Fri Jun 11 12:25:46 CEST 2021 cd /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1 setenv SUBJECTS_DIR /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/bin/recon-all -s AIDAB_2017_T1 -i T1analysis/TNU_AIDAB_2017_T1_t1_fov_brain.nii.gz -all -3T -mprage -wsatlas subjid AIDAB_2017_T1 setenv SUBJECTS_DIR /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results FREESURFER_HOME /mnt/mbServerProjects/HOME/USERS/lea/freesurfer Actual FREESURFER_HOME /mnt/mbServerProjects/HOME/USERS/lea/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Linux mb-kraepelin 5.4.0-73-generic #82~18.04.1-Ubuntu SMP Fri Apr 16 15:10:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 514458 maxlocks unlimited maxsignal 514458 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125G 23G 69G 2.0G 32G 98G Swap: 0B 0B 0B ######################################## 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: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic 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: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic 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: 2021/06/11-10:25:46-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-73-generic 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 /mnt/mbServerProjects/HOME/USERS/lea/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 /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1 mri_convert /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/T1analysis/TNU_AIDAB_2017_T1_t1_fov_brain.nii.gz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig/001.mgz mri_convert /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/T1analysis/TNU_AIDAB_2017_T1_t1_fov_brain.nii.gz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig/001.mgz reading from /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/T1analysis/TNU_AIDAB_2017_T1_t1_fov_brain.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999934, -0.000237523, 0.0115195) j_ras = (-0.000947534, 0.994706, 0.102759) k_ras = (-0.011483, -0.102763, 0.99464) writing to /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig/001.mgz... @#@FSTIME 2021:06:11:12:25:46 mri_convert N 2 e 0.97 S 0.02 U 0.92 P 97% M 39932 F 0 R 8630 W 0 c 98 w 77 I 9112 O 9160 L 8.14 8.21 8.20 @#@FSLOADPOST 2021:06:11:12:25:47 mri_convert N 2 8.21 8.22 8.20 #-------------------------------------------- #@# MotionCor Fri Jun 11 12:25:48 CEST 2021 Found 1 runs /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/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 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig/001.mgz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/rawavg.mgz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1 mri_convert /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/rawavg.mgz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig.mgz --conform mri_convert /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/rawavg.mgz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig.mgz --conform reading from /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999934, -0.000237523, 0.0115195) j_ras = (-0.000947534, 0.994706, 0.102759) k_ras = (-0.011483, -0.102763, 0.99464) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 656.53 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig.mgz... @#@FSTIME 2021:06:11:12:25:51 mri_convert N 3 e 5.61 S 0.01 U 5.59 P 99% M 48164 F 0 R 18978 W 0 c 543 w 65 I 0 O 2664 L 8.21 8.22 8.20 @#@FSLOADPOST 2021:06:11:12:25:56 mri_convert N 3 8.19 8.22 8.20 mri_add_xform_to_header -c /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/transforms/talairach.xfm /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig.mgz /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2021:06:11:12:25:56 mri_add_xform_to_header N 4 e 0.74 S 0.00 U 0.73 P 99% M 23340 F 0 R 4590 W 0 c 71 w 82 I 0 O 2664 L 8.19 8.22 8.20 @#@FSLOADPOST 2021:06:11:12:25:57 mri_add_xform_to_header N 4 8.18 8.22 8.20 #-------------------------------------------- #@# Talairach Fri Jun 11 12:25:57 CEST 2021 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/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 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri /mnt/mbServerProjects/HOME/USERS/lea/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 mb-kraepelin 5.4.0-73-generic #82~18.04.1-Ubuntu SMP Fri Apr 16 15:10:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Fri Jun 11 12:25:57 CEST 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.1062978 cd /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.1062978/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.1062978/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.1062978/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.1062978/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-10, -9.31323e-10) j_ras = (0, 0, -1) k_ras = (1.16415e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Fri Jun 11 12:28:48 CEST 2021 mri_nu_correct.mni done @#@FSTIME 2021:06:11:12:25:57 mri_nu_correct.mni N 12 e 171.04 S 0.25 U 170.74 P 99% M 491104 F 0 R 146890 W 0 c 16425 w 276 I 0 O 2656 L 8.18 8.22 8.20 @#@FSLOADPOST 2021:06:11:12:28:48 mri_nu_correct.mni N 12 8.11 8.19 8.19 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Fri Jun 11 12:28:48 CEST 2021 Ended at Fri Jun 11 12:29:12 CEST 2021 talairach_avi done @#@FSTIME 2021:06:11:12:28:48 talairach_avi N 6 e 23.29 S 1.18 U 15.60 P 72% M 256024 F 0 R 396076 W 0 c 1723 w 11920 I 262144 O 296016 L 8.11 8.19 8.19 @#@FSLOADPOST 2021:06:11:12:29:12 talairach_avi N 6 8.01 8.16 8.18 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /mnt/mbServerProjects/HOME/USERS/lea/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: /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.15325 -0.00952 0.02152 -0.68060; 0.00498 1.05031 0.33119 -34.20124; -0.01498 -0.22755 1.16681 -17.10867; 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 Fri Jun 11 12:29:14 CEST 2021 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7960, pval=0.8469 >= threshold=0.0050) @#@FSTIME 2021:06:11:12:29:14 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 80% M 5660 F 0 R 212 W 0 c 0 w 9 I 0 O 0 L 7.92 8.14 8.17 @#@FSLOADPOST 2021:06:11:12:29:14 talairach_afd N 4 7.92 8.14 8.17 awk -f /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/transforms/talairach_avi.log tal_QC_AZS /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/transforms/talairach_avi.log TalAviQA: 0.96879 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Fri Jun 11 12:29:14 CEST 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 /usr/bin/bc /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 nIters 1 mri_nu_correct.mni 7.1.1 Linux mb-kraepelin 5.4.0-73-generic #82~18.04.1-Ubuntu SMP Fri Apr 16 15:10:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Fri Jun 11 12:29:14 CEST 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.1063509 cd /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.1063509/ones.mgz 7.1.1 cwd /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.1063509/ones.mgz sysname Linux hostname mb-kraepelin machine x86_64 user ewahelene input /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.1063509/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.1063509/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.1063509/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.1063509/input.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.1063509/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.1063509/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.1063509/input.mean.dat sysname Linux hostname mb-kraepelin machine x86_64 user ewahelene whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.1063509/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.1063509/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.1063509/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.1063509/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.1063509/output.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.1063509/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.1063509/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.1063509/output.mean.dat sysname Linux hostname mb-kraepelin machine x86_64 user ewahelene whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.1063509/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.1063509/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.1063509/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz mul .92362524985663284417 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.1063509/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.16415e-10, -9.31323e-10) j_ras = (0, 0, -1) k_ras = (1.16415e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping (57, 236) to ( 3, 110) Fri Jun 11 12:32:30 CEST 2021 mri_nu_correct.mni done @#@FSTIME 2021:06:11:12:29:14 mri_nu_correct.mni N 13 e 195.98 S 0.59 U 195.29 P 99% M 614584 F 0 R 513850 W 0 c 19108 w 659 I 0 O 9728 L 7.92 8.14 8.17 @#@FSLOADPOST 2021:06:11:12:32:30 mri_nu_correct.mni N 13 8.10 8.13 8.16 mri_add_xform_to_header -c /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2021:06:11:12:32:30 mri_add_xform_to_header N 4 e 0.77 S 0.01 U 0.75 P 99% M 23424 F 0 R 4593 W 0 c 78 w 84 I 0 O 2056 L 8.10 8.13 8.16 @#@FSLOADPOST 2021:06:11:12:32:31 mri_add_xform_to_header N 4 8.10 8.13 8.16 #-------------------------------------------- #@# Intensity Normalization Fri Jun 11 12:32:31 CEST 2021 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/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... talairach transform 1.15325 -0.00952 0.02152 -0.68060; 0.00498 1.05031 0.33119 -34.20124; -0.01498 -0.22755 1.16681 -17.10867; 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 = 11 Starting OpenSpline(): npoints = 11 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 141 white matter peak found at 142 gm peak at 100 (100), valley at 54 (54) csf peak at 50, setting threshold to 83 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 36 seconds. @#@FSTIME 2021:06:11:12:32:31 mri_normalize N 7 e 97.33 S 0.28 U 96.98 P 99% M 584056 F 0 R 263301 W 0 c 9523 w 67 I 0 O 1920 L 8.10 8.13 8.16 @#@FSLOADPOST 2021:06:11:12:34:08 mri_normalize N 7 8.17 8.15 8.16 #-------------------------------------------- #@# Skull Stripping Fri Jun 11 12:34:08 CEST 2021 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri mri_em_register -skull nu.mgz /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/mnt/mbServerProjects/HOME/USERS/lea/freesurfer/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (68, 68, 41) --> (190, 193, 196) finding center of left hemi white matter using (109, 110, 119) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (94,95,100) --> (123, 125,138) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 110 +- 2.3 after smoothing, mri peak at 110, scaling input intensities by 0.982 scaling channel 0 by 0.981818 initial log_p = -4.637 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.632531 @ (0.000, 0.000, 0.000) max log p = -4.577526 @ (-5.263, -5.263, -5.263) max log p = -4.577526 @ (0.000, 0.000, 0.000) max log p = -4.540471 @ (3.947, 3.947, 1.316) max log p = -4.540471 @ (0.000, 0.000, 0.000) max log p = -4.540471 @ (0.000, 0.000, 0.000) max log p = -4.540471 @ (0.000, 0.000, 0.000) max log p = -4.540471 @ (0.000, 0.000, 0.000) Found translation: (-1.3, -1.3, -3.9): log p = -4.540 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.076, old_max_log_p =-4.540 (thresh=-4.5) 1.15000 0.00000 0.00000 -20.27852; 0.00000 1.11081 0.29764 -51.47247; 0.00000 -0.29764 1.11081 18.48578; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 53 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.076, old_max_log_p =-4.076 (thresh=-4.1) 1.15000 0.00000 0.00000 -20.27852; 0.00000 1.11081 0.29764 -51.47247; 0.00000 -0.29764 1.11081 18.48578; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 49 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.999, old_max_log_p =-4.076 (thresh=-4.1) 1.12783 0.03731 0.00865 -25.49422; -0.03763 1.16161 0.26940 -46.49535; 0.00000 -0.25760 1.09869 15.96475; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 42 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.999, old_max_log_p =-3.999 (thresh=-4.0) 1.12783 0.03731 0.00865 -25.49422; -0.03763 1.16161 0.26940 -46.49535; 0.00000 -0.25760 1.09869 15.96475; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 42 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.994, old_max_log_p =-3.999 (thresh=-4.0) 1.13203 0.02582 0.01545 -25.24708; -0.02838 1.16186 0.26954 -47.73031; -0.00924 -0.25699 1.09472 17.53586; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 23 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.990, old_max_log_p =-3.994 (thresh=-4.0) 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01850 -0.25689 1.09328 19.34893; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 22 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.989, old_max_log_p =-3.990 (thresh=-4.0) 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 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 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.989 (old=-4.637) transform before final EM align: 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 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 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 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: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.13590 0.02381 0.02448 -26.53793; -0.02841 1.16322 0.26985 -47.95278; -0.01848 -0.25659 1.09200 19.45652; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 803096 FSRUNTIME@ mri_em_register 0.2039 hours 1 threads registration took 12 minutes and 14 seconds. @#@FSTIME 2021:06:11:12:34:08 mri_em_register N 4 e 734.01 S 0.63 U 732.79 P 99% M 629040 F 0 R 166548 W 0 c 70962 w 21 I 0 O 24 L 8.17 8.15 8.16 @#@FSLOADPOST 2021:06:11:12:46:22 mri_em_register N 4 8.31 8.22 8.19 mri_watershed -T1 -brain_atlas /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta -atlas T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) Mode: Atlas analysis ********************************************************* 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=130 y=123 z=111 r=53 first estimation of the main basin volume: 650350 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=110, y=102, z=87, Imax=255 CSF=14, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=8051601593 voxels, voxel volume =1.000 = 8051601593 mmm3 = 8051601.408 cm3 done. PostAnalyze...Basin Prior 16 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=122, z=112, r=8650 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ mri_watershed Error: GLOBAL region of the brain empty ! Command exited with non-zero status 1 @#@FSTIME 2021:06:11:12:46:22 mri_watershed N 7 e 5.05 S 0.20 U 4.84 P 99% M 788232 F 0 R 198766 W 0 c 499 w 17 I 0 O 0 L 8.31 8.22 8.19 @#@FSLOADPOST 2021:06:11:12:46:27 mri_watershed N 7 8.29 8.21 8.19 Linux mb-kraepelin 5.4.0-73-generic #82~18.04.1-Ubuntu SMP Fri Apr 16 15:10:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AIDAB_2017_T1 exited with ERRORS at Fri Jun 11 12:46:27 CEST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Sun Oct 10 21:54:41 CEST 2021 cd /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1 setenv SUBJECTS_DIR /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/bin/recon-all -autorecon-pial -subjid AIDAB_2017_T1 subjid AIDAB_2017_T1 setenv SUBJECTS_DIR /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results FREESURFER_HOME /mnt/mbServerProjects/HOME/USERS/lea/freesurfer Actual FREESURFER_HOME /mnt/mbServerProjects/HOME/USERS/lea/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Linux mb-kraepelin 5.4.0-77-generic #86~18.04.1-Ubuntu SMP Fri Jun 18 01:23:22 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 514409 maxlocks unlimited maxsignal 514409 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125G 29G 9.3G 1.4G 87G 93G Swap: 0B 0B 0B ######################################## 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: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic 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: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic 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: 2021/10/10-19:54:41-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: ewahelene Machine: mb-kraepelin Platform: Linux PlatformVersion: 5.4.0-77-generic 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 /mnt/mbServerProjects/HOME/USERS/lea/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 /mnt/mbServerProjects/HOME/USERS/lea/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Mask BFS Sun Oct 10 21:54:42 CEST 2021 /mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 error: mghRead(/mnt/mbServerProjects/SCRATCH/GROUPS/AiDA_HippoSubfields/AiDA_struct/Freesurfer_results/AIDAB_2017_T1/mri/brain.mgz, -1): could not open file error: mri_mask: could not read source volume brain.mgz Command exited with non-zero status 252 @#@FSTIME 2021:10:10:21:54:42 mri_mask N 5 e 0.03 S 0.00 U 0.00 P 12% M 6168 F 0 R 261 W 0 c 1 w 16 I 0 O 0 L 52.81 81.57 165.70 @#@FSLOADPOST 2021:10:10:21:54:42 mri_mask N 5 52.81 81.57 165.70 Linux mb-kraepelin 5.4.0-77-generic #86~18.04.1-Ubuntu SMP Fri Jun 18 01:23:22 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AIDAB_2017_T1 exited with ERRORS at Sun Oct 10 21:54:42 CEST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting