Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

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recon-all ERROR on new installation UBUNTU 22.04 Ubuntu 22 amd64 (64b) DEB installer 7.3.2 release
by Steinbacher Jürgen 21 Oct '22

21 Oct '22

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.deb<https://secure-web.cisco.com/1Jp0hfngKh-YNvOboZak8vNQYbnpzGL438b30mGK2ULBJy…> 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

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Any differences by Freesurfer version for hippocampal subfields and nuclei of the amygdala ?
by ANNA FINLEY 20 Oct '22

20 Oct '22

External Email - Use Caution Hello Freesurfer experts! We have previously extracted hippocampal subfields and nuclei of the amygdala using the beta version of segmentHA_T1.sh routine with Freesurfer 6 beta. We are wondering if there is any reason to expect volumetric differences between the beta and current version of this routine? In other words, would it be necessary to rerun with the current version in Freesurfer 7, or are the initial values extracted with the beta version sufficient? Thank you for your help! Anna Finley

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Innovative and Exciting Postdoc Opportunity in Brain Gut Interactions at UCLA
by Arpana Annie Gupta 20 Oct '22

20 Oct '22

External Email - Use Caution Dear Freesurfer Community, We are looking for a postdoc fr this exciting position (2-3 years)- details below https://secure-web.cisco.com/1NqyC0HHvTzTL8vtP-76M31wmRU55O0-zkFkTH6mg8np2S… <https://secure-web.cisco.com/1NqyC0HHvTzTL8vtP-76M31wmRU55O0-zkFkTH6mg8np2S…> https://secure-web.cisco.com/1PFqQVrKs9jjs09X7XH-7mUKj7ML_xxlvjYM4LHGMXpcHV… <https://secure-web.cisco.com/1PFqQVrKs9jjs09X7XH-7mUKj7ML_xxlvjYM4LHGMXpcHV…> Thanks Annie The Center for Neurobiology of Stress and Resilience in the Division of Digestive Diseases at the University of California Los Angeles is seeking a full time Post-Doctoral Research Fellow for a U54-funded project studying sex-related differences in the brain-gut-microbiome interactions related to visceral pain. This project is focused on the sex-specific effect of gut microbial metabolites, and estrogen levels on ascending arousal pathways originating in distinct brainstem nuclei to change the activity and connectivity of brain networks involved in symptom generation in irritable bowel syndrome. As a part of an multidisciplinary research team the fellow will apply advanced computational, neuroimaging, biostatistical, and bioinformatics approaches to assess the interaction between various levels of biological data (e.g., microbiota, metabolites, sex hormones, multimodal brain and brainstem imaging data), clinical variables (symptom severity, widespread pain) and sex. There will be opportunities to develop translational and clinical neuroscience research skills (e.g., target discovery, individualized treatment development and biomarker/predictor development), in addition to state-of-the-art analytical skills to address basic and pathophysiological systems biology questions. The G Oppenheimer Center for Neurobiology of Stress and Resilience (CNSR) is an interdisciplinary, translational Center funded by the National Institutes of Health, and by philanthropic support. The overall research goals of the CNSR are to better understand the interactions between mind brain and body in health and disease, and to develop novel management strategies for optimal health and for complex chronic disorders. Center investigators are conducting clinical, translational and basic research with human populations, using interventions (e.g., diet, cognitive behavioral therapy) alongside deep phenotyping including neuroimaging, mutli-omics profiling (gut microbiome, metabolomics, inflammatory biomarkers, psychosocial and behavioral assessments. You will work directly with Arpana “Annie” Gupta, PhD and Jennifer Labus, PhD and an array of faculty collaborators across UCLA, and beyond. There will be many opportunities to lead high impact publications starting on day one, working with existing rich and unique datasets in addition to creating new ones. Extensive mentorship will be provided to facilitate the transition to an independent research career. Duties and Responsibilities: The Post-Doctoral Fellow’s responsibilities will include, but are not limited to: Develop longitudinal multimodal MRI data analysis streams (functional connectivity, task-based fMRI, diffusion tractography and volumetrics). Analyze complex multi-omics datasets including imaging, gut microbiome, metabolomics, behavioral and clinical data. Prepare and submit manuscripts Mentor graduate and undergraduate students Be inquisitive, curious and publish! Required Qualifications: Ph.D. in Neuroscience, Neuropsychology, Bioinformatics, Biostatistics, Engineering, Computer Science or a related field. Strong proficiency and independence with various neuroimaging analysis platforms, multivariate modeling strategies and network connectivity analyses. Established quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments. Experience with R, Linux, Matlab or Python preferred. Background in systems/cognitive neuroscience, neuroanatomy and psychological/clinical constructs. A demonstrated capacity to drive first author publications. Excellent communication and writing skills, motivated and driven to publish. Preferred Qualifications: Connectomics network analysis and machine learning modeling confer a very significant advantage. Management/coding of neuroimaging databases (XNAT or others). Arpana "Annie" Gupta, Ph.D. Associate Professor Director: Neuroimaging Core G. Oppenheimer Center for Neurobiology of Stress and Resilience Ingestive Behavior and Obesity Program UCLA Vatche and Tamar Manoukian Division of Digestive Diseases David Geffen School of Medicine UCLA CHS 42-210, 10833 Le Conte Avenue | Los Angeles, CA 90095-7378 Email: agupta(a)mednet.ucla.edu https://secure-web.cisco.com/173BZkJOJWRC57VDzzRXag1sxGE_ZY2uqP78zEyxS9KOWZ… | Twitter: @AGuptaCNS This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and any disclosure, copying, or distribution of this message, or the taking of any action based on it, by you is strictly prohibited.

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Re: [Freesurfer] passcode for archive
by fsbuild 20 Oct '22

20 Oct '22

External Email - Use Caution Hello Mohamed, It was sent to you on 10/18 at around 7 PM EDT.  Please check your spam filters. - R. On Oct 20, 2022, at 05:22, KATTA, Mohamed (MOORFIELDS EYE HOSPITAL NHS FOUNDATION TRUST) <mohamed.katta(a)nhs.net> wrote:        External Email - Use Caution        Hi,would really appreciate if you could send me the passcode to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive, thanks in advanceBest wishes,Mohamed KattaClinical Research FellowMoorfields Eye HospitalFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of KATTA, Mohamed (MOORFIELDS EYE HOSPITAL NHS FOUNDATION TRUST) <mohamed.katta@nhs.net>Sent: 17 October 2022 14:43To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] passcode for archive  This message originated from outside of NHSmail. Please do not click links or open attachments unless you recognise the sender and know the content is safe.         External Email - Use Caution        Dear Researchers,can I please have the passcode to open to the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive, many thanksBest wishes,Mohamed KattaClinical Research FellowMoorfields Eye Hospital************************************************************************************** ******************************This message may contain confidential information. If you are not the intended recipient please:i) inform the sender that you have received the message in error before deleting it; and ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful). Thank you for your co-operation.NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.For more information and to find out how you can switch visit Joining NHSmail – NHSmail Support************************************************************************************** ******************************This message may contain confidential information. If you are not the intended recipient please:i) inform the sender that you have received the message in error before deleting it; and ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful). Thank you for your co-operation.NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.For more information and to find out how you can switch visit Joining NHSmail – NHSmail Support_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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passcode for archive
by KATTA, Mohamed (MOORFIELDS EYE HOSPITAL NHS FOUNDATION TRUST) 20 Oct '22

20 Oct '22

External Email - Use Caution Dear Researchers, can I please have the passcode to open to the FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1XUCjyvywpen4WIj_jAXxzK3BMR1zKYvM9qrfuPlzdKU9k…> archive, many thanks Best wishes, Mohamed Katta Clinical Research Fellow Moorfields Eye Hospital ************************************************************************************** ****************************** This message may contain confidential information. If you are not the intended recipient please: i) inform the sender that you have received the message in error before deleting it; and ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful). Thank you for your co-operation. NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services. For more information and to find out how you can switch visit Joining NHSmail - NHSmail Support<https://secure-web.cisco.com/1_ae-cIDHwccpVcfBJR-2phY29VPbwsTlP_pdXUdDoU3tB…>

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Thalamic segmentation error
by Alan Francis 19 Oct '22

19 Oct '22

External Email - Use Caution Hi Eugenio - Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help. Thanks, Alan copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared libraries: libicudata.so.52: cannot open shared object file: No such file or directory Command exited with non-zero status 127 @#@FSTIME 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07 @#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 0.22 0.07 127 Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022 For more details, see the log file /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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mghread : cannot open the file
by priya padma 19 Oct '22

19 Oct '22

External Email - Use Caution Hello Team, I am trying to find the volume of WM, GM, CSF separately and I came across this command namely "mri_compute_volume_fractions" Looking through all the email archives I gave the following line as the command after setting the paths $ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz but I get the following error user-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz supposed to be reproducible but seed not set 7.3.2 sysname Darwin hostname user-MacBook-Pro.local machine x86_64 user <username> setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects cd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129 mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz wsurf white psurf pial TempVolFile /mri/norm.mgz USF 2 Reading in aseg and surfs from /Applications/freesurfer/7.3.2/subjects/tester Loading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz error: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz, -1): could not open file I set all the paths so why am I not able to read the mgz file? Could anyone help me with this ? Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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Upgrading Operating System (OS)
by Boa Sorte Silva, Narlon 19 Oct '22

19 Oct '22

External Email - Use Caution Dear FreeSurfer team: I just wanted to confirm the potential issues of upgrading the OS. We are running FreeSurfer 7.1.1 on MacOS 10.4.6 and wanted to upgrade to MacOS 10.15. Our data have been analyzed cross-sectionally and we’ll soon run longitudinal analysis. Would upgrading the MacOS on the same machine and same version of FreeSurfer be detrimental to the analysis results of the same data? In particular, would it bias longitudinal analysis results? Thank you for your help Best regards, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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trac-all -prep: set: Variable name error
by Ashwati Vipin 19 Oct '22

19 Oct '22

External Email - Use Caution Re-posting this. Please help! Dear Freesurfer Developers, My trac-all -prep with the following command: trac-all -prep -debug -c /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/BIOC_0001_v01_DTI_FS_Sept -no-isrunning |& tee log.txt keeps ending abruptly without any error warning as below: [cid:ce34364b-acd7-48a2-88d6-c8745491c8ab] The subject’s scripts folder still has an IsRunning.trac file. I ran the trac-all -prep command with a debug and have attached the log file for that. I’ve also attached my configuration file. Not sure what’s going wrong? Really appreciate your help! Best, Ashwati Notice: This email is generated from the account of an NUS alumnus. Contents, views, and opinions therein are solely those of the sender.

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Re: [Freesurfer] QXcb connection error 170 (was Freeview: missing voxels in reconstructed surfaces)
by fsbuild 18 Oct '22

18 Oct '22

External Email - Use Caution These errors can happen when the remote machine is running Windows or Linux, but it’s a known issue with some X servers that run on Windows.  When the X windows (graphics/windowing) software trying to remotely display images (which is not freeview) to a machine over the network cannot get the resources it needs, rendering images can be incomplete and report various errors. It could be something is going wrong with trying to remotely render graphics using OpenGL.  You could try setting this to see if it makes a difference, $ export LIBGL_ALWAYS_INDIRECT=0 If you have an IT department, they night be able to help troubleshoot a remote connection.   It could be useful to know that freeview displays images just fine when run directly on the machine you are remotely connecting to -  just as you say it does on your own Mac. - R. On Oct 18, 2022, at 11:32, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:This appears to be a rendering artifact that happens sometimes with remote display. Are you viewing remotely from a Windows machine?RuopengOn Oct 18, 2022, at 9:45 AM, Sarah Lavelle <lavells1(a)tcd.ie> wrote:        External Email - Use Caution        Dear Freesurfer,I have an issue when viewing my reconstructed surfaces on Freeview my linux version : freesurfer-linux-ubuntu18_x86_64-devfreesurfer 7-devThe surfaces have a large number of empty voxels. This is not a problem with the recon-all function as I can see the same surface file perfectly on my Mac with the fully working mac version. It seems to be a problem with my Freeview.Some additional information that may help finding the cause:When I open Freeview from Ubuntu, I get the following errors:QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-lavells1'QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20There are no other errors in ubuntu after I load Freeview i.e. No errors in Ubuntu when I then load the surface.I hope you can help me fix this issue as soon as possible. Many thanks,Sarah<image.png><Empty_Voxels_PialSurface_CloseUp.PNG><Empty_Voxels_PialSurface.PNG>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer October 2022