External Email - Use Caution
Hello Everyone,
due to new hardware my old freesurfer did not work anymore, so I have new UBUNTU 22.04 and freesurfer_ubuntu22-7.3.2_amd64.debhttps://secure-web.cisco.com/1Jp0hfngKh-YNvOboZak8vNQYbnpzGL438b30mGK2ULBJyWv29ATncea4ZvZzUuUVopMNBYVb8ZyS_tIHo-dxFJrjLQwpqVAjXQk8pyfuCrWBZQOPPYWerSpnL0eWtdb7LmEQP_K7Ho2ldMrX3pALdsQskhY8QCez8JjaeGTEFQePjEVMjd4hRTMclZ0DMIRcOaDehDdUkoo-lYehxBos-d9AL0I4wdAGGObK4pMtHtOj27jVgv39pFrB3M0VwSaeh1-bDolOCqD_IuNAeSiINxYUiqiiDNkVe0jexMHnjXQpmCuSjWsMWDxVD6xfzky1/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer_ubuntu22-7.3.2_amd64.deb istalled..
machine is Intel i7-4790 28 GB + GeForce GTX 1650 4 GB
I tried just to run one job, autorecon1 "finished without error"
and autorecon2 stops with ERROR: cannot find or read transforms/talairach.m3z
I have seen this error in other cases here, but I did not calculate multiple patients.. and have more memory..
Do you have an idea?
Many thanks jürgen
(I wanted to try the Virtual Box version too, but the download file from here can not be unzipped because of broken header?? Downloaded it twice.. )
Thu Oct 20 09:47:31 CEST 2022 cd /usr/local/freesurfer/7.3.2/subjects/Wen.23.9.21 setenv SUBJECTS_DIR /usr/local/freesurfer/7.3.2/subjects /usr/local/freesurfer/7.3.2/bin/recon-all -s Wen.23.9.21 -autorecon2
subjid Wen.23.9.21 setenv SUBJECTS_DIR /usr/local/freesurfer/7.3.2/subjects FREESURFER_HOME /usr/local/freesurfer/7.3.2 Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 Linux ph 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 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 3579276 kbytes maxproc 111576 maxlocks unlimited maxsignal 111576 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 27Gi 2.7Gi 12Gi 46Mi 12Gi 24Gi Swap: 2.0Gi 3.0Mi 2.0Gi
######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275) 7.3.2
ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2
ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2
ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2022/10/20-07:47:31-GMT BuildTime: Aug 4 2022 06:17:15 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 User: jstein Machine: ph Platform: Linux PlatformVersion: 5.15.0-47-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/7.3.2/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/7.3.2/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Thu Oct 20 09:47:32 CEST 2022 /usr/local/freesurfer/7.3.2/subjects/Wen.23.9.21/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.lta
setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (65, 40, 29) --> (190, 157, 194) finding center of left hemi white matter using (107, 79, 112) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (92,65,92) --> (122, 93,132) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.6 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.409 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.179493 @ (-10.526, 31.579, 10.526) max log p = -3.847481 @ (5.263, -5.263, -15.789) max log p = -3.789743 @ (2.632, -2.632, 7.895) max log p = -3.783289 @ (-1.316, -1.316, -3.947) max log p = -3.767843 @ (-0.658, 0.658, 0.658) max log p = -3.751431 @ (0.329, 0.987, 2.303) max log p = -3.751431 @ (0.000, 0.000, 0.000) max log p = -3.751431 @ (0.000, 0.000, 0.000) Found translation: (-4.3, 24.0, 1.6): log p = -3.751 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.483, old_max_log_p =-3.751 (thresh=-3.7) 1.14016 0.01457 -0.13007 -3.03827; 0.00000 1.13509 0.16902 -6.39816; 0.15011 -0.11066 0.98799 -6.24083; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 3 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.483, old_max_log_p =-3.483 (thresh=-3.5) 1.14016 0.01457 -0.13007 -3.03827; 0.00000 1.13509 0.16902 -6.39816; 0.15011 -0.11066 0.98799 -6.24083; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 4 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.303, old_max_log_p =-3.483 (thresh=-3.5) 1.08330 -0.03102 -0.06606 -1.99714; 0.03359 1.18041 0.13938 -13.78753; 0.07799 -0.07696 1.03685 -7.45414; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 56 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.303, old_max_log_p =-3.303 (thresh=-3.3) 1.08330 -0.03102 -0.06606 -1.99714; 0.03359 1.18041 0.13938 -13.78753; 0.07799 -0.07696 1.03685 -7.45414; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 56 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.258, old_max_log_p =-3.303 (thresh=-3.3) 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 53 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.258, old_max_log_p =-3.258 (thresh=-3.3) 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.258 (old=-4.409) transform before final EM align: 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000;
************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 782540 FSRUNTIME@ mri_em_register 0.1087 hours 1 threads registration took 6 minutes and 31 seconds. @#@FSTIME 2022:10:20:09:47:32 mri_em_register N 7 e 391.20 S 0.74 U 390.19 P 99% M 616456 F 0 R 166634 W 0 c 6814 w 3 I 139952 O 24 L 0.14 0.61 0.85 @#@FSLOADPOST 2022:10:20:09:54:03 mri_em_register N 7 1.00 0.91 0.92 #-------------------------------------- #@# CA Normalize Thu Oct 20 09:54:03 CEST 2022 /usr/local/freesurfer/7.3.2/subjects/Wen.23.9.21/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz
writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (65, 40, 29) --> (190, 157, 194) finding center of left hemi white matter using (107, 79, 112) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (92,65,92) --> (122, 93,132) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.6 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246437 sample points... INFO: compute sample coordinates transform 1.08485 -0.04014 -0.07586 -0.25772; 0.04536 1.17974 0.17286 -17.37174; 0.08573 -0.11603 1.03483 -4.00474; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 38, 30) --> (189, 135, 190) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 2 of 7911 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 41, 32) --> (131, 138, 192) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 6 of 7829 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 112, 53) --> (173, 151, 106) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 492 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 112, 54) --> (127, 151, 109) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 372 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 105, 89) --> (145, 163, 119) Brain_Stem: limiting intensities to 92.0 --> 132.0 0 of 693 (0.0%) samples deleted using 17297 total control points for intensity normalization... bias field = 0.973 +- 0.067 90 of 17289 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 38, 30) --> (189, 135, 190) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 2 of 8050 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 41, 32) --> (131, 138, 192) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 9 of 8000 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 112, 53) --> (173, 151, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 534 (0.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 112, 54) --> (127, 151, 109) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 449 (0.2%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 105, 89) --> (145, 163, 119) Brain_Stem: limiting intensities to 88.0 --> 132.0 32 of 785 (4.1%) samples deleted using 17818 total control points for intensity normalization... bias field = 1.020 +- 0.051 86 of 17674 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 38, 30) --> (189, 135, 190) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 3 of 8055 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 41, 32) --> (131, 138, 192) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 12 of 7977 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 112, 53) --> (173, 151, 106) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 536 (7.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (87, 112, 54) --> (127, 151, 109) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 67 of 467 (14.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 105, 89) --> (145, 163, 119) Brain_Stem: limiting intensities to 88.0 --> 132.0 299 of 819 (36.5%) samples deleted using 17854 total control points for intensity normalization... bias field = 1.017 +- 0.039 47 of 17278 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 52 seconds. @#@FSTIME 2022:10:20:09:54:03 mri_ca_normalize N 8 e 52.10 S 0.39 U 51.70 P 99% M 715064 F 7 R 408272 W 0 c 275 w 5 I 1584 O 3824 L 1.00 0.91 0.92 @#@FSLOADPOST 2022:10:20:09:54:55 mri_ca_normalize N 8 1.00 0.92 0.92 #-------------------------------------- #@# SubCort Seg Thu Oct 20 09:54:55 CEST 2022
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
sysname Linux hostname ph machine x86_64
setenv SUBJECTS_DIR /usr/local/freesurfer/7.3.2/subjects cd /usr/local/freesurfer/7.3.2/subjects/Wen.23.9.21/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500
== Number of threads available to for OpenMP = 1 == reading 1 input volumes reading classifier array from /usr/local/freesurfer/7.3.2/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform\00 Command exited with non-zero status 255 @#@FSTIME 2022:10:20:09:54:55 mri_ca_label N 10 e 12.53 S 0.17 U 12.35 P 99% M 466964 F 9 R 115489 W 0 c 108 w 10 I 1712 O 0 L 1.00 0.92 0.92 @#@FSLOADPOST 2022:10:20:09:55:07 mri_ca_label N 10 1.59 1.06 0.97 Linux ph 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Wen.23.9.21 exited with ERRORS at Thu Oct 20 09:55:07 CEST 2022