Tue Jul 11 10:07:58 EDT 2023 cd /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR setenv SUBJECTS_DIR /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/recon-all -subjid HCA6429272_V1_MR -i /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz -all subjid HCA6429272_V1_MR setenv SUBJECTS_DIR /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/7.2.0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/7.2.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Linux r440-31.nmr.mgh.harvard.edu 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 8388608 kbytes vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1539499 maxlocks unlimited maxsignal 1539499 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 375Gi 10Gi 321Gi 52Mi 43Gi 362Gi Swap: 31Gi 3.0Mi 31Gi SLURM_JOB_ID 2795997 ######################################## program versions used 7.2.0 (freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b) 7.2.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:58-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:07:59-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:00-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.2.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2023/07/11-14:08:01-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: r440-31.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-477.15.1.el8_8.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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 /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR mri_convert /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig/001.mgz mri_convert /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig/001.mgz reading from /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.997218, -0.0267984, -0.0695567) j_ras = (0.0478479, 0.945649, 0.32165) k_ras = (0.0571566, -0.324083, 0.9443) writing to /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig/001.mgz... @#@FSTIME 2023:07:11:10:08:02 mri_convert N 2 e 4.71 S 0.04 U 4.32 P 92% M 46488 F 0 R 1091 W 0 c 32 w 1001 I 49320 O 49312 L 18.47 17.50 17.74 @#@FSLOADPOST 2023:07:11:10:08:07 mri_convert N 2 18.43 17.51 17.74 #-------------------------------------------- #@# MotionCor Tue Jul 11 10:08:08 EDT 2023 Found 1 runs /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/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 /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig/001.mgz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/rawavg.mgz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR mri_convert /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/rawavg.mgz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig.mgz --conform mri_convert /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/rawavg.mgz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig.mgz --conform reading from /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/rawavg.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.997218, -0.0267984, -0.0695567) j_ras = (0.0478479, 0.945649, 0.32165) k_ras = (0.0571566, -0.324083, 0.9443) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 3662 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig.mgz... @#@FSTIME 2023:07:11:10:08:12 mri_convert N 3 e 4.11 S 0.03 U 3.90 P 95% M 66132 F 0 R 6615 W 0 c 21 w 176 I 0 O 12888 L 18.55 17.55 17.75 @#@FSLOADPOST 2023:07:11:10:08:16 mri_convert N 3 18.67 17.59 17.76 mri_add_xform_to_header -c /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/transforms/talairach.xfm /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig.mgz /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2023:07:11:10:08:16 mri_add_xform_to_header N 4 e 1.30 S 0.02 U 1.02 P 80% M 22948 F 0 R 965 W 0 c 12 w 209 I 5816 O 12880 L 18.67 17.59 17.76 @#@FSLOADPOST 2023:07:11:10:08:18 mri_add_xform_to_header N 4 18.22 17.51 17.74 #-------------------------------------------- #@# Talairach Tue Jul 11 10:08:18 EDT 2023 /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/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 /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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 7.2.0 Linux r440-31.nmr.mgh.harvard.edu 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Jul 11 10:08:18 EDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.838665 cd /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.838665/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.838665/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.838665/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.838665/nu0.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 0) j_ras = (-7.45058e-09, -2.98023e-08, -1) k_ras = (5.58794e-09, 1, 2.98023e-08) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Jul 11 10:11:46 EDT 2023 mri_nu_correct.mni done @#@FSTIME 2023:07:11:10:08:18 mri_nu_correct.mni N 12 e 208.51 S 0.21 U 207.17 P 99% M 504800 F 0 R 22467 W 0 c 863 w 712 I 7216 O 21184 L 18.22 17.51 17.74 @#@FSLOADPOST 2023:07:11:10:11:47 mri_nu_correct.mni N 12 19.47 18.56 18.12 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Jul 11 10:11:47 EDT 2023 Ended at Tue Jul 11 10:12:15 EDT 2023 talairach_avi done @#@FSTIME 2023:07:11:10:11:47 talairach_avi N 4 e 28.66 S 0.86 U 19.35 P 70% M 255944 F 0 R 28344 W 0 c 183 w 5877 I 270960 O 296104 L 19.47 18.56 18.12 @#@FSLOADPOST 2023:07:11:10:12:15 talairach_avi N 4 19.81 18.73 18.19 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.2.0 --src: orig.mgz src image (geometry). --trg: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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 1.07280 -0.02927 -0.08382 -4.64026; 0.05793 0.99234 0.17149 -27.30109; 0.04552 -0.24399 1.12810 24.25870; 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 Tue Jul 11 10:12:17 EDT 2023 /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7785, pval=0.8469 >= threshold=0.0050) @#@FSTIME 2023:07:11:10:12:18 talairach_afd N 4 e 0.03 S 0.01 U 0.00 P 48% M 5188 F 0 R 193 W 0 c 1 w 25 I 5912 O 0 L 19.74 18.73 18.19 @#@FSLOADPOST 2023:07:11:10:12:18 talairach_afd N 4 19.74 18.73 18.19 awk -f /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/extract_talairach_avi_QA.awk /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/transforms/talairach_avi.log TalAviQA: 0.95779 z-score: -4 #-------------------------------------------- #@# Nu Intensity Correction Tue Jul 11 10:12:18 EDT 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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 7.2.0 Linux r440-31.nmr.mgh.harvard.edu 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Jul 11 10:12:18 EDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.839162 cd /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.839162/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.839162/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.839162/ones.mgz 7.2.0 cwd /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.839162/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.839162/ones.mgz sysname Linux hostname r440-31.nmr.mgh.harvard.edu machine x86_64 user jj1006 input ./tmp.mri_nu_correct.mni.839162/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.839162/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.839162/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.839162/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.839162/sum.junk --avgwf ./tmp.mri_nu_correct.mni.839162/input.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.839162/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.839162/sum.junk --avgwf ./tmp.mri_nu_correct.mni.839162/input.mean.dat sysname Linux hostname r440-31.nmr.mgh.harvard.edu machine x86_64 user jj1006 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.839162/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.839162/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.839162/ones.mgz --i ./tmp.mri_nu_correct.mni.839162/nu0.mgz --sum ./tmp.mri_nu_correct.mni.839162/sum.junk --avgwf ./tmp.mri_nu_correct.mni.839162/output.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.839162/ones.mgz --i ./tmp.mri_nu_correct.mni.839162/nu0.mgz --sum ./tmp.mri_nu_correct.mni.839162/sum.junk --avgwf ./tmp.mri_nu_correct.mni.839162/output.mean.dat sysname Linux hostname r440-31.nmr.mgh.harvard.edu machine x86_64 user jj1006 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.839162/ones.mgz Loading ./tmp.mri_nu_correct.mni.839162/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.839162/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.839162/nu0.mgz ./tmp.mri_nu_correct.mni.839162/nu0.mgz mul 1.81563546039940996255 Saving result to './tmp.mri_nu_correct.mni.839162/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.839162/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.839162/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.839162/nu0.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 0) j_ras = (-7.45058e-09, -2.98023e-08, -1) k_ras = (5.58794e-09, 1, 2.98023e-08) 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 6 seconds. mapping (18, 119) to ( 3, 110) Tue Jul 11 10:16:11 EDT 2023 mri_nu_correct.mni done @#@FSTIME 2023:07:11:10:12:18 mri_nu_correct.mni N 9 e 232.91 S 0.62 U 230.62 P 99% M 613608 F 0 R 166744 W 0 c 1006 w 1403 I 5168 O 55448 L 19.74 18.73 18.19 @#@FSLOADPOST 2023:07:11:10:16:11 mri_nu_correct.mni N 9 19.86 18.94 18.36 mri_add_xform_to_header -c /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2023:07:11:10:16:11 mri_add_xform_to_header N 4 e 0.63 S 0.01 U 0.57 P 92% M 22988 F 0 R 965 W 0 c 10 w 128 I 0 O 6656 L 19.86 18.94 18.36 @#@FSLOADPOST 2023:07:11:10:16:11 mri_add_xform_to_header N 4 19.86 18.94 18.36 #-------------------------------------------- #@# Intensity Normalization Tue Jul 11 10:16:11 EDT 2023 /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/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 1.07280 -0.02927 -0.08382 -4.64026; 0.05793 0.99234 0.17149 -27.30109; 0.04552 -0.24399 1.12810 24.25870; 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 = 4 Starting OpenSpline(): npoints = 4 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 90 gm peak at 40 (40), valley at 28 (28) csf peak at 20, setting threshold to 33 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 89 gm peak at 42 (42), valley at 29 (29) csf peak at 22, setting threshold to 35 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 3 seconds. @#@FSTIME 2023:07:11:10:16:11 mri_normalize N 7 e 123.55 S 0.20 U 122.97 P 99% M 583656 F 0 R 15033 W 0 c 509 w 140 I 0 O 6968 L 19.86 18.94 18.36 @#@FSLOADPOST 2023:07:11:10:18:15 mri_normalize N 7 18.75 18.83 18.40 #-------------------------------------------- #@# Skull Stripping Tue Jul 11 10:18:15 EDT 2023 /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer/HCA6429272_V1_MR/mri mri_em_register -skull nu.mgz /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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 '/autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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=20.0 skull bounding box = (50, 48, 30) --> (210, 176, 235) finding center of left hemi white matter using (103, 91, 133) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (83,75,108) --> (122, 106,158) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 102 +- 13.7 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.742 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.589674 @ (-10.526, -10.526, -31.579) max log p = -4.406190 @ (5.263, 5.263, 5.263) max log p = -4.406190 @ (0.000, 0.000, 0.000) max log p = -4.361103 @ (1.316, 1.316, 3.947) max log p = -4.361103 @ (0.000, 0.000, 0.000) max log p = -4.361103 @ (0.000, 0.000, 0.000) max log p = -4.361103 @ (0.000, 0.000, 0.000) max log p = -4.361103 @ (0.000, 0.000, 0.000) Found translation: (-3.9, -3.9, -22.4): log p = -4.361 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.168, old_max_log_p =-4.361 (thresh=-4.4) 1.15000 0.00000 0.00000 -23.30484; 0.00000 1.14016 0.13053 -41.84895; 0.00000 -0.15011 0.99144 0.69797; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 37 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.168, old_max_log_p =-4.168 (thresh=-4.2) 1.15000 0.00000 0.00000 -23.30484; 0.00000 1.14016 0.13053 -41.84895; 0.00000 -0.15011 0.99144 0.69797; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 43 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.075, old_max_log_p =-4.168 (thresh=-4.2) 1.12670 -0.03956 0.02530 -17.77491; 0.03816 1.11760 0.13124 -41.77084; -0.04272 -0.16094 1.04691 0.38615; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 34 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.074, old_max_log_p =-4.075 (thresh=-4.1) 1.12466 -0.04600 0.05939 -21.12428; 0.03743 1.13258 0.16852 -48.81091; -0.07927 -0.19234 1.02116 13.06729; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 37 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.045, old_max_log_p =-4.074 (thresh=-4.1) 1.12649 -0.06496 0.05705 -18.32426; 0.05651 1.13198 0.16038 -49.63589; -0.07904 -0.18180 1.01898 10.86841; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 31 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.043, old_max_log_p =-4.045 (thresh=-4.0) 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 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 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 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: 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.043 (old=-4.742) transform before final EM align: 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 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 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 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) = 4.5 tol 0.000000 final transform: 1.12517 -0.06489 0.05699 -18.15578; 0.05644 1.13065 0.16019 -49.41119; -0.07895 -0.18158 1.01778 11.45470; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 799948 FSRUNTIME@ mri_em_register 0.1790 hours 1 threads registration took 10 minutes and 44 seconds. @#@FSTIME 2023:07:11:10:18:15 mri_em_register N 4 e 644.27 S 0.67 U 641.75 P 99% M 628804 F 0 R 117636 W 0 c 2553 w 65 I 149672 O 40 L 18.75 18.83 18.40 @#@FSLOADPOST 2023:07:11:10:29:01 mri_em_register N 4 20.12 18.88 18.42 mri_watershed -T1 -brain_atlas /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/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=129 y=102 z=156 r=92 first estimation of the main basin volume: 3321986 voxelsWM coord (212, 114, 268) out of bounds (256, 256, 256), normalization failed? mri_watershed Error: indices out of bounds Command exited with non-zero status 1 @#@FSTIME 2023:07:11:10:29:01 mri_watershed N 6 e 2.40 S 0.33 U 2.05 P 99% M 779000 F 0 R 181616 W 0 c 25 w 22 I 0 O 0 L 20.12 18.88 18.42 @#@FSLOADPOST 2023:07:11:10:29:03 mri_watershed N 6 20.03 18.88 18.42 Linux r440-31.nmr.mgh.harvard.edu 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HCA6429272_V1_MR exited with ERRORS at Tue Jul 11 10:29:03 EDT 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting