices, nripped=9301 mean border=84.1, 220 (71) missing vertices, mean dist -0.1 [0.4 (%56.4)->0. 3 (%43.6))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0280 min Finding expansion regions mean absolute distance = 0.33 +- 0.57 4475 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chang, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=304504.8, rms=1.949 034: dt: 0.5000, sse=296084.3, rms=1.807 (7.289%) rms = 2.4378/1.8072, sse=354140.3/296084.3, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=241556.9, rms=1.150 (36.374%) 036: dt: 0.2500, sse=232064.5, rms=0.920 (19.978%) 037: dt: 0.2500, sse=224740.8, rms=0.842 (8.469%) rms = 0.8400/0.8422, sse=222657.9/224740.8, time step reduction 2 of 3 to 0. 125 0 0 1 038: dt: 0.2500, sse=222657.9, rms=0.840 (0.270%) 039: dt: 0.1250, sse=220650.0, rms=0.771 (8.155%) rms = 0.7644/0.7715, sse=220726.5/220649.9, time step reduction 3 of 3 to 0. 062 0 1 1 040: dt: 0.1250, sse=220726.5, rms=0.764 (0.914%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 2.63 minutes Writing output to ../surf/rh.white #VMPC# mris_place_surfaces VmPeak 2174856 mris_place_surface done @#@FSTIME 2024:08:07:17:57:03 mris_place_surface N 25 e 162.20 S 0.55 U 161.63 P 99% M 1916156 F 0 R 517087 W 0 c 559 w 140 I 0 O 9344 L 10.39 10.47 10.61 @#@FSLOADPOST 2024:08:07:17:59:45 mris_place_surface N 25 10.78 10.46 10.57 #-------------------------------------------- #@# T1PialSurf lh 公曆 20廿四年八月七日週三十七時59分45秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 272746 0.34084 0.13137 0.001104 3.1137 Corner 818238 60.00000 14.68941 0.256211 179.1172 Edge 409119 0.89911 0.21080 0.018905 3.5050 Hinge 409119 9.83579 11.02995 0.000006 179.9860 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 60.756 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 7099/136375 vertices (129276 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 68188: xyz = (-28.7963,-16.4263,32.6041) oxyz = (-28.7963,-16.4263,32.6041) wxzy = (-28.7963,-16.4263,32.6041) pxyz = (-28.7963,-16.4263,32.6041) CBVO Creating mask 136375 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 51.2911300; border_low = 25.8733980; outside_low = 10.0000000; outside_hi = 44.9366990; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=2 had to be increased for 193 vertices, nripped=7099 mean border=50.5, 235 (235) missing vertices, mean dist 1.8 [3.5 (%0.0)->2.9 (%100.0))] %11 local maxima, %49 large gradients and %35 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0859 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chang, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=32054922.0, rms=35.135 001: dt: 0.5000, sse=23047766.0, rms=29.756 (15.309%) 002: dt: 0.5000, sse=16248795.0, rms=24.938 (16.191%) 003: dt: 0.5000, sse=11582516.0, rms=21.001 (15.790%) 004: dt: 0.5000, sse=8732515.0, rms=18.179 (13.435%) 005: dt: 0.5000, sse=7042099.5, rms=16.276 (10.471%) 006: dt: 0.5000, sse=5795407.0, rms=14.714 (9.598%) 007: dt: 0.5000, sse=4917989.0, rms=13.505 (8.213%) 008: dt: 0.5000, sse=4178076.2, rms=12.393 (8.231%) 009: dt: 0.5000, sse=3623495.2, rms=11.489 (7.297%) 010: dt: 0.5000, sse=3114657.2, rms=10.591 (7.818%) 011: dt: 0.5000, sse=2738036.0, rms=9.873 (6.777%) 012: dt: 0.5000, sse=2378002.0, rms=9.134 (7.486%) 013: dt: 0.5000, sse=2122419.2, rms=8.570 (6.177%) 014: dt: 0.5000, sse=1861151.5, rms=7.952 (7.212%) 015: dt: 0.5000, sse=1684708.1, rms=7.505 (5.622%) 016: dt: 0.5000, sse=1505404.0, rms=7.022 (6.439%) 017: dt: 0.5000, sse=1405290.0, rms=6.735 (4.080%) 018: dt: 0.5000, sse=1295281.2, rms=6.406 (4.886%) 019: dt: 0.5000, sse=1255644.8, rms=6.281 (1.949%) 020: dt: 0.5000, sse=1192210.8, rms=6.078 (3.231%) rms = 6.0467/6.0782, sse=1183253.1/1192210.8, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=1183253.1, rms=6.047 (0.517%) 022: dt: 0.2500, sse=1003253.0, rms=5.424 (10.304%) 023: dt: 0.2500, sse=970316.9, rms=5.302 (2.244%) rms = 5.2785/5.3019, sse=964385.9/970316.9, time step reduction 2 of 3 to 0. 125 0 0 1 024: dt: 0.2500, sse=964385.9, rms=5.278 (0.443%) 025: dt: 0.1250, sse=930701.1, rms=5.150 (2.436%) rms = 5.1288/5.1499, sse=925395.8/930701.1, time step reduction 3 of 3 to 0. 062 0 0 1 026: dt: 0.1250, sse=925395.8, rms=5.129 (0.409%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 51.2911300; border_low = 25.8733980; outside_low = 10.0000000; outside_hi = 44.9366990; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=1 had to be increased for 10620 vertices, nripped=7099 mean border=50.4, 1984 (52) missing vertices, mean dist 0.2 [0.1 (%55.2)->0. 8 (%44.8))] %20 local maxima, %42 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0320 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chang, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=916715.8, rms=4.806 rms = 4.8533/4.8065, sse=927440.3/916715.8, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=871876.8, rms=4.621 (3.863%) 028: dt: 0.2500, sse=839656.2, rms=4.483 (2.984%) 029: dt: 0.2500, sse=825045.9, rms=4.420 (1.408%) rms = 4.4004/4.4198, sse=820530.0/825045.9, time step reduction 2 of 3 to 0. 125 0 0 1 030: dt: 0.2500, sse=820530.0, rms=4.400 (0.440%) 031: dt: 0.1250, sse=803860.4, rms=4.323 (1.750%) rms = 4.3035/4.3234, sse=799592.2/803860.4, time step reduction 3 of 3 to 0. 062 0 0 1 032: dt: 0.1250, sse=799592.1, rms=4.304 (0.459%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 51.2911300; border_low = 25.8733980; outside_low = 10.0000000; outside_hi = 44.9366990; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 10489 vertices, nripped=7099 mean border=49.8, 2600 (42) missing vertices, mean dist 0.2 [0.1 (%49.6)->0. 7 (%50.4))] %29 local maxima, %32 large gradients and %31 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0167 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chang, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=860412.1, rms=4.562 rms = 4.7047/4.5625, sse=893308.5/860412.0, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=823442.2, rms=4.402 (3.518%) 034: dt: 0.2500, sse=799969.7, rms=4.299 (2.344%) rms = 4.2575/4.2987, sse=790532.7/799969.7, time step reduction 2 of 3 to 0. 125 0 0 1 035: dt: 0.2500, sse=790532.7, rms=4.257 (0.960%) rms = 4.2120/4.2575, sse=781022.3/790532.7, time step reduction 3 of 3 to 0. 062 0 0 1 036: dt: 0.1250, sse=781022.3, rms=4.212 (1.068%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 51.2911300; border_low = 25.8733980; outside_low = 10.0000000; outside_hi = 44.9366990; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=136375 Gdiag_no=-1 vno start=0, stop=136375 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8152 vertices, nripped=7099 mean border=48.9, 5501 (37) missing vertices, mean dist 0.2 [0.1 (%48.3)->0. 6 (%51.7))] %35 local maxima, %26 large gradients and %30 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0100 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chang, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=828618.9, rms=4.425 rms = 4.5791/4.4247, sse=862726.1/828618.9, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=798232.6, rms=4.289 (3.065%) 038: dt: 0.2500, sse=775404.8, rms=4.189 (2.345%) rms = 4.1457/4.1885, sse=765501.3/775404.7, time step reduction 2 of 3 to 0. 125 0 0 1 039: dt: 0.2500, sse=765501.4, rms=4.146 (1.023%) 040: dt: 0.1250, sse=753654.8, rms=4.089 (1.377%) rms = 4.0643/4.0886, sse=748361.4/753654.8, time step reduction 3 of 3 to 0. 062 0 0 1 041: dt: 0.1250, sse=748361.4, rms=4.064 (0.593%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 4 intersecting step 1 with no progress (num=5, old_num=4) 001: 5 intersecting terminating search with 0 intersecting #ET# mris_place_surface 2.45 minutes Writing output to ../surf/lh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1359888 mris_place_surface done @#@FSTIME 2024:08:07:17:59:45 mris_place_surface N 28 e 151.41 S 0.39 U 151.00 P 99% M 1102040 F 0 R 303927 W 0 c 506 w 101 I 0 O 9592 L 10.78 10.46 10.57 @#@FSLOADPOST 2024:08:07:18:02:17 mris_place_surface N 28 9.94 10.20 10.45 #-------------------------------------------- #@# T1PialSurf rh 公曆 20廿四年八月七日週三十八時二分十七秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 265582 0.34629 0.13997 0.000323 3.8735 Corner 796746 60.00000 14.67677 0.116431 179.7091 Edge 398373 0.90606 0.21889 0.029829 4.4605 Hinge 398373 10.07644 11.42100 0.000069 179.9864 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 59.756 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 7437/132793 vertices (125356 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 66397: xyz = (50.097,-13.6992,19.1422) oxyz = (50.097,-13.6992,19.1422) wxzy = (50.097,-13.6992,19.1422) pxyz = (50.097,-13.6992,19.1422) CBVO Creating mask 132793 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 49.2911300; border_low = 23.8733980; outside_low = 10.0000000; outside_hi = 42.9366990; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=2 had to be increased for 181 vertices, nripped=7437 mean border=49.2, 199 (199) missing vertices, mean dist 1.7 [6.5 (%0.0)->2.8 (%100.0))] % 9 local maxima, %47 large gradients and %38 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0838 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chang, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=32014970.0, rms=35.655 001: dt: 0.5000, sse=23031894.0, rms=30.205 (15.284%) 002: dt: 0.5000, sse=16270871.0, rms=25.341 (16.103%) 003: dt: 0.5000, sse=11645042.0, rms=21.384 (15.616%) 004: dt: 0.5000, sse=8802490.0, rms=18.536 (13.318%) 005: dt: 0.5000, sse=7115731.5, rms=16.617 (10.357%) 006: dt: 0.5000, sse=5865234.0, rms=15.035 (9.521%) 007: dt: 0.5000, sse=4949200.0, rms=13.760 (8.480%) 008: dt: 0.5000, sse=4153327.5, rms=12.546 (8.820%) 009: dt: 0.5000, sse=3542935.8, rms=11.529 (8.111%) 010: dt: 0.5000, sse=2991820.8, rms=10.525 (8.704%) 011: dt: 0.5000, sse=2581933.5, rms=9.711 (7.733%) 012: dt: 0.5000, sse=2207837.2, rms=8.903 (8.323%) 013: dt: 0.5000, sse=1952614.8, rms=8.306 (6.706%) 014: dt: 0.5000, sse=1716964.6, rms=7.713 (7.138%) 015: dt: 0.5000, sse=1582487.5, rms=7.352 (4.676%) 016: dt: 0.5000, sse=1443075.6, rms=6.958 (5.362%) 017: dt: 0.5000, sse=1377451.9, rms=6.764 (2.796%) 018: dt: 0.5000, sse=1292741.0, rms=6.504 (3.839%) 019: dt: 0.5000, sse=1269601.9, rms=6.429 (1.148%) 020: dt: 0.5000, sse=1214033.4, rms=6.250 (2.785%) rms = 6.2391/6.2502, sse=1211384.8/1214033.3, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=1211384.8, rms=6.239 (0.178%) 022: dt: 0.2500, sse=1035584.1, rms=5.633 (9.718%) 023: dt: 0.2500, sse=1003745.6, rms=5.516 (2.068%) rms = 5.4824/5.5163, sse=994897.9/1003745.6, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=994897.9, rms=5.482 (0.614%) 025: dt: 0.1250, sse=963334.8, rms=5.363 (2.183%) rms = 5.3400/5.3628, sse=957516.0/963334.7, time step reduction 3 of 3 to 0. 062 0 0 1 026: dt: 0.1250, sse=957516.0, rms=5.340 (0.424%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 49.2911300; border_low = 23.8733980; outside_low = 10.0000000; outside_hi = 42.9366990; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=1 had to be increased for 10496 vertices, nripped=7437 mean border=49.2, 2207 (71) missing vertices, mean dist 0.2 [0.1 (%57.0)->0. 9 (%43.0))] %16 local maxima, %43 large gradients and %34 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0277 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chang, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=922258.7, rms=4.927 rms = 4.9731/4.9268, sse=932681.6/922258.7, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=879512.6, rms=4.749 (3.611%) 028: dt: 0.2500, sse=846388.3, rms=4.607 (2.990%) 029: dt: 0.2500, sse=831249.0, rms=4.541 (1.426%) rms = 4.5147/4.5413, sse=825042.8/831249.0, time step reduction 2 of 3 to 0. 125 0 0 1 030: dt: 0.2500, sse=825042.8, rms=4.515 (0.585%) 031: dt: 0.1250, sse=807034.6, rms=4.431 (1.850%) rms = 4.4059/4.4312, sse=801523.7/807034.6, time step reduction 3 of 3 to 0. 062 0 0 1 032: dt: 0.1250, sse=801523.7, rms=4.406 (0.571%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 49.2911300; border_low = 23.8733980; outside_low = 10.0000000; outside_hi = 42.9366990; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 10618 vertices, nripped=7437 mean border=48.7, 2785 (62) missing vertices, mean dist 0.2 [0.1 (%53.9)->0. 7 (%46.1))] %24 local maxima, %34 large gradients and %34 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0166 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chang, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=839688.4, rms=4.567 rms = 4.6865/4.5672, sse=865966.7/839688.4, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=812164.3, rms=4.445 (2.683%) 034: dt: 0.2500, sse=793196.5, rms=4.360 (1.899%) rms = 4.3242/4.3603, sse=785038.4/793196.5, time step reduction 2 of 3 to 0. 125 0 0 1 035: dt: 0.2500, sse=785038.4, rms=4.324 (0.827%) rms = 4.2764/4.3242, sse=775138.5/785038.4, time step reduction 3 of 3 to 0. 062 0 0 1 036: dt: 0.1250, sse=775138.4, rms=4.276 (1.106%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.6386870; border_hi = 49.2911300; border_low = 23.8733980; outside_low = 10.0000000; outside_hi = 42.9366990; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=132793 Gdiag_no=-1 vno start=0, stop=132793 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8190 vertices, nripped=7437 mean border=47.9, 5858 (54) missing vertices, mean dist 0.2 [0.1 (%50.8)->0. 6 (%49.2))] %31 local maxima, %27 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0102 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chang, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=819963.5, rms=4.480 rms = 4.6214/4.4800, sse=850271.0/819963.5, time step reduction 1 of 3 to 0. 250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=791578.9, rms=4.351 (2.877%) 038: dt: 0.2500, sse=769586.8, rms=4.253 (2.247%) 039: dt: 0.2500, sse=757910.2, rms=4.201 (1.222%) rms = 4.1760/4.2014, sse=751819.4/757910.2, time step reduction 2 of 3 to 0. 125 0 0 1 040: dt: 0.2500, sse=751819.4, rms=4.176 (0.605%) 041: dt: 0.1250, sse=739447.6, rms=4.115 (1.472%) rms = 4.0920/4.1145, sse=734682.5/739447.5, time step reduction 3 of 3 to 0. 062 0 0 1 042: dt: 0.1250, sse=734682.5, rms=4.092 (0.546%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 33 intersecting terminating search with 0 intersecting #ET# mris_place_surface 2.41 minutes Writing output to ../surf/rh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1340224 mris_place_surface done @#@FSTIME 2024:08:07:18:02:17 mris_place_surface N 28 e 149.24 S 0.37 U 148.85 P 99% M 1081700 F 0 R 298663 W 0 c 547 w 112 I 0 O 9344 L 9.94 10.20 10.45 @#@FSLOADPOST 2024:08:07:18:04:46 mris_place_surface N 28 10.19 10.14 10.39 #@# white curv lh 公曆 20廿四年八月七日週三十八時四分46秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2024:08:07:18:04:46 mris_place_surface N 5 e 1.08 S 0.07 U 1.01 P 99% M 187416 F 0 R 49954 W 0 c 7 w 1 I 0 O 1072 L 10.19 10.14 10.39 @#@FSLOADPOST 2024:08:07:18:04:47 mris_place_surface N 5 10.19 10.14 10.39 #@# white area lh 公曆 20廿四年八月七日週三十八時四分47秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:08:07:18:04:47 mris_place_surface N 3 e 0.50 S 0.05 U 0.44 P 99% M 187736 F 0 R 49954 W 0 c 1 w 2 I 0 O 1072 L 10.19 10.14 10.39 @#@FSLOADPOST 2024:08:07:18:04:48 mris_place_surface N 3 10.19 10.14 10.39 #@# pial curv lh 公曆 20廿四年八月七日週三十八時四分48秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2024:08:07:18:04:48 mris_place_surface N 5 e 1.02 S 0.05 U 0.96 P 99% M 187484 F 0 R 49954 W 0 c 7 w 2 I 0 O 1072 L 10.19 10.14 10.39 @#@FSLOADPOST 2024:08:07:18:04:49 mris_place_surface N 5 10.09 10.12 10.38 #@# pial area lh 公曆 20廿四年八月七日週三十八時四分49秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:08:07:18:04:49 mris_place_surface N 3 e 0.50 S 0.05 U 0.44 P 99% M 187484 F 0 R 49951 W 0 c 5 w 1 I 0 O 1072 L 10.09 10.12 10.38 @#@FSLOADPOST 2024:08:07:18:04:50 mris_place_surface N 3 10.09 10.12 10.38 #@# thickness lh 公曆 20廿四年八月七日週三十八時四分50秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 136375 vertices processed 25000 of 136375 vertices processed 50000 of 136375 vertices processed 75000 of 136375 vertices processed 100000 of 136375 vertices processed 125000 of 136375 vertices processed 0 of 136375 vertices processed 25000 of 136375 vertices processed 50000 of 136375 vertices processed 75000 of 136375 vertices processed 100000 of 136375 vertices processed 125000 of 136375 vertices processed thickness calculation complete, 964:5945 truncations. 68597 vertices at 0 distance 107371 vertices at 1 distance 55213 vertices at 2 distance 22895 vertices at 3 distance 10159 vertices at 4 distance 4347 vertices at 5 distance 1851 vertices at 6 distance 858 vertices at 7 distance 425 vertices at 8 distance 241 vertices at 9 distance 144 vertices at 10 distance 116 vertices at 11 distance 85 vertices at 12 distance 71 vertices at 13 distance 71 vertices at 14 distance 62 vertices at 15 distance 48 vertices at 16 distance 40 vertices at 17 distance 42 vertices at 18 distance 47 vertices at 19 distance 67 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:08:07:18:04:50 mris_place_surface N 6 e 18.60 S 0.07 U 18.53 P 100% M 186824 F 0 R 57137 W 0 c 52 w 1 I 0 O 1072 L 10.09 10.12 10.38 @#@FSLOADPOST 2024:08:07:18:05:08 mris_place_surface N 6 9.91 10.07 10.36 #@# area and vertex vol lh 公曆 20廿四年八月七日週三十八時五分九秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /home/chang/GBM_Data/VBG/0003/0003/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 0003 lh /home/chang/GBM_Data/VBG/0003/0003/surf/lh.volume masking with /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Total face volume 252503 Total vertex volume 252258 (mask=0) #@# 0003 lh 252258 vertexvol Done @#@FSTIME 2024:08:07:18:05:09 vertexvol N 4 e 1.08 S 0.10 U 0.97 P 99% M 311652 F 8 R 91540 W 0 c 9 w 32 I 1088 O 3216 L 9.91 10.07 10.36 @#@FSLOADPOST 2024:08:07:18:05:10 vertexvol N 4 9.91 10.07 10.36 #@# white curv rh 公曆 20廿四年八月七日週三十八時五分十秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2024:08:07:18:05:10 mris_place_surface N 5 e 1.16 S 0.07 U 1.08 P 99% M 182808 F 0 R 48655 W 0 c 5 w 5 I 0 O 1040 L 9.91 10.07 10.36 @#@FSLOADPOST 2024:08:07:18:05:11 mris_place_surface N 5 9.91 10.07 10.36 #@# white area rh 公曆 20廿四年八月七日週三十八時五分十一秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:08:07:18:05:11 mris_place_surface N 3 e 0.60 S 0.07 U 0.53 P 99% M 183060 F 0 R 48694 W 0 c 2 w 44 I 0 O 1040 L 9.91 10.07 10.36 @#@FSLOADPOST 2024:08:07:18:05:12 mris_place_surface N 3 9.91 10.07 10.36 #@# pial curv rh 公曆 20廿四年八月七日週三十八時五分十二秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2024:08:07:18:05:12 mris_place_surface N 5 e 1.06 S 0.04 U 1.01 P 99% M 182456 F 0 R 48652 W 0 c 5 w 2 I 0 O 1040 L 9.91 10.07 10.36 @#@FSLOADPOST 2024:08:07:18:05:13 mris_place_surface N 5 9.91 10.07 10.36 #@# pial area rh 公曆 20廿四年八月七日週三十八時五分十三秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:08:07:18:05:13 mris_place_surface N 3 e 0.50 S 0.04 U 0.46 P 99% M 182456 F 0 R 48654 W 0 c 3 w 3 I 0 O 1040 L 10.15 10.12 10.37 @#@FSLOADPOST 2024:08:07:18:05:14 mris_place_surface N 3 10.15 10.12 10.37 #@# thickness rh 公曆 20廿四年八月七日週三十八時五分十四秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 132793 vertices processed 25000 of 132793 vertices processed 50000 of 132793 vertices processed 75000 of 132793 vertices processed 100000 of 132793 vertices processed 125000 of 132793 vertices processed 0 of 132793 vertices processed 25000 of 132793 vertices processed 50000 of 132793 vertices processed 75000 of 132793 vertices processed 100000 of 132793 vertices processed 125000 of 132793 vertices processed thickness calculation complete, 585:4335 truncations. 65093 vertices at 0 distance 102863 vertices at 1 distance 55087 vertices at 2 distance 23493 vertices at 3 distance 10439 vertices at 4 distance 4374 vertices at 5 distance 1809 vertices at 6 distance 779 vertices at 7 distance 422 vertices at 8 distance 290 vertices at 9 distance 206 vertices at 10 distance 145 vertices at 11 distance 87 vertices at 12 distance 86 vertices at 13 distance 77 vertices at 14 distance 77 vertices at 15 distance 64 vertices at 16 distance 47 vertices at 17 distance 51 vertices at 18 distance 46 vertices at 19 distance 51 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:08:07:18:05:14 mris_place_surface N 6 e 18.56 S 0.06 U 18.50 P 99% M 182804 F 0 R 55652 W 0 c 42 w 3 I 0 O 1040 L 10.15 10.12 10.37 @#@FSLOADPOST 2024:08:07:18:05:33 mris_place_surface N 6 9.92 10.06 10.35 #@# area and vertex vol rh 公曆 20廿四年八月七日週三十八時五分33秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /home/chang/GBM_Data/VBG/0003/0003/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 0003 rh /home/chang/GBM_Data/VBG/0003/0003/surf/rh.volume masking with /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Total face volume 244738 Total vertex volume 244461 (mask=0) #@# 0003 rh 244461 vertexvol Done @#@FSTIME 2024:08:07:18:05:33 vertexvol N 4 e 0.96 S 0.10 U 0.86 P 99% M 303864 F 0 R 89215 W 0 c 6 w 26 I 0 O 3120 L 9.92 10.06 10.35 @#@FSLOADPOST 2024:08:07:18:05:34 vertexvol N 4 10.08 10.10 10.36 #----------------------------------------- #@# Curvature Stats lh 公曆 20廿四年八月七日週三十八時五分34秒 /home/chang/GBM_Data/VBG/0003/0003/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0003 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ 0003/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 333 ] Gb_filter = 0 @#@FSTIME 2024:08:07:18:05:34 mris_curvature_stats N 11 e 1.37 S 0.06 U 1.31 P 99% M 187292 F 13 R 50116 W 0 c 8 w 16 I 1504 O 8616 L 10.08 10.10 10.36 @#@FSLOADPOST 2024:08:07:18:05:35 mris_curvature_stats N 11 10.08 10.10 10.36 #----------------------------------------- #@# Curvature Stats rh 公曆 20廿四年八月七日週三十八時五分35秒 /home/chang/GBM_Data/VBG/0003/0003/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0003 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ 0003/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 307 ] Gb_filter = 0 WARN: S lookup min: -0.075386 WARN: S explicit min: 0.000000 vertex = 378 @#@FSTIME 2024:08:07:18:05:35 mris_curvature_stats N 11 e 1.39 S 0.06 U 1.32 P 99% M 182856 F 0 R 48857 W 0 c 8 w 4 I 0 O 8360 L 10.08 10.10 10.36 @#@FSLOADPOST 2024:08:07:18:05:37 mris_curvature_stats N 11 10.08 10.10 10.36 #-------------------------------------------- #@# Cortical ribbon mask 公曆 20廿四年八月七日週三十八時五分37秒 /home/chang/GBM_Data/VBG/0003/0003/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 0003 SUBJECTS_DIR is /home/chang/GBM_Data/VBG/0003 loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 206 writing volume /home/chang/GBM_Data/VBG/0003/0003/mri/ribbon.mgz mris_volmask took 4.57 minutes writing ribbon files @#@FSTIME 2024:08:07:18:05:37 mris_volmask N 12 e 273.96 S 0.59 U 273.30 P 99% M 980936 F 8 R 526315 W 0 c 763 w 326 I 952 O 888 L 10.08 10.10 10.36 @#@FSLOADPOST 2024:08:07:18:10:11 mris_volmask N 12 10.76 10.50 10.48 #----------------------------------------- #@# Cortical Parc 2 lh 公曆 20廿四年八月七日週三十八時十分十一秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0003 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 94 labels changed using aseg relabeling using gibbs priors... 000: 8994 changed, 136375 examined... 001: 2021 changed, 34698 examined... 002: 591 changed, 10861 examined... 003: 239 changed, 3354 examined... 004: 122 changed, 1389 examined... 005: 63 changed, 696 examined... 006: 29 changed, 337 examined... 007: 12 changed, 159 examined... 008: 9 changed, 71 examined... 009: 6 changed, 46 examined... 010: 2 changed, 30 examined... 011: 1 changed, 10 examined... 012: 0 changed, 6 examined... 23 labels changed using aseg 000: 238 total segments, 156 labels (1779 vertices) changed 001: 92 total segments, 10 labels (18 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1205 vertices marked for relabeling... 1205 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 8 seconds. @#@FSTIME 2024:08:07:18:10:11 mris_ca_label N 11 e 7.58 S 0.69 U 6.88 P 99% M 1831100 F 0 R 696459 W 0 c 24 w 6 I 42432 O 2144 L 10.76 10.50 10.48 @#@FSLOADPOST 2024:08:07:18:10:18 mris_ca_label N 11 10.22 10.39 10.44 #----------------------------------------- #@# Cortical Parc 2 rh 公曆 20廿四年八月七日週三十八時十分十八秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0003 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02 .gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 149 labels changed using aseg relabeling using gibbs priors... 000: 8867 changed, 132793 examined... 001: 1937 changed, 34353 examined... 002: 557 changed, 10408 examined... 003: 221 changed, 3235 examined... 004: 95 changed, 1277 examined... 005: 44 changed, 548 examined... 006: 25 changed, 273 examined... 007: 9 changed, 136 examined... 008: 6 changed, 55 examined... 009: 2 changed, 30 examined... 010: 1 changed, 13 examined... 011: 2 changed, 8 examined... 012: 1 changed, 11 examined... 013: 0 changed, 7 examined... 17 labels changed using aseg 000: 247 total segments, 160 labels (2134 vertices) changed 001: 91 total segments, 4 labels (19 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 30 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1005 vertices marked for relabeling... 1005 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 8 seconds. @#@FSTIME 2024:08:07:18:10:18 mris_ca_label N 11 e 8.26 S 0.75 U 7.50 P 99% M 1839540 F 0 R 697586 W 0 c 50 w 24 I 42776 O 2088 L 10.22 10.39 10.44 @#@FSLOADPOST 2024:08:07:18:10:27 mris_ca_label N 11 9.96 10.33 10.42 #----------------------------------------- #@# Cortical Parc 3 lh 公曆 20廿四年八月七日週三十八時十分廿七秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0003 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0 2.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0 2.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1352 labels changed using aseg relabeling using gibbs priors... 000: 1884 changed, 136375 examined... 001: 454 changed, 9043 examined... 002: 142 changed, 2601 examined... 003: 76 changed, 829 examined... 004: 52 changed, 409 examined... 005: 40 changed, 271 examined... 006: 31 changed, 215 examined... 007: 22 changed, 179 examined... 008: 12 changed, 117 examined... 009: 7 changed, 66 examined... 010: 6 changed, 42 examined... 011: 7 changed, 32 examined... 012: 3 changed, 41 examined... 013: 4 changed, 24 examined... 014: 4 changed, 18 examined... 015: 3 changed, 22 examined... 016: 3 changed, 17 examined... 017: 2 changed, 17 examined... 018: 1 changed, 17 examined... 019: 1 changed, 6 examined... 020: 1 changed, 7 examined... 021: 0 changed, 6 examined... 465 labels changed using aseg 000: 44 total segments, 11 labels (175 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 744 vertices marked for relabeling... 744 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 6 seconds. @#@FSTIME 2024:08:07:18:10:27 mris_ca_label N 11 e 5.88 S 0.29 U 5.58 P 99% M 895172 F 0 R 292399 W 0 c 17 w 6 I 42976 O 2136 L 9.96 10.33 10.42 @#@FSLOADPOST 2024:08:07:18:10:32 mris_ca_label N 11 9.81 10.29 10.41 #----------------------------------------- #@# Cortical Parc 3 rh 公曆 20廿四年八月七日週三十八時十分32秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0003 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0 2.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.4.1 7.4.1 reading atlas from /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-0 2.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized reading surface from /home/chang/GBM_Data/VBG/0003/0003/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1462 labels changed using aseg relabeling using gibbs priors... 000: 1941 changed, 132793 examined... 001: 491 changed, 9038 examined... 002: 152 changed, 2697 examined... 003: 75 changed, 859 examined... 004: 33 changed, 417 examined... 005: 22 changed, 193 examined... 006: 16 changed, 113 examined... 007: 16 changed, 91 examined... 008: 16 changed, 94 examined... 009: 12 changed, 78 examined... 010: 9 changed, 59 examined... 011: 8 changed, 46 examined... 012: 12 changed, 46 examined... 013: 7 changed, 59 examined... 014: 7 changed, 42 examined... 015: 7 changed, 37 examined... 016: 7 changed, 38 examined... 017: 5 changed, 38 examined... 018: 5 changed, 25 examined... 019: 3 changed, 27 examined... 020: 2 changed, 21 examined... 021: 3 changed, 13 examined... 022: 2 changed, 20 examined... 023: 3 changed, 12 examined... 024: 2 changed, 13 examined... 025: 2 changed, 15 examined... 026: 1 changed, 14 examined... 027: 0 changed, 7 examined... 446 labels changed using aseg 000: 54 total segments, 21 labels (323 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 607 vertices marked for relabeling... 607 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 6 seconds. @#@FSTIME 2024:08:07:18:10:32 mris_ca_label N 11 e 5.91 S 0.27 U 5.64 P 99% M 931196 F 0 R 300341 W 0 c 19 w 3 I 42952 O 2080 L 9.81 10.29 10.41 @#@FSLOADPOST 2024:08:07:18:10:38 mris_ca_label N 11 9.74 10.27 10.40 #----------------------------------------- #@# WM/GM Contrast lh 公曆 20廿四年八月七日週三十八時十分38秒 /home/chang/GBM_Data/VBG/0003/0003/scripts pctsurfcon --s 0003 --lh-only Log file is /home/chang/GBM_Data/VBG/0003/0003/scripts/pctsurfcon.log 公曆 20廿四年八月七日週三十八時十分38秒 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 cd /home/chang/GBM_Data/VBG/0003/0003/scripts /usr/local/freesurfer/bin/pctsurfcon pctsurfcon 7.4.1 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.wm.mgh --regheader 0003 --cortex srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 82565 Masking with /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh. wm.mgh Dim: 136375 1 1 mri_vol2surf done mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.gm.mgh --projfrac 0.3 --regheader 0003 --cortex srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Done reading source surface Reading thickness /home/chang/GBM_Data/VBG/0003/0003/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 91251 Masking with /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh. gm.mgh Dim: 136375 1 1 mri_vol2surf done mri_concat /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh. wm.mgh /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684264/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/chang/GBM_Data/VBG/0003/0003/surf/lh. w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh mri_segstats --in /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh --annot 0003 lh aparc --sum /home/chang/GBM_Data/VBG/0003/0003/stats/lh.w-g. pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh --annot 0003 lh aparc --sum /home/chang/GBM_Data/VBG/0003/0003/stats/lh.w-g.pct.stats --snr sysname Linux hostname chang-System-Product-Name machine x86_64 user chang whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot Seg base 1000 MRISannot2seg(): nhits = 127585 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.w-g.pct.mgh Vertex Area is 0.681666 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2024:08:07:18:10:38 pctsurfcon N 3 e 1.94 S 0.19 U 1.74 P 99% M 232776 F 19 R 171874 W 0 c 19 w 87 I 47384 O 3328 L 9.74 10.27 10.40 @#@FSLOADPOST 2024:08:07:18:10:40 pctsurfcon N 3 10.08 10.33 10.42 #----------------------------------------- #@# WM/GM Contrast rh 公曆 20廿四年八月七日週三十八時十分40秒 /home/chang/GBM_Data/VBG/0003/0003/scripts pctsurfcon --s 0003 --rh-only Log file is /home/chang/GBM_Data/VBG/0003/0003/scripts/pctsurfcon.log 公曆 20廿四年八月七日週三十八時十分40秒 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 cd /home/chang/GBM_Data/VBG/0003/0003/scripts /usr/local/freesurfer/bin/pctsurfcon pctsurfcon 7.4.1 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.wm.mgh --regheader 0003 --cortex srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 81281 Masking with /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh. wm.mgh Dim: 132793 1 1 mri_vol2surf done mri_vol2surf --mov /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.gm.mgh --projfrac 0.3 --regheader 0003 --cortex srcvol = /home/chang/GBM_Data/VBG/0003/0003/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Reading surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Done reading source surface Reading thickness /home/chang/GBM_Data/VBG/0003/0003/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 88541 Masking with /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh. gm.mgh Dim: 132793 1 1 mri_vol2surf done mri_concat /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh. wm.mgh /home/chang/GBM_Data/VBG/0003/0003/surf/tmp.pctsurfcon.684326/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/chang/GBM_Data/VBG/0003/0003/surf/rh. w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh mri_segstats --in /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh --annot 0003 rh aparc --sum /home/chang/GBM_Data/VBG/0003/0003/stats/rh.w-g. pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh --annot 0003 rh aparc --sum /home/chang/GBM_Data/VBG/0003/0003/stats/rh.w-g.pct.stats --snr sysname Linux hostname chang-System-Product-Name machine x86_64 user chang whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot Seg base 2000 MRISannot2seg(): nhits = 123901 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.w-g.pct.mgh Vertex Area is 0.692561 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2024:08:07:18:10:40 pctsurfcon N 3 e 1.86 S 0.17 U 1.69 P 100% M 228936 F 0 R 176581 W 0 c 18 w 68 I 8 O 3256 L 10.08 10.33 10.42 @#@FSLOADPOST 2024:08:07:18:10:42 pctsurfcon N 3 10.08 10.33 10.42 #----------------------------------------- #@# Relabel Hypointensities 公曆 20廿四年八月七日週三十八時十分42秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 5774 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 4516 voxels changed to hypointensity... 9889 hypointense voxels neighboring cortex changed @#@FSTIME 2024:08:07:18:10:42 mri_relabel_hypointensities N 3 e 8.01 S 0.29 U 7.71 P 99% M 470264 F 12 R 331528 W 0 c 31 w 10 I 1880 O 688 L 10.08 10.33 10.42 @#@FSLOADPOST 2024:08:07:18:10:50 mri_relabel_hypointensities N 3 10.07 10.32 10.41 #----------------------------------------- #@# APas-to-ASeg 公曆 20廿四年八月七日週三十八時十分50秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /home/chang/GBM_Data/VBG/0003/0003/mri/ribbon.mgz --threads 1 --lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label --lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label --rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 outvol aseg.mgz 32 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /home/chang/GBM_Data/VBG/0003/0003/mri/ribbon.mgz Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 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rhCerebralWM 241770.5 #CBVS2 SubCortGMVol 51153.0 #CBVS2 CerebellumVol 130049.0 #CBVS2 CerebellumGMVol 107015.0 #CBVS2 VentChorVol 47962.0 #CBVS2 3rd4th5thCSF 4771.0 #CBVS2 AllCSF 52733.0 #CBVS2 CCVol 3379.0 @#@FSTIME 2024:08:07:18:11:01 mri_brainvol_stats N 2 e 2.99 S 0.13 U 2.85 P 99% M 223188 F 25 R 123971 W 0 c 18 w 35 I 4312 O 8 L 9.97 10.29 10.40 @#@FSLOADPOST 2024:08:07:18:11:04 mri_brainvol_stats N 2 9.97 10.29 10.40 #----------------------------------------- #@# AParc-to-ASeg aparc 公曆 20廿四年八月七日週三十八時十一分四秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot 1000 --lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label --lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot 2000 --rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label --rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 outvol aparc+aseg.mgz 32 avail.processors, using 1 Loading aseg.mgz Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8790 vertices from lh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8892 vertices from rh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 0 ndotcheck = 31232 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 897072 mri_surf2volseg done @#@FSTIME 2024:08:07:18:11:04 mri_surf2volseg N 25 e 111.80 S 0.30 U 111.49 P 99% M 877596 F 0 R 244170 W 0 c 323 w 21 I 0 O 832 L 10.22 10.34 10.42 @#@FSLOADPOST 2024:08:07:18:12:55 mri_surf2volseg N 25 10.68 10.48 10.46 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s 公曆 20廿四年八月七日週三十八時十二分55秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label --lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label --rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 outvol aparc.a2009s+aseg.mgz 32 avail.processors, using 1 Loading aseg.mgz Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8790 vertices from lh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.a2009s.annot Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8892 vertices from rh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.a2009s.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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2024:08:07:18:14:48 mri_surf2volseg N 25 11.28 10.71 10.55 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas 公曆 20廿四年八月七日週三十八時十四分48 秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label --lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label --rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 outvol aparc.DKTatlas+aseg.mgz 32 avail.processors, using 1 Loading aseg.mgz Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8790 vertices from lh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.DKTatlas.annot Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8892 vertices from rh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.DKTatlas.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 0 ndotcheck = 31232 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 897072 mri_surf2volseg done @#@FSTIME 2024:08:07:18:14:48 mri_surf2volseg N 25 e 110.19 S 0.25 U 109.87 P 99% M 877636 F 0 R 244522 W 0 c 223 w 370 I 0 O 832 L 11.28 10.71 10.55 @#@FSLOADPOST 2024:08:07:18:16:39 mri_surf2volseg N 25 10.87 10.78 10.59 #----------------------------------------- #@# WMParc 公曆 20廿四年八月七日週三十八時十六分39秒 /home/chang/GBM_Data/VBG/0003/0003/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot 3000 --lh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label --lh-white /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white --lh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial --rh-annot /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot 4000 --rh-cortex-mask /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label --rh-white /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white --rh-pial /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 outvol wmparc.mgz 32 avail.processors, using 1 Loading aparc+aseg.mgz Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8790 vertices from lh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/lh.aparc.annot Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8892 vertices from rh hemi Loading /home/chang/GBM_Data/VBG/0003/0003/label/rh.aparc.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 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setting seed for random number genererator to 1234 7.4.1 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0003 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname chang-System-Product-Name machine x86_64 user chang whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:08:07:18:17:04 mri_segstats N 24 e 261.79 S 0.37 U 261.40 P 99% M 239872 F 0 R 1207400 W 0 c 1035 w 80 I 56 O 24 L 10.64 10.74 10.58 @#@FSLOADPOST 2024:08:07:18:21:26 mri_segstats N 24 9.90 10.36 10.47 #----------------------------------------- #@# Parcellation Stats lh 公曆 20廿四年八月七日週三十八時廿一分廿六秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0003 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 252503 Total vertex volume 252258 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 1304 892 1817 2.190 0.719 0.105 0.028 9 1.4 bankssts 1245 843 2068 2.199 0.808 0.109 0.017 13 1.0 caudalanteriorcingulate 3778 2473 5494 2.344 0.747 0.117 0.032 28 5.1 caudalmiddlefrontal 2203 1629 3520 2.169 0.611 0.144 0.040 21 3.9 cuneus 667 501 2183 2.889 1.022 0.135 0.036 6 1.1 entorhinal 4001 2849 8385 2.477 0.829 0.126 0.030 40 5.3 fusiform 5117 3504 10274 2.511 0.873 0.118 0.031 42 6.7 inferiorparietal 4310 3127 11690 2.728 1.045 0.135 0.040 45 6.8 inferiortemporal 1648 1104 3009 2.356 1.005 0.102 0.023 12 1.4 isthmuscingulate 6682 4516 14585 2.522 0.930 0.125 0.034 65 9.6 lateraloccipital 2572 1780 7036 3.051 1.115 0.106 0.028 20 2.5 lateralorbitofrontal 4366 3132 7497 2.097 0.772 0.129 0.040 47 7.0 lingual 2443 1824 7304 3.044 1.053 0.125 0.029 30 2.9 medialorbitofrontal 4260 3036 11963 2.707 0.992 0.133 0.037 44 7.0 middletemporal 973 599 1879 2.550 0.928 0.075 0.015 5 0.5 parahippocampal 1925 1276 2564 1.995 0.615 0.120 0.034 14 2.8 paracentral 2259 1449 4971 2.719 0.921 0.097 0.025 15 2.0 parsopercularis 980 775 3628 2.824 1.130 0.174 0.051 16 2.2 parsorbitalis 1791 1185 3570 2.258 0.873 0.114 0.029 16 2.0 parstriangularis 1893 1530 2587 1.853 0.566 0.157 0.049 19 4.5 pericalcarine 7502 4922 10684 1.886 0.765 0.111 0.029 58 8.9 postcentral 1196 766 1720 2.029 0.687 0.101 0.020 10 1.0 posteriorcingulate 9510 6119 13990 2.166 0.788 0.112 0.030 67 12.4 precentral 6453 4548 10700 2.207 0.735 0.121 0.028 52 7.5 precuneus 1226 854 2888 2.633 1.091 0.108 0.024 11 1.2 rostralanteriorcingulate 8682 5889 18865 2.454 0.958 0.121 0.033 81 11.7 rostralmiddlefrontal 10940 7300 23050 2.658 0.888 0.123 0.035 102 15.7 superiorfrontal 10345 7133 14862 1.911 0.700 0.119 0.030 86 13.5 superiorparietal 5851 4029 13885 2.665 1.022 0.097 0.022 50 5.1 superiortemporal 5967 4130 11744 2.340 0.874 0.116 0.032 49 7.7 supramarginal 356 285 1990 3.659 1.207 0.163 0.038 6 0.5 frontalpole 696 561 2628 3.376 0.832 0.122 0.028 7 0.9 temporalpole 643 450 1197 2.344 0.673 0.122 0.030 6 0.7 transversetemporal 3801 2621 8030 2.934 1.016 0.107 0.027 30 4.2 insula @#@FSTIME 2024:08:07:18:21:26 mris_anatomical_stats N 14 e 6.59 S 0.16 U 6. 42 P 99% M 482384 F 9 R 138973 W 0 c 18 w 36 I 1464 O 24 L 9.90 10.36 10.47 @#@FSLOADPOST 2024:08:07:18:21:32 mris_anatomical_stats N 14 9.99 10.37 10.47 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0003 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 252503 Total vertex volume 252258 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 1304 880 1817 2.190 0.719 0.123 0.040 26 1.7 bankssts 1245 1050 2068 2.199 0.808 0.165 0.038 40 2.2 caudalanteriorcingulate 3778 2476 5494 2.344 0.747 0.112 0.028 74 4.4 caudalmiddlefrontal 2203 1807 3520 2.169 0.611 0.149 0.045 108 4.0 cuneus 667 981 2183 2.889 1.022 0.361 0.111 34 4.0 entorhinal 4001 3678 8385 2.477 0.829 0.160 0.044 86 7.2 fusiform 5117 4605 10274 2.511 0.873 0.153 0.039 3421 8.7 inferiorparietal 4310 5034 11690 2.728 1.045 0.199 0.049 97 9.5 inferiortemporal 1648 1348 3009 2.356 1.005 0.134 0.037 38 2.4 isthmuscingulate 6682 6605 14585 2.522 0.930 0.161 0.042 143 12.4 lateraloccipital 2572 2596 7036 3.051 1.115 0.174 0.045 55 5.5 lateralorbitofrontal 4366 4043 7497 2.097 0.772 0.159 0.040 79 8.4 lingual 2443 2786 7304 3.044 1.053 0.198 0.045 46 5.1 medialorbitofrontal 4260 5269 11963 2.707 0.992 0.192 0.044 77 8.9 middletemporal 973 897 1879 2.550 0.928 0.157 0.042 13 2.2 parahippocampal 1925 1418 2564 1.995 0.615 0.117 0.030 19 2.3 paracentral 2259 2056 4971 2.719 0.921 0.133 0.028 23 2.8 parsopercularis 980 1614 3628 2.824 1.130 0.256 0.057 19 2.9 parsorbitalis 1791 1721 3570 2.258 0.873 0.159 0.032 27 3.0 parstriangularis 1893 1344 2587 1.853 0.566 0.130 0.039 31 2.8 pericalcarine 7502 6237 10684 1.886 0.765 0.122 0.027 66 8.1 postcentral 1196 909 1720 2.029 0.687 0.116 0.032 23 1.5 posteriorcingulate 9510 6748 13990 2.166 0.788 0.109 0.028 141 10.8 precentral 6453 5271 10700 2.207 0.735 0.145 0.040 117 10.6 precuneus 1226 1218 2888 2.633 1.091 0.172 0.047 28 2.2 rostralanteriorcingulate 8682 8401 18865 2.454 0.958 0.160 0.038 147 14.6 rostralmiddlefrontal 10940 9382 23050 2.658 0.888 0.140 0.036 404 15.5 superiorfrontal 10345 8736 14862 1.911 0.700 0.130 0.031 119 13.5 superiorparietal 5851 5791 13885 2.665 1.022 0.147 0.032 71 8.7 superiortemporal 5967 5625 11744 2.340 0.874 0.155 0.037 118 10.1 supramarginal 356 677 1990 3.659 1.207 0.259 0.040 5 0.8 frontalpole 696 1013 2628 3.376 0.832 0.200 0.038 10 1.2 temporalpole 643 640 1197 2.344 0.673 0.174 0.047 12 1.5 transversetemporal 3801 2768 8030 2.934 1.016 0.170 0.052 129 10.6 insula @#@FSTIME 2024:08:07:18:21:32 mris_anatomical_stats N 14 e 6.53 S 0.21 U 6. 30 P 99% M 482160 F 0 R 139017 W 0 c 36 w 68 I 0 O 24 L 9.99 10.37 10.47 @#@FSLOADPOST 2024:08:07:18:21:39 mris_anatomical_stats N 14 10.07 10.38 10. 48 #----------------------------------------- #@# Parcellation Stats rh 公曆 20廿四年八月七日週三十八時廿一分39秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0003 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 244738 Total vertex volume 244461 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 1065 756 1907 2.829 0.675 0.105 0.025 8 0.9 bankssts 1123 757 2363 2.443 0.858 0.122 0.024 11 1.2 caudalanteriorcingulate 4355 3012 7349 2.354 0.790 0.139 0.038 45 7.6 caudalmiddlefrontal 2344 1693 3608 2.024 0.694 0.146 0.040 23 4.1 cuneus 534 473 2074 2.904 0.962 0.185 0.054 8 1.5 entorhinal 3760 2876 8824 2.550 0.830 0.148 0.044 48 6.9 fusiform 6063 4287 13987 2.670 0.831 0.123 0.034 58 8.1 inferiorparietal 3434 2556 9856 2.808 0.967 0.147 0.047 39 6.4 inferiortemporal 1246 816 2552 2.738 1.020 0.109 0.031 9 1.5 isthmuscingulate 8091 6001 16825 2.344 0.854 0.144 0.046 90 15.7 lateraloccipital 2905 2036 6628 2.751 0.892 0.121 0.031 25 3.8 lateralorbitofrontal 3598 2753 7600 2.224 0.806 0.141 0.045 44 7.1 lingual 2315 1620 6326 2.831 1.186 0.115 0.024 23 2.2 medialorbitofrontal 4064 3005 11573 2.789 0.900 0.132 0.033 46 5.7 middletemporal 938 572 1717 2.346 0.834 0.088 0.018 6 0.6 parahippocampal 2283 1420 2936 2.003 0.608 0.111 0.026 16 2.4 paracentral 2181 1464 3828 2.381 0.716 0.113 0.030 20 2.8 parsopercularis 967 672 3041 3.020 1.041 0.135 0.032 10 1.4 parsorbitalis 1780 1220 3577 2.347 0.963 0.122 0.032 17 2.3 parstriangularis 1890 1361 2455 2.003 0.541 0.152 0.056 123 5.4 pericalcarine 6564 4165 9082 1.923 0.838 0.099 0.024 46 6.4 postcentral 1660 1118 2573 2.159 0.788 0.129 0.037 15 2.6 posteriorcingulate 9064 5712 12212 2.015 0.748 0.116 0.031 77 12.1 precentral 6185 4358 10614 2.286 0.860 0.125 0.034 54 8.5 precuneus 692 495 2113 3.293 0.916 0.097 0.019 6 0.5 rostralanteriorcingulate 8417 5885 15312 2.103 0.863 0.132 0.038 84 13.2 rostralmiddlefrontal 12088 8265 23709 2.480 0.844 0.126 0.034 107 16.6 superiorfrontal 9409 6658 13995 1.939 0.725 0.129 0.037 88 15.1 superiorparietal 5340 3739 12789 2.733 1.021 0.106 0.024 41 5.4 superiortemporal 4534 3145 9172 2.397 0.936 0.112 0.030 37 5.5 supramarginal 361 268 1955 3.713 1.060 0.153 0.043 6 0.7 frontalpole 648 523 3312 3.939 0.662 0.156 0.044 10 1.0 temporalpole 511 346 1036 2.492 0.659 0.114 0.030 5 0.6 transversetemporal 3492 2507 7560 2.933 0.831 0.113 0.027 29 3.7 insula @#@FSTIME 2024:08:07:18:21:39 mris_anatomical_stats N 14 e 5.77 S 0.15 U 5. 61 P 99% M 470024 F 0 R 135436 W 0 c 31 w 1 I 0 O 48 L 10.07 10.38 10.48 @#@FSLOADPOST 2024:08:07:18:21:45 mris_anatomical_stats N 14 9.76 10.30 10.45 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0003 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 244738 Total vertex volume 244461 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 1065 661 1907 2.829 0.675 0.124 0.043 27 1.5 bankssts 1123 1054 2363 2.443 0.858 0.186 0.048 40 2.3 caudalanteriorcingulate 4355 3345 7349 2.354 0.790 0.128 0.033 74 6.3 caudalmiddlefrontal 2344 2004 3608 2.024 0.694 0.143 0.041 31 4.2 cuneus 534 945 2074 2.904 0.962 0.349 0.081 15 2.4 entorhinal 3760 3936 8824 2.550 0.830 0.182 0.049 106 7.5 fusiform 6063 5916 13987 2.670 0.831 0.171 0.044 137 11.6 inferiorparietal 3434 4086 9856 2.808 0.967 0.204 0.052 81 8.1 inferiortemporal 1246 1068 2552 2.738 1.020 0.143 0.042 18 2.0 isthmuscingulate 8091 8079 16825 2.344 0.854 0.167 0.044 250 15.4 lateraloccipital 2905 2702 6628 2.751 0.892 0.199 0.062 179 8.6 lateralorbitofrontal 3598 3995 7600 2.224 0.806 0.182 0.044 61 7.4 lingual 2315 2551 6326 2.831 1.186 0.199 0.048 49 5.2 medialorbitofrontal 4064 5010 11573 2.789 0.900 0.216 0.053 141 10.1 middletemporal 938 881 1717 2.346 0.834 0.174 0.045 16 2.3 parahippocampal 2283 1579 2936 2.003 0.608 0.116 0.029 28 2.8 paracentral 2181 1862 3828 2.381 0.716 0.136 0.035 26 3.1 parsopercularis 967 1239 3041 3.020 1.041 0.204 0.048 18 2.6 parsorbitalis 1780 1768 3577 2.347 0.963 0.169 0.037 25 3.2 parstriangularis 1890 1213 2455 2.003 0.541 0.148 0.058 75 4.2 pericalcarine 6564 5221 9082 1.923 0.838 0.118 0.024 64 6.9 postcentral 1660 1290 2573 2.159 0.788 0.137 0.043 30 3.0 posteriorcingulate 9064 6464 12212 2.015 0.748 0.112 0.027 113 10.4 precentral 6185 4912 10614 2.286 0.860 0.142 0.040 114 10.7 precuneus 692 738 2113 3.293 0.916 0.161 0.042 12 1.0 rostralanteriorcingulate 8417 7898 15312 2.103 0.863 0.160 0.038 135 14.6 rostralmiddlefrontal 12088 10399 23709 2.480 0.844 0.149 0.038 241 19.3 superiorfrontal 9409 8212 13995 1.939 0.725 0.141 0.034 135 13.9 superiorparietal 5340 5208 12789 2.733 1.021 0.149 0.031 68 7.3 superiortemporal 4534 4429 9172 2.397 0.936 0.157 0.032 64 7.0 supramarginal 361 687 1955 3.713 1.060 0.265 0.051 6 1.0 frontalpole 648 1137 3312 3.939 0.662 0.286 0.061 19 2.0 temporalpole 511 506 1036 2.492 0.659 0.131 0.032 4 0.7 transversetemporal 3492 2641 7560 2.933 0.831 0.163 0.044 85 6.3 insula @#@FSTIME 2024:08:07:18:21:45 mris_anatomical_stats N 14 e 6.37 S 0.16 U 6. 20 P 100% M 470528 F 0 R 135437 W 0 c 18 w 1 I 0 O 24 L 9.76 10.30 10.45 @#@FSLOADPOST 2024:08:07:18:21:51 mris_anatomical_stats N 14 9.78 10.30 10.45 #----------------------------------------- #@# Parcellation Stats 2 lh 公曆 20廿四年八月七日週三十八時廿一分51秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0003 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 252503 Total vertex volume 252258 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 953 670 2462 2.514 1.070 0.120 0.028 8 1.1 G_and_S_frontomargin 1352 891 3563 2.734 0.943 0.126 0.034 14 1.7 G_and_S_occipital_inf 1644 1091 2194 1.850 0.537 0.121 0.035 13 2.3 G_and_S_paracentral 1641 1127 4308 2.714 0.914 0.122 0.032 15 2.0 G_and_S_subcentral 703 552 3178 3.361 1.182 0.154 0.044 10 1.2 G_and_S_transv_frontopol 2302 1680 4750 2.419 0.893 0.122 0.027 22 2.5 G_and_S_cingul-Ant 1420 981 2231 2.161 0.655 0.117 0.024 13 1.4 G_and_S_cingul-Mid-Ant 1015 672 1598 2.389 0.750 0.106 0.023 6 0.9 G_and_S_cingul-Mid-Post 532 368 1356 2.928 0.940 0.125 0.031 6 0.7 G_cingul-Post-dorsal 372 267 867 2.616 0.763 0.125 0.027 5 0.3 G_cingul-Post-ventral 1927 1449 3314 2.114 0.700 0.150 0.045 21 3.8 G_cuneus 1283 820 3828 3.077 0.914 0.112 0.034 12 1.5 G_front_inf-Opercular 508 355 1970 3.069 0.911 0.142 0.036 6 0.9 G_front_inf-Orbital 1081 751 2959 2.502 0.944 0.133 0.040 14 1.6 G_front_inf-Triangul 5007 3439 12255 2.537 0.938 0.145 0.044 63 9.3 G_front_middle 7142 4761 17818 2.813 0.932 0.131 0.041 80 11.9 G_front_sup 705 532 1879 3.037 1.059 0.144 0.043 10 1.1 G_Ins_lg_and_S_cent_ins 792 597 2605 3.456 0.993 0.134 0.040 11 1.6 G_insular_short 1924 1279 6478 3.010 1.012 0.134 0.041 23 2.9 G_occipital_middle 1708 1250 3329 2.394 0.842 0.134 0.036 15 2.8 G_occipital_sup 1578 1199 3539 2.323 0.803 0.145 0.044 23 2.9 G_oc-temp_lat-fusifor 2993 2236 6202 2.254 0.822 0.148 0.050 40 6.1 G_oc-temp_med-Lingual 1451 977 4433 2.969 0.955 0.111 0.026 12 1.6 G_oc-temp_med-Parahip 1781 1320 6854 3.379 1.071 0.138 0.042 23 2.7 G_orbital 2045 1495 4942 2.528 0.932 0.138 0.041 24 3.8 G_pariet_inf-Angular 3351 2400 8834 2.524 1.027 0.133 0.037 38 5.4 G_pariet_inf-Supramar 4069 2803 6711 1.989 0.739 0.126 0.034 40 6.1 G_parietal_sup 2845 1809 4370 1.985 0.684 0.130 0.040 28 4.8 G_postcentral 3970 2474 6253 2.106 0.806 0.122 0.037 34 6.6 G_precentral 3057 2299 6837 2.264 0.858 0.137 0.034 34 4.2 G_precuneus 746 635 3711 3.613 0.781 0.165 0.037 16 1.3 G_rectus 678 418 1117 2.935 1.139 0.096 0.033 5 0.8 G_subcallosal 499 344 1101 2.441 0.801 0.123 0.032 5 0.7 G_temp_sup-G_T_transv 2052 1479 7818 3.348 1.095 0.132 0.036 35 2.8 G_temp_sup-Lateral 683 511 1556 2.938 0.907 0.079 0.020 3 0.6 G_temp_sup-Plan_polar 901 626 1767 2.504 0.954 0.095 0.026 5 0.8 G_temp_sup-Plan_tempo 2126 1610 7803 3.062 1.134 0.146 0.050 28 4.1 G_temporal_inf 2569 1860 9006 2.956 1.021 0.142 0.042 32 4.8 G_temporal_middle 302 198 364 2.191 0.473 0.096 0.018 2 0.3 Lat_Fis-ant-Horizont 205 139 236 1.662 0.476 0.087 0.013 1 0.1 Lat_Fis-ant-Vertical 1111 700 1222 2.175 0.512 0.097 0.020 5 0.9 Lat_Fis-post 1842 1311 3162 2.158 0.858 0.122 0.038 19 2.9 Pole_occipital 1351 1126 5150 3.066 0.982 0.158 0.042 18 2.6 Pole_temporal 2757 2076 3312 1.798 0.536 0.130 0.038 21 5.0 S_calcarine 3832 2513 3678 1.737 0.603 0.096 0.021 18 3.8 S_central 997 660 1098 1.891 0.478 0.093 0.017 5 0.7 S_cingul-Marginalis 568 382 742 2.164 0.750 0.093 0.016 2 0.4 S_circular_insula_ant 1679 1093 2418 2.770 0.862 0.075 0.011 5 0.8 S_circular_insula_inf 1959 1246 2466 2.207 0.786 0.086 0.017 7 1.2 S_circular_insula_sup 851 553 1573 2.790 0.650 0.105 0.016 5 0.7 S_collat_transv_ant 503 338 563 2.396 0.468 0.135 0.029 4 0.8 S_collat_transv_post 2291 1466 2626 2.033 0.725 0.088 0.019 12 1.7 S_front_inf 1863 1266 2837 2.285 0.681 0.115 0.026 12 2.4 S_front_middle 3425 2204 5150 2.426 0.744 0.100 0.026 20 3.5 S_front_sup 127 93 130 1.451 0.272 0.091 0.013 0 0.1 S_interm_prim-Jensen 2990 1975 3421 1.998 0.727 0.100 0.021 16 2.5 S_intrapariet_and_P_trans 751 495 929 2.112 0.571 0.115 0.027 4 0.8 S_oc_middle_and_Lunatus 1317 869 1651 2.211 0.503 0.107 0.021 8 1.1 S_oc_sup_and_transversal 785 524 1466 2.401 0.799 0.128 0.035 7 1.4 S_occipital_ant 1002 665 1326 2.463 0.508 0.099 0.019 5 0.8 S_oc-temp_lat 1697 1097 2042 2.031 0.658 0.089 0.017 8 1.0 S_oc-temp_med_and_Lingual 251 174 343 2.116 0.679 0.115 0.032 1 0.3 S_orbital_lateral 397 280 1257 3.290 1.026 0.087 0.022 3 0.2 S_orbital_med-olfact 837 579 1958 2.968 1.223 0.110 0.030 6 0.9 S_orbital-H_Shaped 2652 1790 3595 2.292 0.627 0.114 0.025 16 3.0 S_parieto_occipital 1347 782 1347 2.016 0.898 0.078 0.012 7 0.5 S_pericallosal 4404 2974 4353 1.606 0.514 0.103 0.024 28 4.1 S_postcentral 1449 937 2016 2.634 0.779 0.086 0.018 6 1.0 S_precentral-inf-part 2156 1402 2639 2.324 0.701 0.099 0.021 11 2.0 S_precentral-sup-part 645 433 915 2.502 0.885 0.097 0.013 3 0.3 S_suborbital 1267 837 1601 2.076 0.697 0.110 0.023 8 1.2 S_subparietal 1459 993 2016 2.062 0.735 0.112 0.027 9 1.5 S_temporal_inf 4876 3259 6533 2.183 0.676 0.097 0.022 27 4.6 S_temporal_sup 235 175 328 2.130 0.661 0.130 0.029 2 0.2 S_temporal_transverse @#@FSTIME 2024:08:07:18:21:51 mris_anatomical_stats N 14 e 7.16 S 0.15 U 7. 01 P 99% M 482288 F 0 R 138312 W 0 c 31 w 1 I 0 O 40 L 9.78 10.30 10.45 @#@FSLOADPOST 2024:08:07:18:21:58 mris_anatomical_stats N 14 10.04 10.34 10. 46 #----------------------------------------- #@# Parcellation Stats 2 rh 公曆 20廿四年八月七日週三十八時廿一分58秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0003 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 244738 Total vertex volume 244461 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 840 627 2112 2.582 0.973 0.152 0.045 12 1.8 G_and_S_frontomargin 1379 988 3671 2.751 0.885 0.133 0.041 13 2.3 G_and_S_occipital_inf 1248 815 2143 2.112 0.716 0.128 0.041 10 2.0 G_and_S_paracentral 1463 963 3142 2.717 0.934 0.117 0.032 12 1.6 G_and_S_subcentral 1127 844 3264 2.595 1.151 0.150 0.041 15 2.0 G_and_S_transv_frontopol 2592 1799 6095 2.904 1.000 0.109 0.023 18 2.5 G_and_S_cingul-Ant 1578 1095 2634 2.229 0.635 0.134 0.032 14 2.2 G_and_S_cingul-Mid-Ant 1437 932 1999 2.061 0.752 0.110 0.024 9 1.4 G_and_S_cingul-Mid-Post 465 297 1317 3.234 0.951 0.118 0.037 4 0.6 G_cingul-Post-dorsal 379 260 909 2.982 0.927 0.127 0.024 4 0.4 G_cingul-Post-ventral 2284 1703 4033 2.090 0.772 0.154 0.048 24 4.6 G_cuneus 1456 1031 3501 2.428 0.884 0.138 0.042 20 2.7 G_front_inf-Opercular 264 189 1063 3.100 1.088 0.154 0.040 4 0.4 G_front_inf-Orbital 745 524 2016 2.586 1.042 0.132 0.043 10 1.2 G_front_inf-Triangul 5022 3598 11623 2.342 0.954 0.159 0.051 69 11.4 G_front_middle 7838 5371 17684 2.509 0.888 0.136 0.038 83 12.1 G_front_sup 652 525 1574 2.976 0.673 0.161 0.050 8 1.4 G_Ins_lg_and_S_cent_ins 778 640 2636 3.163 0.863 0.150 0.040 12 1.2 G_insular_short 2110 1611 6670 2.839 0.926 0.161 0.056 32 4.8 G_occipital_middle 1867 1437 3329 2.035 0.713 0.159 0.054 27 4.4 G_occipital_sup 1768 1414 4735 2.632 0.761 0.166 0.054 27 4.0 G_oc-temp_lat-fusifor 1975 1628 5532 2.512 0.872 0.159 0.054 34 4.7 G_oc-temp_med-Lingual 1212 895 3889 2.832 0.919 0.147 0.043 16 2.3 G_oc-temp_med-Parahip 2002 1468 6814 3.133 0.908 0.132 0.034 23 2.9 G_orbital 1795 1369 5037 2.570 0.897 0.151 0.050 24 3.5 G_pariet_inf-Angular 2262 1677 6567 2.673 0.968 0.136 0.041 27 4.0 G_pariet_inf-Supramar 3320 2419 5627 1.910 0.718 0.147 0.046 39 6.3 G_parietal_sup 2278 1374 3715 2.146 0.864 0.114 0.032 24 3.1 G_postcentral 3550 2170 5582 2.130 0.817 0.118 0.037 36 5.5 G_precentral 2682 2035 5771 2.252 0.944 0.149 0.040 30 4.7 G_precuneus 587 458 2875 3.515 0.905 0.144 0.034 9 0.8 G_rectus 420 275 839 2.811 1.339 0.088 0.028 3 0.3 G_subcallosal 398 259 956 2.673 0.623 0.132 0.039 5 0.7 G_temp_sup-G_T_transv 1721 1276 6268 3.413 1.013 0.137 0.037 21 2.7 G_temp_sup-Lateral 753 541 2122 3.387 0.874 0.073 0.017 3 0.3 G_temp_sup-Plan_polar 809 560 1496 2.315 0.879 0.078 0.014 3 0.5 G_temp_sup-Plan_tempo 1797 1441 6556 3.018 1.017 0.174 0.061 28 4.5 G_temporal_inf 2469 1897 9012 2.999 0.987 0.149 0.040 36 4.1 G_temporal_middle 309 207 349 2.020 0.569 0.114 0.023 2 0.3 Lat_Fis-ant-Horizont 198 134 234 2.130 0.812 0.127 0.032 1 0.3 Lat_Fis-ant-Vertical 1348 850 1828 2.802 0.621 0.075 0.015 4 0.7 Lat_Fis-post 3616 2726 6895 2.120 0.805 0.145 0.046 36 7.8 Pole_occipital 1271 1041 6112 3.426 0.943 0.164 0.044 17 2.4 Pole_temporal 2223 1576 2647 1.970 0.567 0.130 0.043 122 5.4 S_calcarine 3089 1988 2717 1.595 0.497 0.091 0.019 16 2.6 S_central 1216 830 1240 1.627 0.391 0.118 0.034 9 2.0 S_cingul-Marginalis 618 411 787 2.332 0.449 0.094 0.019 2 0.6 S_circular_insula_ant 1447 917 1844 2.257 0.829 0.074 0.010 4 0.7 S_circular_insula_inf 1577 996 2234 2.747 0.898 0.086 0.017 6 1.0 S_circular_insula_sup 950 617 1747 2.820 0.655 0.098 0.024 6 0.7 S_collat_transv_ant 546 357 685 2.507 0.481 0.117 0.028 3 0.7 S_collat_transv_post 2050 1360 1989 1.743 0.521 0.113 0.028 15 2.2 S_front_inf 2345 1544 2495 1.755 0.511 0.103 0.023 12 2.2 S_front_middle 3294 2206 4954 2.545 0.729 0.106 0.025 19 3.2 S_front_sup 291 196 443 1.775 0.692 0.065 0.013 1 0.1 S_interm_prim-Jensen 3387 2203 4152 2.108 0.799 0.099 0.021 19 3.2 S_intrapariet_and_P_trans 889 644 1275 2.140 0.558 0.132 0.042 8 1.3 S_oc_middle_and_Lunatus 1462 1005 1647 1.914 0.534 0.114 0.028 11 1.7 S_oc_sup_and_transversal 705 474 1060 2.721 0.704 0.125 0.037 6 1.0 S_occipital_ant 716 517 1118 2.265 0.687 0.128 0.033 7 0.9 S_oc-temp_lat 1694 1152 2030 1.909 0.521 0.106 0.026 13 1.7 S_oc-temp_med_and_Lingual 542 366 661 1.861 0.656 0.125 0.028 4 0.8 S_orbital_lateral 545 398 846 2.134 0.724 0.148 0.039 6 1.0 S_orbital_med-olfact 947 635 1983 2.916 0.876 0.099 0.023 5 0.9 S_orbital-H_Shaped 2511 1666 3262 2.355 0.638 0.111 0.026 16 2.7 S_parieto_occipital 1191 717 1258 2.135 0.709 0.104 0.029 9 1.4 S_pericallosal 3049 1976 2836 1.583 0.461 0.093 0.018 17 2.2 S_postcentral 2247 1454 2793 2.148 0.601 0.106 0.023 15 2.1 S_precentral-inf-part 1910 1218 2022 1.970 0.588 0.113 0.027 13 2.3 S_precentral-sup-part 352 229 465 2.172 1.001 0.092 0.012 2 0.2 S_suborbital 1465 1019 2097 2.002 0.897 0.126 0.034 11 2.1 S_subparietal 981 661 1733 2.432 0.791 0.106 0.026 5 0.9 S_temporal_inf 5304 3631 8903 2.570 0.707 0.103 0.022 36 4.7 S_temporal_sup 294 206 315 1.762 0.620 0.113 0.012 2 0.2 S_temporal_transverse @#@FSTIME 2024:08:07:18:21:58 mris_anatomical_stats N 14 e 6.67 S 0.13 U 6. 53 P 99% M 470488 F 0 R 134816 W 0 c 31 w 1 I 0 O 40 L 10.04 10.34 10.46 @#@FSLOADPOST 2024:08:07:18:22:05 mris_anatomical_stats N 14 9.65 10.25 10.43 #----------------------------------------- #@# Parcellation Stats 3 lh 公曆 20廿四年八月七日週三十八時廿二分五秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0003 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 252503 Total vertex volume 252258 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 2025 1374 3305 2.241 0.771 0.115 0.021 21 1.8 caudalanteriorcingulate 4057 2654 5935 2.336 0.749 0.118 0.033 31 5.7 caudalmiddlefrontal 3132 2253 4914 2.232 0.636 0.135 0.036 28 4.7 cuneus 603 444 1983 2.866 1.043 0.135 0.034 5 0.9 entorhinal 3695 2612 7243 2.398 0.791 0.125 0.031 37 4.9 fusiform 5181 3535 10314 2.501 0.879 0.119 0.032 43 6.9 inferiorparietal 4257 3136 12385 2.824 1.039 0.137 0.040 45 6.9 inferiortemporal 1656 1111 2981 2.360 0.998 0.105 0.023 12 1.4 isthmuscingulate 6807 4612 14781 2.515 0.923 0.125 0.034 67 9.5 lateraloccipital 2869 2003 8225 3.066 1.129 0.114 0.032 25 3.3 lateralorbitofrontal 4425 3171 7572 2.102 0.770 0.128 0.039 47 7.1 lingual 1839 1396 6094 3.234 0.990 0.127 0.029 24 2.1 medialorbitofrontal 5548 3920 13897 2.623 0.950 0.129 0.036 54 8.9 middletemporal 1055 655 2062 2.548 0.933 0.074 0.014 5 0.5 parahippocampal 2370 1579 3337 2.100 0.688 0.121 0.034 19 3.5 paracentral 2124 1344 4634 2.744 0.933 0.098 0.026 15 2.0 parsopercularis 1113 828 3279 2.624 1.000 0.139 0.038 13 1.7 parsorbitalis 2167 1429 3991 2.204 0.847 0.114 0.029 19 2.4 parstriangularis 1889 1522 2569 1.852 0.561 0.157 0.049 19 4.5 pericalcarine 8674 5701 12060 1.868 0.754 0.111 0.028 66 10.2 postcentral 1298 832 1825 2.078 0.682 0.104 0.023 11 1.2 posteriorcingulate 9349 6012 13938 2.180 0.788 0.113 0.030 68 12.4 precentral 6219 4451 10754 2.180 0.743 0.125 0.029 52 7.8 precuneus 1722 1176 3687 2.584 1.079 0.107 0.025 14 1.7 rostralanteriorcingulate 6508 4442 14357 2.435 0.977 0.124 0.034 64 9.2 rostralmiddlefrontal 11777 7944 27056 2.692 0.928 0.122 0.035 109 16.6 superiorfrontal 8370 5751 11847 1.891 0.700 0.116 0.030 68 10.9 superiorparietal 7503 5244 17872 2.670 1.021 0.100 0.023 65 6.8 superiortemporal 5581 3869 11048 2.354 0.871 0.117 0.032 46 7.3 supramarginal 629 441 1180 2.354 0.672 0.121 0.030 5 0.7 transversetemporal 3143 2191 7132 3.062 1.010 0.105 0.026 24 3.3 insula @#@FSTIME 2024:08:07:18:22:05 mris_anatomical_stats N 14 e 6.66 S 0.15 U 6. 50 P 99% M 482132 F 0 R 138330 W 0 c 24 w 17 I 0 O 24 L 9.65 10.25 10.43 @#@FSLOADPOST 2024:08:07:18:22:12 mris_anatomical_stats N 14 9.43 10.19 10.41 #----------------------------------------- #@# Parcellation Stats 3 rh 公曆 20廿四年八月七日週三十八時廿二分十二秒 /home/chang/GBM_Data/VBG/0003/0003/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0003 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 244738 Total vertex volume 244461 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 1210 815 2531 2.463 0.849 0.121 0.024 12 1.2 caudalanteriorcingulate 4551 3145 7605 2.338 0.795 0.138 0.037 46 7.7 caudalmiddlefrontal 2868 2052 4423 2.059 0.719 0.143 0.042 27 5.0 cuneus 497 447 1845 2.793 0.906 0.193 0.058 7 1.5 entorhinal 3543 2707 8029 2.510 0.810 0.148 0.045 45 6.6 fusiform 6010 4239 13643 2.643 0.816 0.124 0.034 57 8.2 inferiorparietal 3676 2738 10922 2.859 0.949 0.145 0.045 41 6.6 inferiortemporal 1252 818 2588 2.723 1.032 0.106 0.028 9 1.4 isthmuscingulate 8173 6105 16919 2.331 0.854 0.145 0.046 92 16.1 lateraloccipital 3084 2207 7582 2.812 0.905 0.130 0.035 32 4.8 lateralorbitofrontal 3514 2685 7434 2.224 0.813 0.141 0.045 46 7.0 lingual 1611 1145 5205 3.065 1.240 0.119 0.027 16 1.7 medialorbitofrontal 4842 3557 13265 2.826 0.891 0.126 0.031 50 6.3 middletemporal 991 620 1872 2.375 0.859 0.091 0.019 6 0.8 parahippocampal 2366 1475 3093 2.015 0.611 0.111 0.027 16 2.5 paracentral 2404 1615 4129 2.360 0.738 0.112 0.030 21 3.1 parsopercularis 935 654 2740 2.820 1.040 0.124 0.029 9 1.2 parsorbitalis 1711 1151 3372 2.350 0.971 0.119 0.030 17 2.0 parstriangularis 1838 1331 2389 1.981 0.524 0.153 0.056 119 5.3 pericalcarine 7211 4608 9881 1.897 0.818 0.100 0.024 51 7.2 postcentral 1737 1159 2605 2.134 0.781 0.131 0.038 15 2.8 posteriorcingulate 8568 5402 11753 2.031 0.764 0.115 0.031 73 11.3 precentral 6364 4548 11022 2.253 0.866 0.128 0.035 57 9.5 precuneus 964 657 2591 3.067 1.090 0.091 0.019 7 0.7 rostralanteriorcingulate 6238 4296 11281 2.089 0.878 0.134 0.041 64 10.5 rostralmiddlefrontal 14895 10275 29674 2.441 0.864 0.126 0.033 134 20.1 superiorfrontal 7890 5514 11656 1.957 0.729 0.126 0.035 73 11.7 superiorparietal 6814 4816 17356 2.846 1.016 0.112 0.026 58 7.2 superiortemporal 4382 3045 8898 2.411 0.939 0.113 0.031 37 5.5 supramarginal 508 345 1041 2.458 0.683 0.109 0.030 5 0.6 transversetemporal 3254 2362 7116 2.928 0.836 0.114 0.027 27 3.5 insula @#@FSTIME 2024:08:07:18:22:12 mris_anatomical_stats N 14 e 5.81 S 0.12 U 5. 68 P 99% M 470448 F 0 R 134816 W 0 c 30 w 1 I 0 O 24 L 9.43 10.19 10.41 @#@FSLOADPOST 2024:08:07:18:22:18 mris_anatomical_stats N 14 9.64 10.22 10.42 #-------------------------------------------- #@# ASeg Stats 公曆 20廿四年八月七日週三十八時廿二分十八秒 /home/chang/GBM_Data/VBG/0003/0003 mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 0003 setting seed for random number genererator to 1234 7.4.1 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 0003 sysname Linux hostname chang-System-Product-Name machine x86_64 user chang whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) Computing euler number orig.nofix lheno = -62, rheno = -62 orig.nofix lhholes = 32, rhholes = 32 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:08:07:18:22:18 mri_segstats N 32 e 143.11 S 0.34 U 142.75 P 99% M 290072 F 0 R 753890 W 0 c 481 w 66 I 0 O 24 L 9.64 10.22 10.42 @#@FSLOADPOST 2024:08:07:18:24:41 mri_segstats N 32 10.18 10.29 10.42 /home/chang/GBM_Data/VBG/0003/0003/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/chang/GBM_Data/VBG/0003; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh 公曆 20廿四年八月七日週三十八時廿四分41秒 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0003 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 343 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4472 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:41 mri_label2label N 12 e 2.25 S 0.16 U 2.08 P 99% M 557012 F 0 R 165787 W 0 c 15 w 11 I 16720 O 312 L 10.18 10.29 10.42 @#@FSLOADPOST 2024:08:07:18:24:43 mri_label2label N 12 10.18 10.29 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0003 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 1619 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9528 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:43 mri_label2label N 12 e 3.17 S 0.13 U 3.04 P 99% M 556908 F 0 R 165867 W 0 c 24 w 3 I 632 O 696 L 10.18 10.29 10.42 @#@FSLOADPOST 2024:08:07:18:24:46 mri_label2label N 12 10.24 10.30 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0003 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4272 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:46 mri_label2label N 12 e 2.75 S 0.18 U 2.57 P 99% M 557620 F 0 R 165781 W 0 c 14 w 3 I 320 O 272 L 10.24 10.30 10.42 @#@FSLOADPOST 2024:08:07:18:24:49 mri_label2label N 12 10.24 10.30 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0003 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 395 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6378 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:49 mri_label2label N 12 e 2.75 S 0.18 U 2.57 P 99% M 557736 F 0 R 165817 W 0 c 12 w 2 I 472 O 432 L 10.24 10.30 10.42 @#@FSLOADPOST 2024:08:07:18:24:52 mri_label2label N 12 10.06 10.26 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0003 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 894 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6678 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:52 mri_label2label N 12 e 2.90 S 0.20 U 2.69 P 99% M 557164 F 0 R 165818 W 0 c 29 w 2 I 456 O 472 L 10.06 10.26 10.41 @#@FSLOADPOST 2024:08:07:18:24:55 mri_label2label N 12 10.14 10.27 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0003 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 385 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4455 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:55 mri_label2label N 12 e 2.70 S 0.18 U 2.52 P 99% M 557824 F 0 R 165786 W 0 c 9 w 2 I 320 O 312 L 10.14 10.27 10.41 @#@FSLOADPOST 2024:08:07:18:24:57 mri_label2label N 12 10.14 10.27 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0003 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 2204 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15793 mri_label2label: Done @#@FSTIME 2024:08:07:18:24:57 mri_label2label N 12 e 3.43 S 0.18 U 3.24 P 99% M 558504 F 0 R 165970 W 0 c 11 w 4 I 1056 O 1136 L 10.14 10.27 10.41 @#@FSLOADPOST 2024:08:07:18:25:01 mri_label2label N 12 10.05 10.25 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0003 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 233 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4414 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:01 mri_label2label N 12 e 2.78 S 0.20 U 2.58 P 99% M 557264 F 0 R 165787 W 0 c 16 w 2 I 328 O 264 L 10.05 10.25 10.41 @#@FSLOADPOST 2024:08:07:18:25:04 mri_label2label N 12 10.05 10.25 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0003 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 455 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3877 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:04 mri_label2label N 12 e 2.65 S 0.15 U 2.49 P 99% M 556904 F 0 R 165768 W 0 c 28 w 3 I 272 O 280 L 10.05 10.25 10.41 @#@FSLOADPOST 2024:08:07:18:25:06 mri_label2label N 12 9.96 10.23 10.40 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.label --trgsubject 0003 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 866 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5507 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:06 mri_label2label N 12 e 2.98 S 0.17 U 2.80 P 99% M 557624 F 0 R 165858 W 0 c 15 w 62 I 376 O 432 L 9.96 10.23 10.40 @#@FSLOADPOST 2024:08:07:18:25:09 mri_label2label N 12 9.96 10.23 10.40 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.label --trgsubject 0003 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 2231 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10345 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:09 mri_label2label N 12 e 3.04 S 0.15 U 2.88 P 99% M 557516 F 0 R 165874 W 0 c 14 w 5 I 664 O 848 L 9.97 10.23 10.40 @#@FSLOADPOST 2024:08:07:18:25:12 mri_label2label N 12 9.97 10.23 10.40 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.label --trgsubject 0003 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 217 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2235 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:12 mri_label2label N 12 e 2.52 S 0.19 U 2.32 P 100% M 557644 F 0 R 166517 W 0 c 15 w 2 I 168 O 168 L 9.97 10.23 10.40 @#@FSLOADPOST 2024:08:07:18:25:15 mri_label2label N 12 9.81 10.19 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0003 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1358 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:15 mri_label2label N 12 e 2.60 S 0.21 U 2.39 P 99% M 557008 F 0 R 165729 W 0 c 9 w 3 I 264 O 88 L 9.81 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:17 mri_label2label N 12 9.81 10.19 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0003 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1268 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:17 mri_label2label N 12 e 2.66 S 0.20 U 2.45 P 99% M 557208 F 0 R 165725 W 0 c 10 w 4 I 112 O 88 L 9.81 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:20 mri_label2label N 12 9.82 10.19 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 455 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:20 mri_label2label N 12 e 2.90 S 0.18 U 2.71 P 99% M 557340 F 0 R 165725 W 0 c 10 w 2 I 40 O 40 L 9.82 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:23 mri_label2label N 12 9.82 10.19 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 751 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:23 mri_label2label N 12 e 2.57 S 0.20 U 2.36 P 99% M 557272 F 0 R 165717 W 0 c 10 w 3 I 72 O 56 L 9.82 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:26 mri_label2label N 12 10.00 10.22 10.39 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1946 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:26 mri_label2label N 12 e 2.05 S 0.19 U 1.86 P 99% M 557668 F 0 R 165743 W 0 c 8 w 2 I 176 O 136 L 10.00 10.22 10.39 @#@FSLOADPOST 2024:08:07:18:25:28 mri_label2label N 12 10.00 10.22 10.39 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 358 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2459 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:28 mri_label2label N 12 e 2.42 S 0.16 U 2.26 P 100% M 557468 F 0 R 165745 W 0 c 10 w 3 I 200 O 200 L 10.00 10.22 10.39 @#@FSLOADPOST 2024:08:07:18:25:30 mri_label2label N 12 9.84 10.18 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 694 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4571 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:30 mri_label2label N 12 e 2.76 S 0.17 U 2.59 P 99% M 557836 F 0 R 165787 W 0 c 9 w 3 I 360 O 360 L 9.84 10.18 10.38 @#@FSLOADPOST 2024:08:07:18:25:33 mri_label2label N 12 9.84 10.18 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 951 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3870 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:33 mri_label2label N 12 e 2.64 S 0.18 U 2.46 P 100% M 557352 F 0 R 166535 W 0 c 14 w 4 I 272 O 320 L 9.84 10.18 10.38 @#@FSLOADPOST 2024:08:07:18:25:36 mri_label2label N 12 10.01 10.21 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 496 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1782 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:36 mri_label2label N 12 e 2.67 S 0.21 U 2.46 P 100% M 557240 F 0 R 165733 W 0 c 14 w 2 I 128 O 160 L 10.01 10.21 10.38 @#@FSLOADPOST 2024:08:07:18:25:38 mri_label2label N 12 10.01 10.21 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject 0003 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 174 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1180 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:38 mri_label2label N 12 e 2.60 S 0.21 U 2.39 P 99% M 557468 F 0 R 165728 W 0 c 10 w 3 I 96 O 96 L 10.01 10.21 10.38 @#@FSLOADPOST 2024:08:07:18:25:41 mri_label2label N 12 9.93 10.19 10.38 mris_label2annot --s 0003 --ctab /usr/local/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl. label --l lh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/label cmdline mris_label2annot --s 0003 --ctab /usr/local/freesurfer/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl. label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname chang-System-Product-Name machine x86_64 user chang subject 0003 hemi lh SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 ColorTable /usr/local/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig Index Offset 0 0 reading lh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading lh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading lh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading lh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading lh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading lh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading lh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading lh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 121569 unhit vertices Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/lh.mpm.vpnl.annot @#@FSTIME 2024:08:07:18:25:41 mris_label2annot N 26 e 0.40 S 0.06 U 0.33 P 99% M 158036 F 8 R 42714 W 0 c 3 w 7 I 1328 O 2136 L 9.93 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:41 mris_label2annot N 26 9.93 10.19 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1058 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:41 mri_label2label N 12 e 2.73 S 0.16 U 2.55 P 99% M 557732 F 0 R 165810 W 0 c 11 w 87 I 96 O 80 L 9.93 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:44 mri_label2label N 12 9.93 10.19 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 511 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2603 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:44 mri_label2label N 12 e 2.73 S 0.16 U 2.56 P 99% M 556856 F 0 R 165750 W 0 c 20 w 3 I 192 O 208 L 9.93 10.19 10.38 @#@FSLOADPOST 2024:08:07:18:25:47 mri_label2label N 12 10.10 10.22 10.39 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1531 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:47 mri_label2label N 12 e 2.51 S 0.21 U 2.29 P 99% M 556712 F 0 R 166505 W 0 c 15 w 3 I 136 O 96 L 10.10 10.22 10.39 @#@FSLOADPOST 2024:08:07:18:25:49 mri_label2label N 12 10.09 10.22 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2066 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:49 mri_label2label N 12 e 2.48 S 0.17 U 2.31 P 99% M 557284 F 0 R 165746 W 0 c 10 w 3 I 184 O 144 L 10.09 10.22 10.38 @#@FSLOADPOST 2024:08:07:18:25:52 mri_label2label N 12 10.09 10.22 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 346 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2665 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:52 mri_label2label N 12 e 2.67 S 0.17 U 2.49 P 99% M 557416 F 0 R 165750 W 0 c 10 w 4 I 208 O 192 L 10.09 10.22 10.38 @#@FSLOADPOST 2024:08:07:18:25:55 mri_label2label N 12 10.24 10.25 10.39 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 158 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1707 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:55 mri_label2label N 12 e 2.60 S 0.18 U 2.42 P 100% M 557748 F 0 R 165736 W 0 c 11 w 5 I 144 O 128 L 10.24 10.25 10.39 @#@FSLOADPOST 2024:08:07:18:25:57 mri_label2label N 12 10.24 10.25 10.39 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 1215 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8250 mri_label2label: Done @#@FSTIME 2024:08:07:18:25:57 mri_label2label N 12 e 3.27 S 0.18 U 3.09 P 100% M 557944 F 0 R 165842 W 0 c 16 w 3 I 616 O 608 L 10.24 10.25 10.39 @#@FSLOADPOST 2024:08:07:18:26:00 mri_label2label N 12 10.14 10.22 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1940 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:00 mri_label2label N 12 e 2.57 S 0.18 U 2.38 P 100% M 557760 F 0 R 165737 W 0 c 8 w 3 I 168 O 112 L 10.14 10.22 10.38 @#@FSLOADPOST 2024:08:07:18:26:03 mri_label2label N 12 10.14 10.22 10.38 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1345 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:03 mri_label2label N 12 e 2.86 S 0.19 U 2.67 P 99% M 557452 F 0 R 165723 W 0 c 8 w 3 I 104 O 104 L 10.14 10.22 10.38 @#@FSLOADPOST 2024:08:07:18:26:06 mri_label2label N 12 10.61 10.32 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 616 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4021 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:06 mri_label2label N 12 e 2.91 S 0.16 U 2.74 P 99% M 557816 F 0 R 165769 W 0 c 14 w 3 I 304 O 320 L 10.61 10.32 10.41 @#@FSLOADPOST 2024:08:07:18:26:09 mri_label2label N 12 10.61 10.32 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 1050 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4384 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:09 mri_label2label N 12 e 2.72 S 0.21 U 2.51 P 99% M 557052 F 0 R 165774 W 0 c 21 w 4 I 296 O 368 L 10.61 10.32 10.41 @#@FSLOADPOST 2024:08:07:18:26:12 mri_label2label N 12 10.64 10.33 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0003 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 543 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:12 mri_label2label N 12 e 1.94 S 0.17 U 1.77 P 99% M 557104 F 0 R 165713 W 0 c 9 w 2 I 48 O 40 L 10.64 10.33 10.42 @#@FSLOADPOST 2024:08:07:18:26:14 mri_label2label N 12 10.64 10.33 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.thresh.la bel --trgsubject 0003 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.entorhinal_exvivo.thresh.la bel srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 505 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:14 mri_label2label N 12 e 2.26 S 0.19 U 2.06 P 100% M 556700 F 0 R 165710 W 0 c 18 w 2 I 48 O 40 L 10.64 10.33 10.42 @#@FSLOADPOST 2024:08:07:18:26:16 mri_label2label N 12 10.51 10.31 10.41 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.thresh.la bel --trgsubject 0003 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/lh.perirhinal_exvivo.thresh.la bel srcsubject = fsaverage trgsubject = 0003 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 136375 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 493 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:16 mri_label2label N 12 e 3.07 S 0.25 U 2.81 P 99% M 556592 F 0 R 166570 W 0 c 39 w 87 I 48 O 40 L 10.51 10.31 10.41 @#@FSLOADPOST 2024:08:07:18:26:19 mri_label2label N 12 10.51 10.31 10.41 mris_label2annot --s 0003 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh. V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/label cmdline mris_label2annot --s 0003 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh. V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chang-System-Product-Name machine x86_64 user chang subject 0003 hemi lh SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 90530 unhit vertices Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/lh.BA_exvivo.annot @#@FSTIME 2024:08:07:18:26:19 mris_label2annot N 38 e 0.47 S 0.05 U 0.41 P 99% M 158300 F 0 R 42933 W 0 c 3 w 7 I 8 O 2136 L 10.51 10.31 10.41 @#@FSLOADPOST 2024:08:07:18:26:19 mris_label2annot N 38 10.39 10.29 10.40 mris_label2annot --s 0003 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/label cmdline mris_label2annot --s 0003 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chang-System-Product-Name machine x86_64 user chang subject 0003 hemi lh SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 109089 unhit vertices Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:08:07:18:26:19 mris_label2annot N 38 e 0.43 S 0.06 U 0.35 P 98% M 158432 F 0 R 42847 W 0 c 6 w 3 I 0 O 2136 L 10.39 10.29 10.40 @#@FSLOADPOST 2024:08:07:18:26:20 mris_label2annot N 38 10.39 10.29 10.40 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 0003 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 252503 Total vertex volume 252258 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 1219 712 2063 2.214 0.736 0.128 0.041 13 2.0 BA1_exvivo 5934 3970 7604 1.790 0.717 0.113 0.029 46 7.2 BA2_exvivo 1212 798 1139 1.886 0.602 0.123 0.030 9 1.4 BA3a_exvivo 2786 1856 4499 1.934 0.880 0.099 0.024 18 2.7 BA3b_exvivo 1912 1210 2756 2.045 0.702 0.116 0.034 14 3.0 BA4a_exvivo 1661 1078 1822 1.846 0.618 0.091 0.023 7 1.8 BA4p_exvivo 11737 7467 20672 2.472 0.869 0.120 0.036 102 18.1 BA6_exvivo 2041 1295 4534 2.984 0.825 0.095 0.025 11 1.7 BA44_exvivo 2851 1883 5563 2.221 0.888 0.111 0.030 25 3.3 BA45_exvivo 3305 2555 4984 1.926 0.739 0.142 0.043 34 6.4 V1_exvivo 8205 5769 14627 2.306 0.786 0.134 0.040 83 14.2 V2_exvivo 1741 1172 3785 2.492 0.817 0.126 0.030 16 2.4 MT_exvivo 676 503 2235 3.124 0.913 0.142 0.039 7 1.2 perirhinal_exvivo 565 407 1837 3.012 1.038 0.110 0.024 4 0.6 entorhinal_exvivo @#@FSTIME 2024:08:07:18:26:20 mris_anatomical_stats N 12 e 2.66 S 0.16 U 2. 49 P 99% M 477632 F 0 R 137191 W 0 c 16 w 1 I 0 O 24 L 10.39 10.29 10.40 @#@FSLOADPOST 2024:08:07:18:26:23 mris_anatomical_stats N 12 10.39 10.29 10. 40 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0003 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 252503 Total vertex volume 252258 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 810 475 1209 2.056 0.573 0.136 0.044 9 1.5 BA1_exvivo 2334 1578 2772 1.649 0.594 0.123 0.033 20 3.3 BA2_exvivo 1014 661 876 1.768 0.475 0.125 0.031 8 1.2 BA3a_exvivo 1615 1057 1577 1.455 0.403 0.079 0.015 6 1.1 BA3b_exvivo 2090 1333 2707 1.932 0.685 0.117 0.034 14 3.5 BA4a_exvivo 1377 902 1508 1.903 0.609 0.101 0.027 7 1.8 BA4p_exvivo 6948 4386 10734 2.311 0.799 0.119 0.034 61 10.1 BA6_exvivo 1238 782 2940 2.940 0.928 0.096 0.026 7 1.1 BA44_exvivo 1186 812 3178 2.533 0.929 0.132 0.041 15 2.0 BA45_exvivo 3483 2694 5373 1.949 0.751 0.137 0.041 34 6.4 V1_exvivo 4106 2975 7313 2.236 0.783 0.145 0.047 49 8.6 V2_exvivo 402 282 838 2.450 0.841 0.144 0.037 5 0.6 MT_exvivo 309 215 832 2.915 0.865 0.106 0.024 2 0.3 perirhinal_exvivo 374 262 1001 2.887 1.087 0.106 0.021 2 0.4 entorhinal_exvivo @#@FSTIME 2024:08:07:18:26:23 mris_anatomical_stats N 12 e 2.68 S 0.13 U 2. 55 P 100% M 478144 F 0 R 141227 W 0 c 8 w 1 I 0 O 24 L 10.39 10.29 10.40 @#@FSLOADPOST 2024:08:07:18:26:25 mris_anatomical_stats N 12 10.76 10.37 10. 43 #-------------------------------------------- #@# BA_exvivo Labels rh 公曆 20廿四年八月七日週三十八時廿六分廿五秒 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0003 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4154 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:25 mri_label2label N 12 e 2.82 S 0.17 U 2.64 P 99% M 549540 F 0 R 163447 W 0 c 11 w 7 I 16160 O 264 L 10.76 10.37 10.43 @#@FSLOADPOST 2024:08:07:18:26:28 mri_label2label N 12 10.76 10.37 10.43 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0003 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7020 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:28 mri_label2label N 12 e 2.99 S 0.20 U 2.79 P 99% M 550148 F 0 R 163497 W 0 c 11 w 5 I 520 O 448 L 10.76 10.37 10.43 @#@FSLOADPOST 2024:08:07:18:26:31 mri_label2label N 12 10.70 10.36 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0003 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4021 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:31 mri_label2label N 12 e 2.91 S 0.19 U 2.71 P 99% M 550052 F 0 R 163447 W 0 c 12 w 3 I 312 O 224 L 10.70 10.36 10.42 @#@FSLOADPOST 2024:08:07:18:26:34 mri_label2label N 12 10.70 10.36 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0003 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4651 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:34 mri_label2label N 12 e 3.01 S 0.19 U 2.81 P 99% M 549816 F 0 R 163455 W 0 c 19 w 4 I 352 O 272 L 10.70 10.36 10.42 @#@FSLOADPOST 2024:08:07:18:26:37 mri_label2label N 12 10.64 10.35 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0003 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 378 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6125 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:37 mri_label2label N 12 e 2.97 S 0.20 U 2.77 P 100% M 550116 F 0 R 163481 W 0 c 9 w 3 I 440 O 392 L 10.64 10.35 10.42 @#@FSLOADPOST 2024:08:07:18:26:40 mri_label2label N 12 10.75 10.38 10.43 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0003 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4553 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:40 mri_label2label N 12 e 2.70 S 0.19 U 2.51 P 99% M 549868 F 0 R 163456 W 0 c 15 w 3 I 344 O 256 L 10.75 10.38 10.43 @#@FSLOADPOST 2024:08:07:18:26:43 mri_label2label N 12 10.75 10.38 10.43 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0003 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 1956 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14212 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:43 mri_label2label N 12 e 3.08 S 0.17 U 2.90 P 100% M 550436 F 0 R 163607 W 0 c 13 w 5 I 936 O 1048 L 10.75 10.38 10.43 @#@FSLOADPOST 2024:08:07:18:26:46 mri_label2label N 12 10.61 10.36 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0003 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 879 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7791 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:46 mri_label2label N 12 e 2.89 S 0.17 U 2.71 P 100% M 549408 F 0 R 163503 W 0 c 18 w 4 I 528 O 528 L 10.61 10.36 10.42 @#@FSLOADPOST 2024:08:07:18:26:49 mri_label2label N 12 10.61 10.36 10.42 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0003 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 381 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5736 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:49 mri_label2label N 12 e 2.96 S 0.20 U 2.75 P 99% M 549388 F 0 R 163476 W 0 c 14 w 9 I 416 O 376 L 10.61 10.36 10.42 @#@FSLOADPOST 2024:08:07:18:26:52 mri_label2label N 12 10.64 10.37 10.43 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.label --trgsubject 0003 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 947 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5674 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:52 mri_label2label N 12 e 3.43 S 0.23 U 3.19 P 99% M 549580 F 0 R 163518 W 0 c 14 w 53 I 376 O 432 L 10.64 10.37 10.43 @#@FSLOADPOST 2024:08:07:18:26:55 mri_label2label N 12 11.07 10.46 10.46 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.label --trgsubject 0003 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 2181 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10197 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:55 mri_label2label N 12 e 2.82 S 0.18 U 2.63 P 100% M 549940 F 0 R 163535 W 0 c 10 w 5 I 640 O 800 L 11.07 10.46 10.46 @#@FSLOADPOST 2024:08:07:18:26:58 mri_label2label N 12 11.07 10.46 10.46 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.label --trgsubject 0003 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2197 mri_label2label: Done @#@FSTIME 2024:08:07:18:26:58 mri_label2label N 12 e 2.07 S 0.14 U 1.92 P 99% M 549312 F 0 R 163410 W 0 c 20 w 3 I 160 O 176 L 11.07 10.46 10.46 @#@FSLOADPOST 2024:08:07:18:27:00 mri_label2label N 12 10.91 10.44 10.45 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0003 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1068 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:00 mri_label2label N 12 e 2.62 S 0.17 U 2.44 P 99% M 548704 F 0 R 163393 W 0 c 23 w 3 I 96 O 72 L 10.91 10.44 10.45 @#@FSLOADPOST 2024:08:07:18:27:03 mri_label2label N 12 10.91 10.44 10.45 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0003 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 777 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:03 mri_label2label N 12 e 2.84 S 0.18 U 2.65 P 100% M 548988 F 0 R 164163 W 0 c 10 w 2 I 72 O 56 L 10.91 10.44 10.45 @#@FSLOADPOST 2024:08:07:18:27:06 mri_label2label N 12 10.99 10.47 10.46 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 663 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:06 mri_label2label N 12 e 2.67 S 0.17 U 2.49 P 99% M 549292 F 0 R 163380 W 0 c 9 w 4 I 56 O 56 L 10.99 10.47 10.46 @#@FSLOADPOST 2024:08:07:18:27:08 mri_label2label N 12 10.99 10.47 10.46 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 958 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:08 mri_label2label N 12 e 2.53 S 0.18 U 2.34 P 100% M 549176 F 0 R 163381 W 0 c 12 w 2 I 72 O 88 L 10.99 10.47 10.46 @#@FSLOADPOST 2024:08:07:18:27:11 mri_label2label N 12 11.07 10.49 10.47 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1592 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:11 mri_label2label N 12 e 2.69 S 0.17 U 2.52 P 99% M 549144 F 0 R 163401 W 0 c 16 w 2 I 144 O 104 L 11.07 10.49 10.47 @#@FSLOADPOST 2024:08:07:18:27:14 mri_label2label N 12 11.07 10.49 10.47 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1705 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:14 mri_label2label N 12 e 2.81 S 0.17 U 2.63 P 99% M 549452 F 0 R 164172 W 0 c 10 w 3 I 152 O 120 L 11.07 10.49 10.47 @#@FSLOADPOST 2024:08:07:18:27:16 mri_label2label N 12 11.15 10.52 10.47 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 640 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4307 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:16 mri_label2label N 12 e 3.06 S 0.22 U 2.84 P 100% M 550044 F 0 R 163447 W 0 c 13 w 4 I 328 O 328 L 11.15 10.52 10.47 @#@FSLOADPOST 2024:08:07:18:27:19 mri_label2label N 12 11.30 10.56 10.49 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 794 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3513 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:20 mri_label2label N 12 e 2.96 S 0.22 U 2.74 P 99% M 549684 F 0 R 163429 W 0 c 24 w 3 I 248 O 288 L 11.30 10.56 10.49 @#@FSLOADPOST 2024:08:07:18:27:22 mri_label2label N 12 11.30 10.56 10.49 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 480 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1708 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:22 mri_label2label N 12 e 2.55 S 0.17 U 2.37 P 99% M 549340 F 0 R 163397 W 0 c 13 w 4 I 112 O 152 L 11.30 10.56 10.49 @#@FSLOADPOST 2024:08:07:18:27:25 mri_label2label N 12 11.43 10.60 10.50 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject 0003 --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 408 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1433 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:25 mri_label2label N 12 e 2.54 S 0.17 U 2.37 P 99% M 549696 F 0 R 163431 W 0 c 9 w 39 I 96 O 128 L 11.43 10.60 10.50 @#@FSLOADPOST 2024:08:07:18:27:28 mri_label2label N 12 11.43 10.60 10.50 mris_label2annot --s 0003 --ctab /usr/local/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl. label --l rh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/label cmdline mris_label2annot --s 0003 --ctab /usr/local/freesurfer/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl. label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname chang-System-Product-Name machine x86_64 user chang subject 0003 hemi rh SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 ColorTable /usr/local/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig Index Offset 0 0 reading rh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading rh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading rh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading rh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading rh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading rh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading rh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading rh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 118945 unhit vertices Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/rh.mpm.vpnl.annot @#@FSTIME 2024:08:07:18:27:28 mris_label2annot N 26 e 0.53 S 0.06 U 0.47 P 99% M 154132 F 0 R 41590 W 0 c 2 w 7 I 0 O 2080 L 11.43 10.60 10.50 @#@FSLOADPOST 2024:08:07:18:27:28 mris_label2annot N 26 11.43 10.60 10.50 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 926 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:28 mri_label2label N 12 e 2.62 S 0.17 U 2.44 P 99% M 549404 F 0 R 163388 W 0 c 13 w 3 I 80 O 64 L 11.43 10.60 10.50 @#@FSLOADPOST 2024:08:07:18:27:31 mri_label2label N 12 11.32 10.59 10.50 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2813 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:31 mri_label2label N 12 e 2.68 S 0.17 U 2.50 P 99% M 549752 F 0 R 164188 W 0 c 9 w 2 I 240 O 184 L 11.32 10.59 10.50 @#@FSLOADPOST 2024:08:07:18:27:33 mri_label2label N 12 11.32 10.59 10.50 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1708 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:34 mri_label2label N 12 e 2.59 S 0.19 U 2.40 P 99% M 549216 F 0 R 164171 W 0 c 12 w 3 I 152 O 96 L 11.32 10.59 10.50 @#@FSLOADPOST 2024:08:07:18:27:36 mri_label2label N 12 11.05 10.55 10.48 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2228 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:36 mri_label2label N 12 e 2.98 S 0.20 U 2.78 P 99% M 549736 F 0 R 164183 W 0 c 15 w 4 I 192 O 144 L 11.05 10.55 10.48 @#@FSLOADPOST 2024:08:07:18:27:39 mri_label2label N 12 11.05 10.55 10.48 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1429 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:39 mri_label2label N 12 e 2.63 S 0.19 U 2.43 P 100% M 549436 F 0 R 163397 W 0 c 10 w 2 I 120 O 88 L 11.05 10.55 10.48 @#@FSLOADPOST 2024:08:07:18:27:42 mri_label2label N 12 11.29 10.60 10.50 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1510 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:42 mri_label2label N 12 e 2.38 S 0.20 U 2.17 P 99% M 548692 F 0 R 163396 W 0 c 20 w 3 I 136 O 96 L 11.29 10.60 10.50 @#@FSLOADPOST 2024:08:07:18:27:44 mri_label2label N 12 11.29 10.60 10.50 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 1207 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8166 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:44 mri_label2label N 12 e 2.53 S 0.16 U 2.37 P 100% M 549484 F 0 R 163508 W 0 c 20 w 3 I 592 O 608 L 11.29 10.60 10.50 @#@FSLOADPOST 2024:08:07:18:27:47 mri_label2label N 12 10.94 10.54 10.48 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1099 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:47 mri_label2label N 12 e 2.67 S 0.21 U 2.46 P 99% M 548920 F 0 R 163393 W 0 c 13 w 3 I 88 O 80 L 10.94 10.54 10.48 @#@FSLOADPOST 2024:08:07:18:27:49 mri_label2label N 12 11.27 10.62 10.51 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1229 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:49 mri_label2label N 12 e 3.21 S 0.21 U 3.00 P 99% M 549328 F 0 R 163392 W 0 c 19 w 3 I 104 O 80 L 11.27 10.62 10.51 @#@FSLOADPOST 2024:08:07:18:27:53 mri_label2label N 12 11.27 10.62 10.51 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 561 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3793 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:53 mri_label2label N 12 e 2.63 S 0.20 U 2.43 P 99% M 550028 F 0 R 164208 W 0 c 10 w 4 I 280 O 288 L 11.27 10.62 10.51 @#@FSLOADPOST 2024:08:07:18:27:55 mri_label2label N 12 10.93 10.56 10.49 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 944 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4381 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:55 mri_label2label N 12 e 2.93 S 0.19 U 2.72 P 99% M 550036 F 0 R 163444 W 0 c 10 w 4 I 296 O 352 L 10.93 10.56 10.49 @#@FSLOADPOST 2024:08:07:18:27:58 mri_label2label N 12 10.93 10.56 10.49 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0003 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 315 mri_label2label: Done @#@FSTIME 2024:08:07:18:27:58 mri_label2label N 12 e 2.68 S 0.21 U 2.47 P 99% M 549432 F 0 R 163379 W 0 c 12 w 3 I 24 O 32 L 10.93 10.56 10.49 @#@FSLOADPOST 2024:08:07:18:28:01 mri_label2label N 12 10.85 10.55 10.49 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.thresh.la bel --trgsubject 0003 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.entorhinal_exvivo.thresh.la bel srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 718 mri_label2label: Done @#@FSTIME 2024:08:07:18:28:01 mri_label2label N 12 e 2.37 S 0.16 U 2.20 P 99% M 549260 F 0 R 163428 W 0 c 19 w 42 I 64 O 48 L 10.85 10.55 10.49 @#@FSLOADPOST 2024:08:07:18:28:03 mri_label2label N 12 10.85 10.55 10.49 mri_label2label --srcsubject fsaverage --srclabel /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.thresh.la bel --trgsubject 0003 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/chang/GBM_Data/VBG/0003/fsaverage/label/rh.perirhinal_exvivo.thresh.la bel srcsubject = fsaverage trgsubject = 0003 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/chang/GBM_Data/VBG/0003/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white Reading target registration /home/chang/GBM_Data/VBG/0003/0003/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 132793 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 302 mri_label2label: Done @#@FSTIME 2024:08:07:18:28:03 mri_label2label N 12 e 2.75 S 0.18 U 2.57 P 99% M 548840 F 0 R 163373 W 0 c 13 w 3 I 32 O 24 L 10.85 10.55 10.49 @#@FSLOADPOST 2024:08:07:18:28:06 mri_label2label N 12 10.95 10.57 10.50 mris_label2annot --s 0003 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh. V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/label cmdline mris_label2annot --s 0003 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh. V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chang-System-Product-Name machine x86_64 user chang subject 0003 hemi rh SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89838 unhit vertices Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/rh.BA_exvivo.annot @#@FSTIME 2024:08:07:18:28:06 mris_label2annot N 38 e 0.46 S 0.04 U 0.41 P 99% M 154456 F 0 R 41813 W 0 c 6 w 3 I 0 O 2080 L 10.95 10.57 10.50 @#@FSLOADPOST 2024:08:07:18:28:07 mris_label2annot N 38 10.95 10.57 10.50 mris_label2annot --s 0003 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /home/chang/GBM_Data/VBG/0003/0003/label cmdline mris_label2annot --s 0003 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chang-System-Product-Name machine x86_64 user chang subject 0003 hemi rh SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/chang/GBM_Data/VBG/0003/0003/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 108567 unhit vertices Writing annot to /home/chang/GBM_Data/VBG/0003/0003/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:08:07:18:28:07 mris_label2annot N 38 e 0.40 S 0.05 U 0.35 P 99% M 154388 F 0 R 41734 W 0 c 4 w 4 I 0 O 2080 L 10.95 10.57 10.50 @#@FSLOADPOST 2024:08:07:18:28:07 mris_label2annot N 38 10.95 10.57 10.50 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 0003 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 244738 Total vertex volume 244461 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 922 537 1782 2.449 0.818 0.128 0.037 12 1.2 BA1_exvivo 3661 2323 3927 1.726 0.653 0.095 0.021 23 3.2 BA2_exvivo 1067 680 946 1.729 0.564 0.124 0.028 9 1.2 BA3a_exvivo 1984 1269 2738 1.741 0.851 0.089 0.019 10 1.6 BA3b_exvivo 1508 974 1961 1.835 0.622 0.095 0.022 9 1.4 BA4a_exvivo 1259 817 1376 1.765 0.596 0.098 0.025 8 1.5 BA4p_exvivo 10950 7049 17297 2.235 0.778 0.124 0.034 96 15.4 BA6_exvivo 4137 2744 6951 2.316 0.782 0.118 0.032 40 5.5 BA44_exvivo 3473 2372 7014 2.230 0.983 0.122 0.031 33 4.5 BA45_exvivo 3396 2572 6040 2.119 0.736 0.145 0.047 134 7.9 V1_exvivo 7835 5913 14311 2.114 0.759 0.152 0.050 101 17.2 V2_exvivo 1909 1327 4358 2.784 0.823 0.124 0.035 16 2.7 MT_exvivo 316 231 1346 3.389 0.927 0.156 0.048 4 0.6 perirhinal_exvivo 538 428 1988 2.989 0.936 0.129 0.030 4 0.7 entorhinal_exvivo @#@FSTIME 2024:08:07:18:28:07 mris_anatomical_stats N 12 e 2.90 S 0.13 U 2. 76 P 100% M 466212 F 0 R 133723 W 0 c 10 w 1 I 0 O 24 L 10.95 10.57 10.50 @#@FSLOADPOST 2024:08:07:18:28:10 mris_anatomical_stats N 12 11.11 10.61 10. 51 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0003 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/chang/GBM_Data/VBG/0003/0003/mri/wm.mgz... reading input surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... reading input pial surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.pial... reading input white surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 244738 Total vertex volume 244461 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1531637 mm^3 (det: 1.271911 ) 625 356 1220 2.488 0.860 0.131 0.040 9 1.0 BA1_exvivo 2095 1340 2433 1.798 0.719 0.097 0.022 14 2.1 BA2_exvivo 973 609 730 1.715 0.481 0.127 0.027 9 1.0 BA3a_exvivo 1579 1022 1511 1.413 0.420 0.074 0.013 6 0.8 BA3b_exvivo 1014 626 1406 2.024 0.633 0.103 0.024 6 0.9 BA4a_exvivo 1039 687 1019 1.615 0.493 0.088 0.022 5 1.1 BA4p_exvivo 7056 4436 11131 2.268 0.782 0.120 0.034 62 9.8 BA6_exvivo 895 630 1925 2.430 0.795 0.121 0.031 10 1.1 BA44_exvivo 878 630 2281 2.524 0.986 0.138 0.042 11 1.6 BA45_exvivo 3265 2474 5407 2.062 0.693 0.146 0.047 133 7.7 V1_exvivo 3979 3043 7904 2.200 0.831 0.157 0.053 50 9.9 V2_exvivo 271 195 871 2.914 0.945 0.150 0.051 4 0.5 MT_exvivo 28 18 94 3.434 0.640 0.118 0.017 0 0.0 perirhinal_exvivo 529 410 1852 3.032 0.860 0.140 0.036 5 0.8 entorhinal_exvivo @#@FSTIME 2024:08:07:18:28:10 mris_anatomical_stats N 12 e 2.68 S 0.15 U 2. 52 P 99% M 466004 F 0 R 133723 W 0 c 25 w 1 I 0 O 24 L 11.11 10.61 10.51 @#@FSLOADPOST 2024:08:07:18:28:13 mris_anatomical_stats N 12 11.11 10.61 10. 51 Started at 公曆 20廿四年八月七日週三十六時二分48秒 Ended at 公曆 20廿四年八月七日週三十八時廿八分十三秒 #@#%# recon-all-run-time-hours 2.424 recon-all -s 0003 finished without error at 公曆 20廿四年八月七日週三十八時廿八分十三秒 #New# invocation of recon-all 公曆 20廿四年八月七日週三十八時廿八分十三秒 cd /home/chang/GBM_Data/VBG/0003/0003 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 /usr/local/freesurfer/bin/recon-all -subjid 0003 -sd /home/chang/GBM_Data/VBG/0003 -T2 /home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz -T2pial subjid 0003 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 16453580 kbytes maxproc 513872 maxlocks unlimited maxsignal 513872 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 16Gi 3.0Gi 2.4Gi 106Gi 105Gi Swap: 2.0Gi 2.0Gi 1.0Mi ######################################## program versions used 7.4.1 (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or 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03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/08/07-10:28:13-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: chang Machine: chang-System-Product-Name Platform: Linux PlatformVersion: 6.5.0-44-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input 公曆 20廿四年八月七日週三十八時廿八分十三秒 /home/chang/GBM_Data/VBG/0003/0003 mri_convert --no_scale 1 /home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz mri_convert --no_scale 1 /home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz reading from /home/chang/GBM_Data/RHUH-GBM_nii_v1/0003/0/0003_0_t2.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz... @#@FSTIME 2024:08:07:18:28:13 mri_convert N 4 e 0.35 S 0.02 U 0.32 P 99% M 42240 F 0 R 9168 W 0 c 5 w 4 I 11280 O 10744 L 11.11 10.61 10.51 @#@FSLOADPOST 2024:08:07:18:28:13 mri_convert N 4 11.11 10.61 10.51 #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR 公曆 20廿四年八月七日週三十八時廿八分十三秒 bbregister --s 0003 --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw. mgz --lta /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask tmp /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180 Log file is /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.log 公曆 20廿四年八月七日週三十八時廿八分十三秒 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 cd /home/chang/GBM_Data/VBG/0003/0003/scripts /usr/local/freesurfer/bin/bbregister --s 0003 --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz --lta /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask bbregister 7.4.1 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii mri_convert /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii reading from /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister. 688180/template.nii... mri_coreg --s 0003 --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii --regdat /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. init.dat --reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/mri_ coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/chang/GBM_Data/VBG/0003/0003/scripts cmdline mri_coreg --s 0003 --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii --regdat /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. init.dat --reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/mri_ coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname chang-System-Product-Name machine x86_64 user chang dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii Reading in ref /home/chang/GBM_Data/VBG/0003/0003/mri/brainmask.mgz Setting cras translation parameters to align volume centers Init matrix params 0.0000 1.0000 -1.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 -1.00000; 0.00000 0.00000 1.00000 1.00000; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 0.0000 1.0000 -1.0000 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 5.4220 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 123.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0833937660 nhits = 137431 out of 16777216, Percent Overlap: 52.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 1.00000; 0.00000 0.00000 1.00000 -1.00000; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 1.00000 0.00000 0.00000 -8.00000; 0.00000 0.00000 -1.00000 247.00000; 0.00000 -1.00000 0.00000 204.50000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 0.00000 1.00000 1.00000 0.00000 0.00000 0.00000 -1.0597895 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0834896564 #@# 4 188 0.00000 1.00000 1.00000 0.00000 0.00000 0.00000 -1.0834897 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.083490 #@# 4 194 0.38197 1.00000 1.00000 0.00000 0.00000 0.00000 -1.0836478 #@# 4 203 0.36268 0.38197 1.00000 0.00000 0.00000 0.00000 -1.0837729 #@# 4 205 0.36268 0.57609 1.00000 0.00000 0.00000 0.00000 -1.0838054 #@# 4 206 0.36268 0.56609 1.00000 0.00000 0.00000 0.00000 -1.0838056 #@# 4 207 0.36268 0.55609 1.00000 0.00000 0.00000 0.00000 -1.0838066 #@# 4 210 0.36268 0.52068 1.00000 0.00000 0.00000 0.00000 -1.0838077 #@# 4 214 0.36268 0.52068 -0.61803 0.00000 0.00000 0.00000 -1.0846199 #@# 4 215 0.36268 0.52068 -0.09597 0.00000 0.00000 0.00000 -1.0850186 #@# 4 219 0.36268 0.52068 -0.03848 0.00000 0.00000 0.00000 -1.0850224 #@# 4 220 0.36268 0.52068 -0.04848 0.00000 0.00000 0.00000 -1.0850245 #@# 4 237 0.36268 0.52068 -0.04848 0.00000 0.01488 0.00000 -1.0850266 powell nthiter 1: fret = -1.085027 #@# 4 254 0.37268 0.52068 -0.04848 0.00000 0.01488 0.00000 -1.0850269 #@# 4 262 0.37268 0.44233 -0.04848 0.00000 0.01488 0.00000 -1.0850277 #@# 4 263 0.37268 0.47741 -0.04848 0.00000 0.01488 0.00000 -1.0850282 #@# 4 264 0.37268 0.46741 -0.04848 0.00000 0.01488 0.00000 -1.0850288 #@# 4 272 0.37268 0.46741 -0.07814 0.00000 0.01488 0.00000 -1.0850306 #@# 4 289 0.37268 0.46741 -0.07814 0.00000 0.02488 0.00000 -1.0850319 #@# 4 298 0.37268 0.46741 -0.07814 0.00000 0.02488 0.01787 -1.0850326 Powell done niters total = 1 OptTimeSec 6.4 sec OptTimeMin 0.11 min nEvals 300 Final optimized parameters 0.37268403 0.46741304 -0.07813513 0.00000000 0.02487876 0.01787130 Final matrix parameters 0.3727 0.4674 -0.0781 0.0000 0.0249 0.0279 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.085032561910817 --------------------------------- Final RefRAS-to-MovRAS 1.00000 0.00031 0.00043 0.37268; -0.00031 1.00000 0.00000 0.46741; -0.00043 -0.00000 1.00000 -0.07814; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 1.00000 0.00043 -0.00031 -8.45911; -0.00031 0.00000 -1.00000 247.53508; 0.00043 -1.00000 -0.00000 205.41837; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters 0.3727 0.4674 -0.0781 0.0000 0.0249 0.0179 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters 0.3727 0.4674 -0.0781 0.0000 0.0249 0.0179 nhits = 137429 out of 16777216, Percent Overlap: 52.4 mri_coreg RunTimeSec 38.5 sec To check run: tkregisterfv --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp. bbregister.688180/template.nii --targ /home/chang/GBM_Data/VBG/0003/0003/mri/brainmask.mgz --reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/mri_ coreg.lta --s 0003 --surfs mri_coreg done mri_segreg --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii --init-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. init.dat --out-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr. pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 cd /home/chang/GBM_Data/VBG/0003/0003/scripts mri_segreg --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii --init-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. init.dat --out-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr. pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 sysname Linux hostname chang-System-Product-Name machine x86_64 user chang movvol /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii regfile /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. init.dat subject 0003 dof 6 outregfile /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister. 688180/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1723607109 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.00000 0.00031 0.00043 0.44350; -0.00043 -0.00000 1.00000 -0.02605; -0.00031 1.00000 -0.00000 0.50484; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.946830 1 -25.0 -25.0 25.0 0.954694 2 -25.0 25.0 -25.0 1.000999 3 -25.0 25.0 25.0 0.982965 4 25.0 -25.0 -25.0 0.948758 5 25.0 -25.0 25.0 0.962045 6 25.0 25.0 -25.0 0.974763 7 25.0 25.0 25.0 0.974663 REL: 8 1.159603 7.745715 0.968214 rel = 1.19767 Initial costs ---------------- Number of surface hits 2512 WM Intensity -0.4722 +/- 0.6719 Ctx Intensity 0.1936 +/- 1.1155 Pct Contrast -2293.4429 +/- 111257.5584 Cost 1.1596 RelCost 1.1977 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9548 0.9548 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9240 0.9240 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9239 0.9239 0.0 219 -4.0000 4.0000 4.0000 -4.0000 0.0000 -4.0000 0.9056 0.9056 0.0 Brute Force -------------------------- Min cost was 0.905642 Number of iterations 729 Search time 0.670579 sec Parameters at best (transmm, rotdeg) -4.000 4.000 4.000 -4.000 0.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 4 2 4 3 -4 4 0 5 -4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.905642 5 -4.618 4.000 4.000 -4.000 0.000 -4.000 0.9008647402 9 -4.531 4.000 4.000 -4.000 0.000 -4.000 0.8996386370 10 -4.520 4.000 4.000 -4.000 0.000 -4.000 0.8986073976 11 -4.470 4.000 4.000 -4.000 0.000 -4.000 0.8979427876 14 -4.458 4.000 4.000 -4.000 0.000 -4.000 0.8975149420 16 -4.460 4.000 4.000 -4.000 0.000 -4.000 0.8974104720 17 -4.464 4.000 4.000 -4.000 0.000 -4.000 0.8972284763 27 -4.464 3.948 4.000 -4.000 0.000 -4.000 0.8947837774 30 -4.464 3.944 4.000 -4.000 0.000 -4.000 0.8942695936 32 -4.464 3.930 4.000 -4.000 0.000 -4.000 0.8937001881 44 -4.464 3.930 4.027 -4.000 0.000 -4.000 0.8921445828 50 -4.464 3.930 4.026 -4.000 0.000 -4.000 0.8921406036 51 -4.464 3.930 4.025 -4.000 0.000 -4.000 0.8921390140 65 -4.464 3.930 4.025 -3.998 0.000 -4.000 0.8913596165 77 -4.464 3.930 4.025 -3.998 0.024 -4.000 0.8897987625 79 -4.464 3.930 4.025 -3.998 0.014 -4.000 0.8897798886 81 -4.464 3.930 4.025 -3.998 0.019 -4.000 0.8889510638 83 -4.464 3.930 4.025 -3.998 0.018 -4.000 0.8889485991 97 -4.464 3.930 4.025 -3.998 0.018 -4.003 0.8882235387 99 -4.464 3.930 4.025 -3.998 0.018 -4.002 0.8881980743 100 -4.464 3.930 4.025 -3.998 0.018 -4.001 0.8881790630 powell nthiter 1: fret = 0.888179 115 -4.463 3.930 4.025 -3.998 0.018 -4.001 0.8881564397 116 -4.462 3.930 4.025 -3.998 0.018 -4.001 0.8881510722 125 -4.462 3.931 4.025 -3.998 0.018 -4.001 0.8881343315 128 -4.462 3.932 4.025 -3.998 0.018 -4.001 0.8881201325 130 -4.462 3.934 4.025 -3.998 0.018 -4.001 0.8881012733 144 -4.462 3.934 4.024 -3.998 0.018 -4.001 0.8880386506 145 -4.462 3.934 4.023 -3.998 0.018 -4.001 0.8880083385 176 -4.462 3.934 4.023 -3.998 0.019 -4.001 0.8880010057 powell nthiter 2: fret = 0.888001 209 -4.461 3.934 4.023 -3.998 0.019 -4.001 0.8879996501 269 -4.461 3.934 4.023 -3.998 0.020 -4.001 0.8879948325 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 1.024492 1 -25.0 -25.0 25.0 1.002858 2 -25.0 25.0 -25.0 0.972662 3 -25.0 25.0 25.0 0.951033 4 25.0 -25.0 -25.0 0.930944 5 25.0 -25.0 25.0 0.959659 6 25.0 25.0 -25.0 0.986401 7 25.0 25.0 25.0 0.958929 REL: 8 0.887995 7.786979 0.973372 rel = 0.912287 Number of iterations 2 Min cost was 0.887995 Number of FunctionCalls 288 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.199039 sec Parameters at optimum (transmm) -4.46100 3.93356 4.02320 Parameters at optimum (rotdeg) -3.99810 0.01986 -4.00143 Final costs ---------------- Number of surface hits 2512 WM Intensity -0.1788 +/- 1.1407 Ctx Intensity -0.2031 +/- 1.4149 Pct Contrast 454.6450 +/- 12168.3811 Cost 0.8880 RelCost 1.1977 Reg at min cost was 0.99753 0.00552 0.07002 -4.01776; -0.07024 0.06951 0.99511 3.91180; -0.00063 0.99757 -0.06972 4.52847; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr. pass1.dat, type = 14 Original Reg 1.00000 0.00031 0.00043 0.44350; -0.00043 -0.00000 1.00000 -0.02605; -0.00031 1.00000 -0.00000 0.50484; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00247 -0.00521 -0.06959 4.46126; 0.06980 -0.06951 0.00489 -3.93784; 0.00032 0.00243 0.06972 -4.02364; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.325218 Computing change in rh position Surface-RMS-Diff-mm 6.808459 2.496179 12.116522 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii --init-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr. pass1.dat --out-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw. auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 cd /home/chang/GBM_Data/VBG/0003/0003/scripts mri_segreg --mov /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii --init-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr. pass1.dat --out-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw. auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/reg. curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname chang-System-Product-Name machine x86_64 user chang movvol /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/temp late.nii regfile /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/tmp.bbregister.688180/bbr. pass1.dat subject 0003 dof 6 outregfile /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjAbs 2.000000 WMProjAbs 1.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1723645545 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99753 0.00552 0.07002 -4.01776; -0.07024 0.06951 0.99511 3.91180; -0.00063 0.99757 -0.06972 4.52847; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz Projecting LH Surfs Loading lh.white surf GM Proj: 0 0.500000 2.000000 WM Proj: 0 0.500000 1.000000 Projecting RH Surfs Loading rh.white surf Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.983531 1 -25.0 -25.0 25.0 0.974198 2 -25.0 25.0 -25.0 0.986685 3 -25.0 25.0 25.0 0.979991 4 25.0 -25.0 -25.0 0.962851 5 25.0 -25.0 25.0 0.974900 6 25.0 25.0 -25.0 0.965208 7 25.0 25.0 25.0 0.957650 REL: 8 0.948762 7.785015 0.973127 rel = 0.974962 Initial costs ---------------- Number of surface hits 251486 WM Intensity -0.1886 +/- 1.1889 Ctx Intensity -0.1968 +/- 1.3948 Pct Contrast -67.6954 +/- 34550.7112 Cost 0.9488 RelCost 0.9750 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9286 0.9286 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.9240 0.9240 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.9206 0.9206 0.0 8 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.9133 0.9133 0.0 179 -0.1000 0.1000 -0.1000 0.0000 0.1000 0.1000 0.9120 0.9120 0.0 522 0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.9108 0.9108 0.0 650 0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.9094 0.9094 0.0 653 0.1000 0.1000 -0.1000 -0.1000 0.0000 0.1000 0.9078 0.9078 0.0 661 0.1000 0.1000 -0.1000 0.0000 0.0000 0.0000 0.9067 0.9067 0.0 Brute Force -------------------------- Min cost was 0.906707 Number of iterations 729 Search time 0.510323 sec Parameters at best (transmm, rotdeg) 0.100 0.100 -0.100 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0.1 2 -0.1 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.947728 3 -1.518 0.100 -0.100 0.000 0.000 0.000 0.9460698791 4 -0.893 0.100 -0.100 0.000 0.000 0.000 0.9447947841 6 -0.513 0.100 -0.100 0.000 0.000 0.000 0.9442331843 8 -0.590 0.100 -0.100 0.000 0.000 0.000 0.9439347554 16 -0.591 0.100 -0.100 0.000 0.000 0.000 0.9439090088 21 -0.591 -0.518 -0.100 0.000 0.000 0.000 0.9417197037 23 -0.591 -0.656 -0.100 0.000 0.000 0.000 0.9412219890 25 -0.591 -0.620 -0.100 0.000 0.000 0.000 0.9409964324 27 -0.591 -0.609 -0.100 0.000 0.000 0.000 0.9409446009 28 -0.591 -0.604 -0.100 0.000 0.000 0.000 0.9409383707 29 -0.591 -0.603 -0.100 0.000 0.000 0.000 0.9409307576 35 -0.591 -0.603 -1.718 0.000 0.000 0.000 0.9396632458 36 -0.591 -0.603 -1.011 0.000 0.000 0.000 0.9387022732 40 -0.591 -0.603 -0.994 0.000 0.000 0.000 0.9386344290 42 -0.591 -0.603 -0.957 0.000 0.000 0.000 0.9384991811 46 -0.591 -0.603 -0.959 0.000 0.000 0.000 0.9384968334 51 -0.591 -0.603 -0.959 1.000 0.000 0.000 0.9384050540 55 -0.591 -0.603 -0.959 0.618 0.000 0.000 0.9371076029 56 -0.591 -0.603 -0.959 0.382 0.000 0.000 0.9366999652 58 -0.591 -0.603 -0.959 0.383 0.000 0.000 0.9366292947 59 -0.591 -0.603 -0.959 0.473 0.000 0.000 0.9363311256 60 -0.591 -0.603 -0.959 0.430 0.000 0.000 0.9359123331 69 -0.591 -0.603 -0.959 0.430 -1.618 0.000 0.9111724936 76 -0.591 -0.603 -0.959 0.430 -2.539 0.000 0.9110926218 77 -0.591 -0.603 -0.959 0.430 -2.084 0.000 0.9105675952 78 -0.591 -0.603 -0.959 0.430 -2.095 0.000 0.9102657296 79 -0.591 -0.603 -0.959 0.430 -2.303 0.000 0.9102144494 80 -0.591 -0.603 -0.959 0.430 -2.393 0.000 0.9100245463 95 -0.591 -0.603 -0.959 0.430 -2.393 0.382 0.9079651798 97 -0.591 -0.603 -0.959 0.430 -2.393 0.409 0.9076807175 100 -0.591 -0.603 -0.959 0.430 -2.393 0.408 0.9076615681 101 -0.591 -0.603 -0.959 0.430 -2.393 0.398 0.9076461921 102 -0.591 -0.603 -0.959 0.430 -2.393 0.403 0.9076148761 103 -0.591 -0.603 -0.959 0.430 -2.393 0.402 0.9075915850 powell nthiter 1: fret = 0.907592 110 -1.209 -0.603 -0.959 0.430 -2.393 0.402 0.9074654142 112 -0.911 -0.603 -0.959 0.430 -2.393 0.402 0.9065864692 114 -1.050 -0.603 -0.959 0.430 -2.393 0.402 0.9063212523 116 -0.984 -0.603 -0.959 0.430 -2.393 0.402 0.9060953652 119 -0.975 -0.603 -0.959 0.430 -2.393 0.402 0.9060028945 120 -0.968 -0.603 -0.959 0.430 -2.393 0.402 0.9059992454 121 -0.971 -0.603 -0.959 0.430 -2.393 0.402 0.9059158367 122 -0.972 -0.603 -0.959 0.430 -2.393 0.402 0.9058846384 141 -0.972 -0.603 -1.577 0.430 -2.393 0.402 0.9039833344 143 -0.972 -0.603 -1.464 0.430 -2.393 0.402 0.9030349066 146 -0.972 -0.603 -1.494 0.430 -2.393 0.402 0.9027854120 152 -0.972 -0.603 -1.496 0.430 -2.393 0.402 0.9027495003 159 -0.972 -0.603 -1.496 0.812 -2.393 0.402 0.9016582789 161 -0.972 -0.603 -1.496 0.758 -2.393 0.402 0.9014010803 173 -0.972 -0.603 -1.496 0.758 -2.011 0.402 0.8998767388 175 -0.972 -0.603 -1.496 0.758 -2.135 0.402 0.8992842416 182 -0.972 -0.603 -1.496 0.758 -2.138 0.402 0.8992707754 191 -0.972 -0.603 -1.496 0.758 -2.138 0.300 0.8992569276 198 -0.972 -0.603 -1.496 0.758 -2.138 0.307 0.8991871153 199 -0.972 -0.603 -1.496 0.758 -2.138 0.311 0.8991616128 201 -0.972 -0.603 -1.496 0.758 -2.138 0.310 0.8991570772 202 -0.972 -0.603 -1.496 0.758 -2.138 0.309 0.8991434627 203 -1.353 -0.603 -2.032 1.085 -1.882 0.216 0.8979631489 powell nthiter 2: fret = 0.899143 227 -0.972 -0.818 -1.496 0.758 -2.138 0.309 0.8978256453 230 -0.972 -0.840 -1.496 0.758 -2.138 0.309 0.8978216686 231 -0.972 -0.829 -1.496 0.758 -2.138 0.309 0.8977918190 232 -0.972 -0.828 -1.496 0.758 -2.138 0.309 0.8977238065 245 -0.972 -0.828 -1.520 0.758 -2.138 0.309 0.8976367220 246 -0.972 -0.828 -1.516 0.758 -2.138 0.309 0.8976278778 247 -0.972 -0.828 -1.514 0.758 -2.138 0.309 0.8975725038 257 -0.972 -0.828 -1.514 0.878 -2.138 0.309 0.8973890101 262 -0.972 -0.828 -1.514 0.871 -2.138 0.309 0.8973410539 263 -0.972 -0.828 -1.514 0.872 -2.138 0.309 0.8973315240 264 -0.972 -0.828 -1.514 0.873 -2.138 0.309 0.8973196642 273 -0.972 -0.828 -1.514 0.873 -2.147 0.309 0.8971610146 274 -0.972 -0.828 -1.514 0.873 -2.157 0.309 0.8971265106 278 -0.972 -0.828 -1.514 0.873 -2.158 0.309 0.8971046587 287 -0.972 -0.828 -1.514 0.873 -2.158 0.319 0.8970466233 289 -0.972 -0.828 -1.514 0.873 -2.158 0.333 0.8970100905 290 -0.972 -0.828 -1.514 0.873 -2.158 0.334 0.8969714709 300 -0.972 -0.914 -1.521 0.917 -2.166 0.344 0.8963434071 302 -0.972 -0.903 -1.520 0.911 -2.165 0.343 0.8962190385 304 -0.972 -0.903 -1.520 0.912 -2.165 0.343 0.8961852573 305 -0.972 -0.908 -1.520 0.914 -2.165 0.343 0.8961830673 307 -0.972 -0.906 -1.520 0.913 -2.165 0.343 0.8961730429 310 -0.972 -0.906 -1.520 0.913 -2.165 0.343 0.8961720930 powell nthiter 3: fret = 0.896172 337 -0.972 -0.906 -1.520 0.913 -2.165 0.346 0.8961067251 383 -0.972 -0.906 -1.520 0.913 -2.164 0.346 0.8960750602 powell nthiter 4: fret = 0.896075 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.975964 1 -25.0 -25.0 25.0 0.967428 2 -25.0 25.0 -25.0 0.981661 3 -25.0 25.0 25.0 0.990489 4 25.0 -25.0 -25.0 0.953759 5 25.0 -25.0 25.0 0.968768 6 25.0 25.0 -25.0 0.976922 7 25.0 25.0 25.0 0.968822 REL: 8 0.896075 7.783812 0.972977 rel = 0.920963 Number of iterations 4 Min cost was 0.896075 Number of FunctionCalls 483 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 13.680996 sec Parameters at optimum (transmm) -0.97176 -0.90599 -1.52009 Parameters at optimum (rotdeg) 0.91314 -2.16414 0.34635 Final costs ---------------- Number of surface hits 251486 WM Intensity -0.2146 +/- 1.0957 Ctx Intensity -0.1295 +/- 1.4043 Pct Contrast 110.8027 +/- 25392.8264 Cost 0.8961 RelCost 0.9750 Reg at min cost was 0.99729 -0.03251 0.06598 -5.18313; -0.06419 0.05341 0.99651 2.90775; 0.03592 0.99804 -0.05117 2.91515; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat, type = 14 Original Reg 0.99753 0.00552 0.07002 -4.01776; -0.07024 0.06951 0.99511 3.91180; -0.00063 0.99757 -0.06972 4.52847; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00024 0.03803 0.00404 1.16536; -0.00605 0.01610 -0.00140 1.00404; -0.03655 -0.00048 -0.01855 1.61332; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.004314 Computing change in rh position Surface-RMS-Diff-mm 2.334677 1.059853 4.406749 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.896075 -0.214632 -0.129454 110.802654 tkregister2_cmdl --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz --reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.dat --noedit --ltaout /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz reg file /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto. dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99729 -0.03251 0.06598 -5.18313; -0.06419 0.05341 0.99651 2.90775; 0.03592 0.99804 -0.05117 2.91515; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 120.00000; 0.00000 0.00000 1.00000 -77.50000; 0.00000 -1.00000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99729 -0.03251 0.06598 -5.18313; -0.06419 0.05341 0.99651 2.90775; 0.03592 0.99804 -0.05117 2.91515; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 0003 RegMat --------------------------- 0.99729 -0.03251 0.06598 -5.18313; -0.06419 0.05341 0.99651 2.90775; 0.03592 0.99804 -0.05117 2.91515; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at 公曆 20廿四年八月七日週三十八時廿八分十三秒 Ended at 公曆 20廿四年八月七日週三十八時廿九分十二秒 BBR-Run-Time-Sec 59 bbregister Done To check results, run: tkregisterfv --mov /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz --reg /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta --surfs --sd /home/chang/GBM_Data/VBG/0003 @#@FSTIME 2024:08:07:18:28:13 bbregister N 13 e 59.04 S 1.71 U 57.30 P 99% M 706656 F 12 R 2218542 W 0 c 213 w 1068 I 1536 O 70784 L 11.11 10.61 10.51 @#@FSLOADPOST 2024:08:07:18:29:12 bbregister N 13 10.89 10.65 10.53 cp /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.auto.lta /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta @#@FSTIME 2024:08:07:18:29:12 cp N 2 e 0.00 S 0.00 U 0.00 P 100% M 2304 F 0 R 189 W 0 c 0 w 1 I 0 O 8 L 10.89 10.65 10.53 @#@FSLOADPOST 2024:08:07:18:29:12 cp N 2 10.89 10.65 10.53 mri_convert -odt float -at /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta -rl /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz reading from /home/chang/GBM_Data/VBG/0003/0003/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) INFO: Reading transformation from file /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /home/chang/GBM_Data/VBG/0003/0003/mri/orig.mgz... INFO: Applying transformation from file /home/chang/GBM_Data/VBG/0003/0003/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99729 0.03592 -0.06419 5.62565; -0.03251 0.99804 0.05341 -11.04095; 0.06598 -0.05117 0.99651 11.87163; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz... @#@FSTIME 2024:08:07:18:29:12 mri_convert N 8 e 1.08 S 0.02 U 1.06 P 99% M 108032 F 0 R 25681 W 0 c 12 w 1 I 0 O 11560 L 10.89 10.65 10.53 @#@FSLOADPOST 2024:08:07:18:29:14 mri_convert N 8 10.89 10.65 10.53 mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /home/chang/GBM_Data/VBG/0003/0003/mri/aseg.presurf.mgz -surface /home/chang/GBM_Data/VBG/0003/0003/surf/lh.white identity.nofile -surface /home/chang/GBM_Data/VBG/0003/0003/surf/rh.white identity.nofile /home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/T2.norm.mgz setting seed for random number genererator to 1234 using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading mri_src from /home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz... Copying mri_dst from mri_src computing distance transform computing distance transform min_dist = 1 Erasing Border planes 4 aseg read with width 256 (src width 256) resampling aseg... Removing non-wm voxels 78821 non wm control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 MRIapplyBiasCorrectionSameGeometry() NaN found at voxel (0, 0, 0, 0) error: Numerical argument out of domain error: WARNING: 16777216 NaNs found in volume /home/chang/GBM_Data/VBG/0003/0003/mri/T2.prenorm.mgz... \00 writing normalized volume to /home/chang/GBM_Data/VBG/0003/0003/mri/T2.norm. mgz #VMPC# mri_normalize VmPeak 877864 mri_normalize done @#@FSTIME 2024:08:07:18:29:14 mri_normalize N 18 e 13.40 S 0.45 U 12.95 P 100% M 745184 F 3 R 487208 W 0 c 49 w 2 I 32 O 136 L 10.89 10.65 10.53 @#@FSLOADPOST 2024:08:07:18:29:27 mri_normalize N 18 11.28 10.75 10.57 mri_mask -transfer 255 -keep_mask_deletion_edits /home/chang/GBM_Data/VBG/0003/0003/mri/T2.norm.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/brain.finalsurfs.mgz /home/chang/GBM_Data/VBG/0003/0003/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 maskval=255, outval=255 Writing masked volume to /home/chang/GBM_Data/VBG/0003/0003/mri/T2.mgz...done. @#@FSTIME 2024:08:07:18:29:27 mri_mask N 6 e 1.07 S 0.05 U 1.02 P 99% M 238076 F 0 R 58376 W 0 c 5 w 2 I 0 O 136 L 11.28 10.75 10.57 @#@FSLOADPOST 2024:08:07:18:29:28 mri_mask N 6 11.28 10.75 10.57 #-------------------------------------------- #@# MMPialSurf lh 公曆 20廿四年八月七日週三十八時廿九分廿八秒 cd /home/chang/GBM_Data/VBG/0003/0003/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 7.4.1 7.4.1 cd /home/chang/GBM_Data/VBG/0003/0003/mri setenv SUBJECTS_DIR /home/chang/GBM_Data/VBG/0003 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --mmvol T2.mgz T2 Reading in input surface ../surf/lh.pial.T1 Not smoothing input surface Area 272746 0.44422 0.37554 0.000119 7.1834 Corner 818238 60.00000 30.10735 0.040969 179.8384 Edge 409119 1.06184 0.52459 0.002581 8.1249 Hinge 409119 18.15251 25.58024 0.000094 179.9970 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19640, wmmin=5, clip=110 MRIfindBrightNonWM(): 1562 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 60.756 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 7099/136375 vertices (129276 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 Reading in multimodal volume T2.mgz using multi modal weights vertex 68188: xyz = (-30.7907,-17.9909,34.3246) oxyz = (-28.7963,-16.4263,32.6041) wxzy = (-28.7963,-16.4263,32.6041) pxyz = (-30.7907,-17.9909,34.3246) CBVO Creating mask 136375 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing pial target locations using multimodal (1) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=1 Changed 500997 aseg cortex voxels to 0 Creating lowres distance volumes t=0.0159976 Creating white distance volumes t=0.153809 (box.dx, box.dy, box.dz) = (136, 234, 316) (region->dx, region->dy, region->dz) = (136, 234, 316) (region->dx, region->dy, region->dz) = (136, 234, 316) Creating pial distance volumes t=0.471721 (box.dx, box.dy, box.dz) = (146, 250, 328) (region->dx, region->dy, region->dz) = (146, 250, 328) (region->dx, region->dy, region->dz) = (146, 250, 328) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 0.849581 Starting loop over 136375 vertices vno = 0, t = 0.849581 error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image\00 error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image\00 Command terminated by signal 11 @#@FSTIME 2024:08:07:18:29:28 mris_place_surface N 31 e 56.54 S 1.26 U 55.14 P 99% M 1937256 F 2 R 1106903 W 0 c 234 w 542 I 272 O 0 L 11.28 10.75 10.57 @#@FSLOADPOST 2024:08:07:18:30:25 mris_place_surface N 31 10.93 10.78 10.59 Linux chang-System-Product-Name 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0003 exited with ERRORS at 公曆 20廿四年八月七日週三十八時卅分廿五秒 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Older tksurfer and tkmedit (FS version 5.0.0) fail to launch: glut issue?
by Raij, Tommi A. 07 Aug '24

07 Aug '24

Dear Surfers, I am trying to launch tksurfer/tkmedit in the stable 5_0_0 environment in the Martinos network, but this fails with glut segmentation errors. FS version 6 tksurfer works on the same machine and data, but I need to create some figures that match version 5. We already tried with a different user and a few years older linux box, same issues. Any suggestions would be greatly appreciated! For example, is there a variable that we could set to point to an older OpenGL version? (My LD_LIBRARY_PATH has not been set, and my PATH does not include anything pointing to /usr/lib or /usr/lib64) Details: on machine rukki (locally at terminal): setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env cd $MY_SUBJECTS_DIR Checking version: freesurfer ... You are running this version of FreeSurfer: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 echo $FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 cp -r $FREESURFER_HOME/subjects/fsaverage $MY_SUBJECTS_DIR/. chmod -R 777 fsaverage [rukki:sphsm10-ffx] (nmr-stable5.0-env) tksurfer fsaverage lh inflated subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: <$MY_SUBJECTS_DIR> surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: <$MY_SUBJECTS_DIR> Reading image info <$MY_SUBJECTS_DIR>/fsaverage) Reading <$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz surfer: Reading header info from /<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz [rukki:sphsm10-ffx] (nmr-stable5.0-env) ... after which there is no screen output. The file xdebug_tksurfer was generated: [rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tksurfer Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut [rukki:sphsm10-ffx] (nmr-stable5.0-env) [rukki:sphsm10-ffx] (nmr-stable5.0-env) echo $DISPLAY :3 setenv DISPLAY :0 does not fix the issue (results in GLUT: Fatal Error in tksurfer.bin: could not open display: 0) I also tried fsaverage4, fsaverage5, fsaverage6, and bert, copied from the same folder into my $SUBJECTS_DIR, same result. The issue is not specific to tksurfer: tkmedit -f fsaverage/mri/T1.mgz =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : [rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tkmedit tkmedit started: Wed Aug 7 16:54:21 2024 tkmedit.bin -f fsaverage/mri/T1.mgz $Id: tkmedit.c,v 1.341.2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5_0_0 $ Set user home dir to ($MY_SUBJECTS_DIR) Set subject home dir to fsaverage/mri/T1.mgz Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x3447db0, isSource=./fsaverage/mri/T1.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=fsaverage/mri/T1.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=tkmedit.bin ) 02: Loading volume fsaverage/mri/T1.mgz 01: main() 01: Parsing command line arguments 00: 00: [rukki:sphsm10-ffx] (nmr-stable5.0-env) My OpenGL version: [rukki:sphsm10-ffx] (nmr-stable5.0-env) glxinfo | grep "OpenGL version" OpenGL version string: 4.6.0 NVIDIA 550.54.14 The other machine we tried had OpenGL version 4.6.0 NVIDIA 535.54.03 Thank you! Best regards, Tommi --- Tommi Raij, MD, PhD Director, TMS Clinical Research MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th st Charlestown, MA 02129

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Re: [Freesurfer] Tksurfer and freeview
by fsbuild 07 Aug '24

07 Aug '24

External Email - Use Caution  The tksurfer command is deprecated and no longer supported.  You could try using freeview directly or run tksurferfv which may use some of the same options as tksurfer, but runs freeview instead.  $ tksurferfv --help This is a script that runs freeview with arguments like tksurfer. Not all tksurfer functionality is replicated. tksurferfv subject hemi surface ... -tksurfer : use tksurfer instead of freeview Can have multiple annotations -all : load white, pial, inflated -vgl : runs freeview with /usr/pubsw/bin/vglrun -no-vgl : does not run freeview with /usr/pubsw/bin/vglrun -no-outline : do not show annots as outline -vtxno vtxno : put cursor on vtxno on the first surface -neuro : use neurological orientation instead of radiological -rotate-around-cursor (-rca) : in 3d view, rotate around cursor (use -no- to turn off) -linear, -linearopaque, -piecewise, -min_to_max (default) : overlay heat scale --keep-sphere-vol-geom : do not ignore sphere volume geometry when loading sphere On 8/7/24 16:01, Hengameh (hennn2023(a)gmail.com) wrote: Hi Ed, I am currently encountering the same issue. Could you please assist in fixing this issue?Thank you for your help. Hengameh  Sent from Mail for Windows 

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Extract surface vertex IDs from significance map
by Dan Levitas 07 Aug '24

07 Aug '24

External Email - Use Caution I may have spoken too soon. It appears that the —olab flag option in mri_surfcluster provides .label files with vertex IDs for each cluster. Dan

1 0

Extract surface vertex IDs from significance map
by Dan Levitas 07 Aug '24

07 Aug '24

External Email - Use Caution I have been using the Matlab LME tutorial to assess several time*group interaction effects in my dataset. I successfully created *sig.mgh files and used *mri_surfcluster* to generate cluster summary (*thickness.clustersummary.txt), which include each cluster's highest peak vertex. I would like to extract all vertices for each cluster to more closely examine the interaction effect of cortical thickness, but am unsure how to do so. The *mri_surfcluster* function doesn't appear to have an option for this, is there some other function or series of steps I can take to achieve this? Thanks, Dan

1 0

Question/potential bug regarding mri_convert and .gca files
by Siegel, Nys Tjade 07 Aug '24

07 Aug '24

External Email - Use Caution Dear Freesurfer community, I'm trying to extract labels from a .gca atlas volume using the following command: mri_convert atlas.gca -nth 1 labels.mgz (from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat) I've found a .gca file in the /average folder for which this works (RB_all_2020-01-02.gca), but for the cortical parcellations I'm actually interested in (e.g. lh.DKTatlas40.gcs), I get the following error: ERROR: cannot determine file type for lh.DKTatlas40.gcs I'm pretty confused, because the documentations, as well as other support requests, are pretty clear on that my problem should be solved using the mentioned command. Notably, mri_convert -u, does not list GCA under the supported file-types, maybe this is a versioning issue? I'm using freesurfer 7.2.0 with Ubunutu 22.04.4. Any help is much appreciated. Best regards, Nys Tjade Siegel

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Postdoctoral Fellow in human 7T and advanced neuroimaging at Emory University
by Wu, Junjie 06 Aug '24

06 Aug '24

External Email - Use Caution Please find attached an ad for a Postdoctoral Fellow in human 7T and advanced neuroimaging at Emory University. Thank you!

1 0

WMH-Synthseg Bad CPU type in Executable
by Vaughn, Stephen 06 Aug '24

06 Aug '24

External Email - Use Caution Hello! I am trying to run the WMH synthseg command. I have successfully downloaded the Atlas files, but when I ran the mri_WMHsynthseg command, I encountered the error: /Applications/freesurfer/dev/bin/fspython: line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable /Applications/freesurfer/dev/bin/fspython: line 30: /Applications/freesurfer/dev/python/bin/python3: Undefined error: 0 >From the other archived emails, I found individuals reporting this from Qdec, tksurfer, and tkmedit because their macOS updated to 64 bit, is that what is happening here? Is there a work around or do I need to use a different computer with 32bit OS? Thanks! Please be aware that e-mail communication can be intercepted in transmission or misdirected. Please consider communicating any sensitive information by telephone, fax, or mail. The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to hipaa.security(a)yale.edu and destroy this message.

1 0

Comparison of "segment_subregions" and "recon-all"
by Yoonho Hwang 06 Aug '24

06 Aug '24

External Email - Use Caution Dear Bruce Fischl and Douglas Greve, Hi all, After completing the "recon-all" process, I have completed the "segment_subregions" process. There is a difference between the total volume (hippocampus, amygdala, thalamus, brainstem) using "asegstats2table" and the total volume (hippocampus, amygdala, thalamus, brainstem) using "segment_subregions". Is there a standard for how much difference is acceptable? Thank you very much Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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Re: [Freesurfer] mri_easyreg --help error: zsh : illegal hardware instruction mri_easyreg --help
by fsbuild 05 Aug '24

05 Aug '24

External Email - Use Caution  Hello Yaozhi, You probably installed the Intel Mac binaries to run on your Silicon Mac with an M1, M2, or M3 arm64 chip.  But not all Intel binaries will run on the newer arm64 Macs.   If you want to run that command you will need to download and install the silicon Mac nightly freesurfer build. To remove your current freesurfer install, you can try running the uninstall script from the command line under what you set FREESURFER_HOME to, $ cd $FREESURFER_HOME$ sudo bash uninstall.sh Once you have removed your current freesurfer installation, you can download and try installing the arm64 pkg, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesu… Right click with the mouse on the .pkg file and select “Open with —> install.app (default)".  Then follow the prompts in the installer windows. - R. On Aug 5, 2024, at 21:45, Yang, Yaozhi <yangyaozhi(a)ufl.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I am trying to use easyreg from the paper--- A ready‑to‑use machine learning tool for symmetric multi‑modality registration of brain MRI and the paper says that I can use freesurfer to get the easyreg function. But after I download freesurfur in my macbook, and run mri_easyreg –-help on the terminal, I get the error saying that zsh : illegal hardware instruction mri_easyreg --help. So can you help me with that? How can I use easyreg method? Thank you very much! Best,Yaozhi_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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