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 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: 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

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

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)

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