External Email - Use Caution
Hello Freesurfer Developers
I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBb...
ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness
Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64
1) freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1
2) platform: bash terminal
3) log file
Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache
subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333
PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.
######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1
ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 7.4.1
ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 7.4.1
ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ####################################### GCADIR /Applications/freesurfer/7.4.1/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 /Applications/freesurfer/7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz
reading from /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii... TR=8.98, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz... #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Tue Nov 21 15:50:39 GMT 2023 /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf \n mris_preproc --s I12250_MP-RAGE_20060321115220_3 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf/lh.thickness Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64
recon-all -s I12250_MP-RAGE_20060321115220_3 exited with ERRORS at Tue Nov 21 15:50:39 GMT 2023
To report a problem, see http://secure-web.cisco.com/1kSmtgzR_pxmyG0Pcf2UmG3i7fQr9HeDya5uym7dX6z6tGZd...
Thank you