Wed Mar 5 15:18:57 CET 2025 cd /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii setenv SUBJECTS_DIR /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8 /bif/software/FREESURFER/freesurfer-8.0.0/bin/recon-all -s sub-AH002_ses-01_T1w.nii -i /bif/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz -all subjid sub-AH002_ses-01_T1w.nii setenv SUBJECTS_DIR /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8 FREESURFER_HOME /bif/software/FREESURFER/freesurfer-8.0.0 Actual FREESURFER_HOME /bif/software/FREESURFER/freesurfer-8.0.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 256366 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 62G 2.8G 42G 127M 17G 59G Swap: 11G 0B 11G ######################################## program versions used 8.0.0 (freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a) 8.0.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 8.0.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 8.0.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mris_convert -all-info ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 8.0.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ####################################### GCADIR /bif/software/FREESURFER/freesurfer-8.0.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /bif/software/FREESURFER/freesurfer-8.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii mri_convert /bif/storage/storage1/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz mri_convert /bif/storage/storage1/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=1) reading from /bif/storage/storage1/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998713, 0.042352, -0.027917) j_ras = (-0.0431906, 0.998612, -0.0301534) k_ras = (0.0266012, 0.0313203, 0.999155) writing to /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz... @#@FSTIME 2025:03:05:15:18:58 mri_convert N 2 e 3.14 S 0.01 U 2.95 P 94% M 48644 F 0 R 1561 W 0 c 13 w 392 I 0 O 19752 L 1.87 0.80 0.48 @#@FSLOADPOST 2025:03:05:15:19:01 mri_convert N 2 1.88 0.82 0.48 #-------------------------------------------- #@# MotionCor Wed Mar 5 15:19:02 CET 2025 Found 1 runs /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/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 /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz mri_info /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 176 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 1 xstart: -88.0, xend: 88.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 0.9987, y_r = -0.0432, z_r = 0.0266, c_r = -0.2881 : x_a = 0.0424, y_a = 0.9986, z_a = 0.0313, c_a = -0.1328 : x_s = -0.0279, y_s = -0.0302, z_s = 0.9992, c_s = 10.3591 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.9987 -0.0432 0.0266 -86.0514 0.0424 0.9986 0.0313 -135.6911 -0.0279 -0.0302 0.9992 -111.2165 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 0.9987 0.0424 -0.0279 88.5825 -0.0432 0.9986 -0.0302 128.4325 0.0266 0.0313 0.9992 117.6615 0.0000 0.0000 0.0000 1.0000 /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii mri_convert /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --conform mri_convert /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --conform reading from /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998713, 0.042352, -0.027917) j_ras = (-0.0431906, 0.998612, -0.0301534) k_ras = (0.0266012, 0.0313203, 0.999155) volume geometry: valid : -85139672 extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : (-0.2881, -0.1328, 10.3591) shears : ( 0.0000, 0.0000, 0.0000) file : /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 774 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz... @#@FSTIME 2025:03:05:15:19:05 mri_convert N 3 e 3.89 S 0.01 U 3.76 P 97% M 60088 F 0 R 3496 W 0 c 12 w 244 I 0 O 9600 L 1.88 0.82 0.48 @#@FSLOADPOST 2025:03:05:15:19:09 mri_convert N 3 1.97 0.86 0.50 mri_add_xform_to_header -c /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/transforms/talairach.xfm /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2025:03:05:15:19:09 mri_add_xform_to_header N 4 e 1.56 S 0.00 U 1.45 P 92% M 19548 F 0 R 1416 W 0 c 13 w 222 I 0 O 9600 L 1.97 0.86 0.50 @#@FSLOADPOST 2025:03:05:15:19:11 mri_add_xform_to_header N 4 1.97 0.87 0.51 mri_info /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz orig.mgz ======================================== Volume information for /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz type: MGH intent: MRI (0) dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.2881 : x_a = -0.0000, y_a = -0.0000, z_a = 1.0000, c_a = -0.1328 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 10.3590 talairach xfm : /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.7119 -0.0000 -0.0000 1.0000 -128.1328 0.0000 -1.0000 0.0000 138.3590 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 -0.0000 127.7119 -0.0000 0.0000 -1.0000 138.3590 -0.0000 1.0000 -0.0000 128.1328 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz --trg /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --outlta /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg2orig.lta 8.0.0 --inlta: identity.nofile input LTA transform. --src: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz src image (geometry). --trg: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz trg image (geometry). --outlta: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg2orig.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg2orig.lta... lta_convert successful. @#@FSTIME 2025:03:05:15:19:11 lta_convert N 8 e 0.21 S 0.00 U 0.20 P 98% M 2204 F 0 R 646 W 0 c 2 w 9 I 0 O 8 L 1.97 0.87 0.51 @#@FSLOADPOST 2025:03:05:15:19:11 lta_convert N 8 1.97 0.87 0.51 mri_synthstrip --threads 1 -i /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz -o /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/synthstrip.mgz If you use SynthStrip in your analysis, please cite: ---------------------------------------------------- SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://doi.org/10.1016/j.neuroimage.2022.119474 Website: https://synthstrip.io @#@FSTIME 2025:03:05:15:19:11 mri_synthstrip N 6 e 33.27 S 2.16 U 28.71 P 92% M 5860760 F 0 R 122244 W 0 c 345 w 7658 I 0 O 2440 L 1.97 0.87 0.51 @#@FSLOADPOST 2025:03:05:15:19:44 mri_synthstrip N 6 1.98 0.98 0.55 mri_synthseg --i /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --o /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/synthseg.rca.mgz --threads 1 --vol /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/stats/synthseg.vol.csv --keepgeom --addctab --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread addctab True predicting 1/1 the following problem occurred with image /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz : Traceback (most recent call last): File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 324, in predict image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i], File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 577, in preprocess im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True) File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 1527, in get_volume_info data_res = np.array(header['pixdim'][1:n_dims + 1]) File "/bif/software/FREESURFER/freesurfer-8.0.0/python/lib/python3.8/site-packages/nibabel/wrapstruct.py", line 310, in __getitem__ return self._structarr[item] ValueError: no field of name pixdim resuming program execution ERROR: some problems occured for the following inputs (see corresponding errors above): /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz @#@FSTIME 2025:03:05:15:19:44 mri_synthseg N 11 e 8.65 S 0.72 U 4.20 P 56% M 575560 F 0 R 117516 W 0 c 260 w 14864 I 0 O 96 L 1.98 0.98 0.55 @#@FSLOADPOST 2025:03:05:15:19:53 mri_synthseg N 11 1.99 1.02 0.57 Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-AH002_ses-01_T1w.nii exited with ERRORS at Wed Mar 5 15:19:53 CET 2025 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting