External Email - Use Caution
Hello FreeSurfer Developers,
When attempting to run "recon-all -long" in subjects with multiple T1 inputs, I
get the following error when "longmc" is run:
concatLtas: Undefined variable.
if: Expression Syntax.
Command exited with non-zero status 1
For the entire log, see attached "longmc_error.log".
The following change at line 188 of "freesurfer/bin/longmc" fixes it
(case-sensitive issue in "$concatLtas"):
set ud = `UpdateNeeded $origvol $CrossList $concatLtas --> set ud =
`UpdateNeeded $origvol $CrossList $ConcatLtas`
Best,
Andrea
Tue Mar 19 03:23:22 UTC 2024
cd /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1.long.sub-005x47481
setenv SUBJECTS_DIR /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE
/home/a_boscutti_gmail_com/freesurfer/bin/recon-all -long sub-005x47481_ses-1 sub-005x47481 -parallel -openmp 4 -all
subjid sub-005x47481_ses-1.long.sub-005x47481
setenv SUBJECTS_DIR /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE
FREESURFER_HOME /home/a_boscutti_gmail_com/freesurfer
Actual FREESURFER_HOME /home/a_boscutti_gmail_com/freesurfer
build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460
Linux instance-20240319-023721 5.15.0-1053-gcp #61~20.04.1-Ubuntu SMP Mon Feb 26 16:50:40 UTC 2024 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 65536 kbytes
maxproc 3611912
maxlocks unlimited
maxsignal 3611912
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 881Gi 3.8Gi 600Gi 1.0Mi 277Gi 872Gi
Swap: 0B 0B 0B
########################################
program versions used
7.4.1 (freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460)
7.4.1
ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
7.4.1
ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:22-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp CompilerName: GCC CompilerVersion: 8.4.0
mri_motion_correct.fsl 7.4.1
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2024/03/19-03:23:23-GMT BuildTime: Jun 14 2023 04:06:48 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 User: a_boscutti_gmail_com Machine: instance-20240319-023721 Platform: Linux PlatformVersion: 5.15.0-1053-gcp 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 /home/a_boscutti_gmail_com/freesurfer/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 /home/a_boscutti_gmail_com/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
longmc -long sub-005x47481_ses-1 sub-005x47481 -s sub-005x47481_ses-1.long.sub-005x47481
Tue Mar 19 03:23:23 UTC 2024
setenv SUBJECTS_DIR /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE
cd /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1.long.sub-005x47481
/home/a_boscutti_gmail_com/freesurfer/bin/longmc -long sub-005x47481_ses-1 sub-005x47481 -s sub-005x47481_ses-1.long.sub-005x47481
freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460
longmc 7.4.1
Linux instance-20240319-023721 5.15.0-1053-gcp #61~20.04.1-Ubuntu SMP Mon Feb 26 16:50:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
pid 26494
cp /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/001.lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/001-iscale.txt /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1.long.sub-005x47481/mri
mri_concatenate_lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/001.lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481/mri/transforms/sub-005x47481_ses-1_to_sub-005x47481.lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/001-to-base.lta
volume geometry:
extent : (208, 240, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : ( 1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 1.0000, 0.0000)
z_(ras) : ( 0.0000, 0.0000, 1.0000)
c_(ras) : ( 0.5000, 32.2279, -22.8056)
file : /apps/psyapps/FREESURFER_OUT/sub-005x47481_ses-1/mri/rawavg.mgz
volume geometry:
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : ( 0.5000, 32.2279, -22.8056)
file : /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/norm.mgz
Read individual LTAs
Warning: dst volume of lta1 doesn't match src volume of lta2
Volume geometry for lta1-dst:
Volume geometry for lta2-src:
Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2...
Writing combined LTA to file /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/001-to-base.lta...
mri_concatenate_lta successful.
cp /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/002.lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/002-iscale.txt /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1.long.sub-005x47481/mri
mri_concatenate_lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/002.lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481/mri/transforms/sub-005x47481_ses-1_to_sub-005x47481.lta /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/002-to-base.lta
volume geometry:
extent : (208, 240, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : ( 1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 1.0000, 0.0000)
z_(ras) : ( 0.0000, 0.0000, 1.0000)
c_(ras) : ( 0.5000, 32.2279, -22.8056)
file : /apps/psyapps/FREESURFER_OUT/sub-005x47481_ses-1/mri/rawavg.mgz
volume geometry:
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : ( 0.5000, 32.2279, -22.8056)
file : /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/norm.mgz
Read individual LTAs
Warning: dst volume of lta1 doesn't match src volume of lta2
Volume geometry for lta1-dst:
Volume geometry for lta2-src:
Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2...
Writing combined LTA to file /home/a_boscutti_gmail_com/FREESURFER_OUT_GOOGLE/sub-005x47481_ses-1/mri/orig/002-to-base.lta...
mri_concatenate_lta successful.
concatLtas: Undefined variable.
if: Expression Syntax.
Command exited with non-zero status 1
@#@FSTIME 2024:03:19:03:23:23 longmc N 5 e 0.36 S 0.16 U 0.12 P 79% M 12024 F 2 R 18258 W 0 c 44 w 237 I 0 O 56 L 1.02 0.92 0.76
@#@FSLOADPOST 2024:03:19:03:23:23 longmc N 5 1.02 0.92 0.76
Linux instance-20240319-023721 5.15.0-1053-gcp #61~20.04.1-Ubuntu SMP Mon Feb 26 16:50:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-005x47481_ses-1.long.sub-005x47481 exited with ERRORS at Tue Mar 19 03:23:23 UTC 2024
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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