Wed May 26 18:23:44 CST 2021 cd /home/liubing/FreeSurfer/data/test_recon/ANDI1 setenv SUBJECTS_DIR /home/liubing/FreeSurfer/data/test_recon /home/liubing/FreeSurfer/freesurfer/bin/recon-all -s ANDI1 -i ./test/ANDI1/ADNI_002_S_0619_MR_MP-RAGE__br_raw_20060601215738863_1_S15147_I16392.nii -all -qcache subjid ANDI1 setenv SUBJECTS_DIR /home/liubing/FreeSurfer/data/test_recon FREESURFER_HOME /home/liubing/FreeSurfer/freesurfer Actual FREESURFER_HOME /home/liubing/FreeSurfer/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 512146 maxlocks unlimited maxsignal 512146 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 11Gi 30Gi 853Mi 83Gi 112Gi Swap: 7.7Gi 49Mi 7.7Gi ######################################## program versions used 7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) 7.1.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.1.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:23:44-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.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 /home/liubing/FreeSurfer/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 /home/liubing/FreeSurfer/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/liubing/FreeSurfer/data/test_recon/ANDI1 mri_convert /home/liubing/FreeSurfer/data/test/ANDI1/ADNI_002_S_0619_MR_MP-RAGE__br_raw_20060601215738863_1_S15147_I16392.nii /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig/001.mgz mri_convert /home/liubing/FreeSurfer/data/test/ANDI1/ADNI_002_S_0619_MR_MP-RAGE__br_raw_20060601215738863_1_S15147_I16392.nii /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig/001.mgz INFO: using NIfTI-1 qform reading from /home/liubing/FreeSurfer/data/test/ANDI1/ADNI_002_S_0619_MR_MP-RAGE__br_raw_20060601215738863_1_S15147_I16392.nii... 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/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig/001.mgz... @#@FSTIME 2021:05:26:18:23:44 mri_convert N 2 e 1.40 S 0.01 U 1.39 P 99% M 28196 F 0 R 651 W 0 c 3 w 33 I 7744 O 32960 L 0.11 0.58 0.87 @#@FSLOADPOST 2021:05:26:18:23:46 mri_convert N 2 0.11 0.58 0.87 #-------------------------------------------- #@# MotionCor Wed May 26 18:23:46 CST 2021 Found 1 runs /home/liubing/FreeSurfer/data/test_recon/ANDI1/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/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig/001.mgz /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/rawavg.mgz /home/liubing/FreeSurfer/data/test_recon/ANDI1 mri_convert /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/rawavg.mgz /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig.mgz --conform mri_convert /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/rawavg.mgz /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig.mgz --conform reading from /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/rawavg.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) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 8856 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig.mgz... @#@FSTIME 2021:05:26:18:23:49 mri_convert N 3 e 2.49 S 0.03 U 2.43 P 98% M 39000 F 0 R 2344 W 0 c 188 w 1 I 0 O 16760 L 0.10 0.57 0.87 @#@FSLOADPOST 2021:05:26:18:23:52 mri_convert N 3 0.10 0.57 0.87 mri_add_xform_to_header -c /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/transforms/talairach.xfm /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig.mgz /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2021:05:26:18:23:52 mri_add_xform_to_header N 4 e 1.09 S 0.01 U 1.06 P 98% M 22800 F 0 R 965 W 0 c 111 w 3 I 0 O 16760 L 0.10 0.57 0.87 @#@FSLOADPOST 2021:05:26:18:23:53 mri_add_xform_to_header N 4 0.17 0.58 0.87 #-------------------------------------------- #@# Talairach Wed May 26 18:23:53 CST 2021 /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri /home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Wed May 26 18:23:53 CST 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.811028 cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.811028/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.811028/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.811028/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.811028/nu0.mgz... TR=0.00, 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... Wed May 26 18:26:41 CST 2021 mri_nu_correct.mni done @#@FSTIME 2021:05:26:18:23:53 mri_nu_correct.mni N 12 e 168.47 S 0.08 U 168.23 P 99% M 488588 F 0 R 24898 W 0 c 76 w 103 I 0 O 14264 L 0.17 0.58 0.87 @#@FSLOADPOST 2021:05:26:18:26:41 mri_nu_correct.mni N 12 1.58 0.92 0.95 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Wed May 26 18:26:41 CST 2021 Ended at Wed May 26 18:27:10 CST 2021 talairach_avi done @#@FSTIME 2021:05:26:18:26:41 talairach_avi N 4 e 28.43 S 0.38 U 21.97 P 78% M 255428 F 0 R 28486 W 0 c 369 w 144 I 0 O 295264 L 1.58 0.92 0.95 @#@FSLOADPOST 2021:05:26:18:27:10 talairach_avi N 4 3.56 1.47 1.14 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /home/liubing/FreeSurfer/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.1.1 --src: orig.mgz src image (geometry). --trg: /home/liubing/FreeSurfer/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 0.97150 0.02218 -0.01546 -204.21016; -0.04161 0.84673 0.42965 -458.30338; -0.00132 -0.36187 0.97350 -400.96991; 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 Wed May 26 18:27:12 CST 2021 /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4532, pval=0.1049 >= threshold=0.0050) @#@FSTIME 2021:05:26:18:27:12 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 5300 F 0 R 200 W 0 c 1 w 1 I 0 O 0 L 3.92 1.58 1.17 @#@FSLOADPOST 2021:05:26:18:27:12 talairach_afd N 4 3.92 1.58 1.17 awk -f /home/liubing/FreeSurfer/freesurfer/bin/extract_talairach_avi_QA.awk /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/transforms/talairach_avi.log tal_QC_AZS /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri/transforms/talairach_avi.log TalAviQA: 0.95965 z-score: #-------------------------------------------- #@# Nu Intensity Correction Wed May 26 18:27:12 CST 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri /home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.1 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Wed May 26 18:27:12 CST 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.811389 cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz 7.1.1 cwd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz sysname Linux hostname HEUBME.com machine x86_64 user liubing input /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811389/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811389/input.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811389/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811389/input.mean.dat sysname Linux hostname HEUBME.com machine x86_64 user liubing whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.811389/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 /dev/shm/tmp.mri_nu_correct.mni.811389/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811389/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811389/output.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.811389/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.811389/output.mean.dat sysname Linux hostname HEUBME.com machine x86_64 user liubing whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.811389/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.811389/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 /dev/shm/tmp.mri_nu_correct.mni.811389/output.mean.dat mri_segstats done Missing parameters. Usage: bc inputImageFile inputSegmentationFile side PathToTrainingFiles outputSegmentationFile side = 0 (left side) or else (right side) mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.811389/nu0.mgz mul Segmentation fault (core dumped) Command exited with non-zero status 1 @#@FSTIME 2021:05:26:18:27:12 mri_nu_correct.mni N 9 e 198.73 S 0.22 U 197.81 P 99% M 503012 F 0 R 27486 W 0 c 437 w 146 I 0 O 16 L 3.92 1.58 1.17 @#@FSLOADPOST 2021:05:26:18:30:31 mri_nu_correct.mni N 9 5.64 3.77 2.13 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ANDI1 exited with ERRORS at Wed May 26 18:30:31 CST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting