External Email - Use Caution
From: Yanez-Ramos, Lupita <yanez-ramos.mariaguadal...@mayo.edu>
Date: Tuesday, February 11, 2025 at 11:53
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Recon-all error - release 8.0.0-beta
Hello FreeSurfer Developers,
I'm attempting to run recon-all and recon-all-clinical, but it is the first
time that I used this since I changed my MacBook.
ERROR:
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
recon-all -s sub-01 exited with ERRORS at Tue Feb 11 10:33:15 CST 2025
I've searched the list and no similar errors have been reported. Does anyone
have any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.
1) FreeSurfer version: FreeSurfer version 8.0.0-beta MacOS X darwin_arm64 (64b)
PKG installer
2) Platform: macOs Sequoia 15.3. Chip Apple M4 Max
3) uname -a: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu
Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
4) recon-all.log: see attached
Thank you so much, I really need to use recon-all to complete my project.
Have a great day,
Lupita
Tue Feb 11 10:06:14 CST 2025
cd
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
setenv SUBJECTS_DIR
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer
/Applications/freesurfer/8.0.0-beta/bin/recon-all -i
/Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii
-s sub-01 -all
subjid sub-01
setenv SUBJECTS_DIR
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer
FREESURFER_HOME /Applications/freesurfer/8.0.0-beta
Actual FREESURFER_HOME /Applications/freesurfer/8.0.0-beta
build-stamp.txt: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8176 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 65535
memorylocked unlimited
maxproc 10666
PhysMem: 96G used (6394M wired, 39G compressor), 31G unused.
########################################
program versions used
dev (freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc)
dev
ProgramName: lta_convert ProgramArguments: lta_convert -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: dev
TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: dev
TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_concat ProgramArguments: mri_concat -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:15-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3
2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: dev
TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_relabel_hypointensities ProgramArguments:
mri_relabel_hypointensities -all-info ProgramVersion: dev TimeStamp:
2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
dev
ProgramName: mri_robust_register ProgramArguments: mri_robust_register
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
dev
ProgramName: mri_robust_template ProgramArguments: mri_robust_template
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
mris_convert -all-info
ProgramName: mris_convert ProgramArguments: mris_convert -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:16-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion:
dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024 19:08:47
BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_divide_parcellation ProgramArguments:
mris_divide_parcellation -all-info ProgramVersion: dev TimeStamp:
2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_segment ProgramArguments: mri_segment -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_left_right_register ProgramArguments:
mris_left_right_register -all-info ProgramVersion: dev TimeStamp:
2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3
2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_register ProgramArguments: mris_register -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3
2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff
-all-info ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime:
Nov 3 2024 19:08:47 BuildStamp:
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc User:
yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:17-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
mri_motion_correct.fsl dev
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info
ProgramVersion: dev TimeStamp: 2025/02/11-16:06:18-GMT BuildTime: Nov 3 2024
19:08:47 BuildStamp: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
User: yanez-ramos.mariaguadalupe Machine: R5523400.local Platform: Darwin
PlatformVersion: 24.3.0 CompilerName: Clang CompilerVersion: 13.0.0
#######################################
GCADIR /Applications/freesurfer/8.0.0-beta/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/8.0.0-beta/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
\n mri_convert
/Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz
\n
mri_convert
/Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz
INFO: using NIfTI-1 sform (sform_code=2)
reading from
/Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii...
TR=0.00, 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/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Feb 11 10:06:19 CST 2025
Found 1 runs
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
\n cp
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
\n
\n mri_info
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
\n
rawavg.mgz ========================================
Volume information for
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
type: MGH
intent: MRI (0)
dimensions: 181 x 217 x 181
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 217.000
dof: 1
xstart: -90.5, xend: 90.5
ystart: -108.5, yend: 108.5
zstart: -90.5, zend: 90.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000
talairach xfm :
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
1.0000 0.0000 0.0000 -90.0000
0.0000 1.0000 0.0000 -126.0000
0.0000 0.0000 1.0000 -72.0000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
1.0000 0.0000 0.0000 90.0000
0.0000 1.0000 0.0000 126.0000
0.0000 0.0000 1.0000 72.0000
0.0000 0.0000 0.0000 1.0000
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
\n mri_convert
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--conform \n
mri_convert
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--conform
reading from
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz...
TR=0.00, 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)
volume geometry:
valid : 0
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, -17.5000, 18.5000)
file :
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 49785.6 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz...
\n mri_add_xform_to_header -c
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/talairach.xfm
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
\n
INFO: extension is mgz
\n mri_info
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
\n
orig.mgz ========================================
Volume information for
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
type: MGH
intent: MRI (0)
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -17.5000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 18.5000
talairach xfm :
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 128.5000
0.0000 0.0000 1.0000 -145.5000
0.0000 -1.0000 0.0000 146.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 -0.0000 128.5000
-0.0000 -0.0000 -1.0000 146.5000
-0.0000 1.0000 -0.0000 145.5000
-0.0000 -0.0000 -0.0000 1.0000
lta_convert --inlta identity.nofile --src
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
--trg
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--outlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg2orig.lta
dev
--inlta: identity.nofile input LTA transform.
--src:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz
src image (geometry).
--trg:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
trg image (geometry).
--outlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg2orig.lta
output LTA.
LTA read, type : 1
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Writing LTA to file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg2orig.lta...
lta_convert successful.
\n mri_synthstrip --threads 1 -i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
-o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz
\n
Configuring model on the CPU
Running SynthStrip model version 1
Input image read from:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
Processing frame (of 1): 1 done
Masked image saved to:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz
If you use SynthStrip in your analysis, please cite:
----------------------------------------------------
SynthStrip: Skull-Stripping for Any Brain Image
A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann
NeuroImage 206 (2022), 119474
https://doi.org/10.1016/j.neuroimage.2022.119474
Website: https://synthstrip.io
\n mri_synthseg --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthseg.rca.mgz
--threads 1 --vol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/stats/synthseg.vol.csv
--keepgeom --addctab --cpu \n
SynthSeg 2.0
using CPU, hiding all CUDA_VISIBLE_DEVICES
using 1 thread
addctab True
predicting 1/1
1/1 [==============================] - ETA:
0s
1/1 [==============================] - 322s 322s/step
Reslicing to have same geom as the input [1. 1. 1.]
segmentation saved in:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthseg.rca.mgz
volumes saved in:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/stats/synthseg.vol.csv
#@# mri_synthseg vmpeak None
If you use this tool in a publication, please cite:
SynthSeg: Segmentation of brain MRI scans of any contrast and resolution
without retraining
B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl,
A.V. Dalca, J.E. Iglesias
Medical Image Analysis, 2023.
Tue Feb 11 10:13:03 CST 2025
setenv SUBJECTS_DIR
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer
cd
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
/Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz
--t /Applications/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz
--affine-only --o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305
--threads 1
-rwxr-xr-x 1 root wheel 30900 Nov 3 18:25
/Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
$Id$
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
pid 96300
Tue Feb 11 10:13:03 CST 2025
\n\n
mri_synthmorph -m affine -t
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz
/Applications/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz -j 1
Thank you for choosing SynthMorph. Please cite us!
SynthMorph: learning contrast-invariant registration without acquired images
Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV
IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022
https://doi.org/10.1109/TMI.2021.3116879
Anatomy-specific acquisition-agnostic affine registration learned from
fictitious images
Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution)
SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023
https://doi.org/10.1117/12.2653251
https://synthmorph.io/#papers (PDF)
Anatomy-aware and acquisition-agnostic joint registration with SynthMorph
Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution)
Imaging Neuroscience, 2, 1-33, 2024
https://doi.org/10.1162/imag_a_00197
Website: https://synthmorph.io
~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305
~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
lta_convert --invert --inlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta
--outlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta
dev
--invert: will invert transform.
--inlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta
input LTA transform.
--outlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta
output LTA.
LTA read, type : 1
1.08684 0.08641 0.04272 -2.30560;
-0.05741 1.05093 -0.07044 -2.13585;
0.01811 -0.01467 1.21110 -3.66046;
0.00000 0.00000 0.00000 1.00000;
Writing LTA to file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta...
lta_convert successful.
\n\n
To check affine registration
tkregisterfv --mov
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz
--targ /Applications/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz
--reg
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta
AffineOnly specified, so exiting now
Started at Tue Feb 11 10:13:03 CST 2025
Ended at Tue Feb 11 10:14:02 CST 2025
Fs-Synthmorph-Reg-Run-Time-Sec 59
Fs-Synthmorph-Reg-Run-Time-Min 0.98
Fs-Synthmorph-Reg-Run-Time-Hours 0.02
fs-synthmorph-reg Done
dev
--ltavox2vox: output LTA as VOX_TO_VOX transform.
--inlta: synthmorph.mni305/aff.lta input LTA transform.
--outlta: talairach.xfm.lta output LTA.
LTA read, type : 1
1.08684 0.08641 0.04272 -2.30560;
-0.05741 1.05093 -0.07044 -2.13585;
0.01811 -0.01467 1.21110 -3.66046;
0.00000 0.00000 0.00000 1.00000;
Writing LTA to file talairach.xfm.lta...
lta_convert successful.
dev
--inlta: talairach.xfm.lta input LTA transform.
--outmni: talairach.xfm output MNI/XFM matrix.
LTA read, type : 1
1.08684 0.08641 0.04272 -2.30562;
-0.05741 1.05093 -0.07044 -2.13585;
0.01811 -0.01467 1.21110 -3.66046;
0.00000 0.00000 0.00000 1.00000;
lta_convert successful.
\n fs-synthmorph-reg --s sub-01 --threads 1 --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--test \n
Tue Feb 11 10:14:03 CST 2025
setenv SUBJECTS_DIR
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer
cd
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01
/Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg --s sub-01 --threads
1 --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--test
-rwxr-xr-x 1 root wheel 30900 Nov 3 18:25
/Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
$Id$
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
pid 96493
mri_mask -bb 3
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
cropping npad = 3
DoAbs = 0
Computing bounding box, npad = 3, 3, 3, 3, 3, 3
35 35 16 180 187 223
maskval=0, outval=0
Writing masked volume to
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done.
lta_convert --inlta identity.nofile --src
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
--trg
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--outlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta
dev
--inlta: identity.nofile input LTA transform.
--src:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
src image (geometry).
--trg:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
trg image (geometry).
--outlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta
output LTA.
LTA read, type : 1
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Writing LTA to file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta...
lta_convert successful.
Tue Feb 11 10:14:03 CST 2025
\n\n
mri_synthmorph -m affine -t
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz
-j 1
[DEBUG] FSNifti1Extension.read(): esize = 1520
[DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1508 (tag = 7, length =
4)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1492 (tag = 45, length =
27)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1453 (tag = 8, length =
48)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1393 (tag = 31, length =
131)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1250 (tag = 3, length =
592)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 646 (tag = 3, length =
607)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 27 (tag = -1, length =
1)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 14 (tag = 0, length =
0)
[DEBUG] FSNifti1Extension.read(): esize = 144
[DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1
[DEBUG] FSNifti1Extension.read(): remaining taglen = 132 (tag = 7, length =
4)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 116 (tag = 45, length =
27)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 77 (tag = 8, length =
48)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 17 (tag = -1, length =
1)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 4
Thank you for choosing SynthMorph. Please cite us!
SynthMorph: learning contrast-invariant registration without acquired images
Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV
IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022
https://doi.org/10.1109/TMI.2021.3116879
Anatomy-specific acquisition-agnostic affine registration learned from
fictitious images
Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution)
SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023
https://doi.org/10.1117/12.2653251
https://synthmorph.io/#papers (PDF)
Anatomy-aware and acquisition-agnostic joint registration with SynthMorph
Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution)
Imaging Neuroscience, 2, 1-33, 2024
https://doi.org/10.1162/imag_a_00197
Website: https://synthmorph.io
Tue Feb 11 10:14:39 CST 2025
\n\n
mri_concatenate_lta -invert1 -invertout
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta
invert the first LTA before applying it
invert the output LTA
Read individual LTAs
Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2...
Inverting output LTA
Writing combined LTA to file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta...
mri_concatenate_lta successful.
\n\n
mri_concatenate_lta -invert2
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta
invert the second LTA before applying it
Read individual LTAs
Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2...
Writing combined LTA to file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta...
mri_concatenate_lta successful.
\n\n
lta_convert --invert --inlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta
--outlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta
dev
--invert: will invert transform.
--inlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta
input LTA transform.
--outlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta
output LTA.
LTA read, type : 1
0.87815 -0.06784 -0.04863 2.87647;
0.03993 0.91526 0.09739 1.04553;
-0.00669 0.01654 0.78237 3.06534;
0.00000 0.00000 0.00000 1.00000;
Writing LTA to file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta...
lta_convert successful.
\n\n
lta_convert --inlta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta
--outmni
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm
dev
--inlta:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta
input LTA transform.
--outmni:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm
output MNI/XFM matrix.
LTA read, type : 1
1.13544 0.08307 0.06023 -3.53753;
-0.05069 1.09134 -0.13900 -0.56914;
0.01077 -0.02236 1.28161 -3.93619;
0.00000 0.00000 0.00000 1.00000;
lta_convert successful.
\n\n
To check affine registration
tkregisterfv --mov
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
--targ
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz
--reg
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta
\n\n
mri_synthmorph -m deform -t
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz
-i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz
-j 1 -o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz
[DEBUG] FSNifti1Extension.read(): esize = 1520
[DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1508 (tag = 7, length =
4)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1492 (tag = 45, length =
27)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1453 (tag = 8, length =
48)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1393 (tag = 31, length =
131)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1250 (tag = 3, length =
592)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 646 (tag = 3, length =
607)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 27 (tag = -1, length =
1)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 14 (tag = 0, length =
0)
[DEBUG] FSNifti1Extension.read(): esize = 144
[DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1
[DEBUG] FSNifti1Extension.read(): remaining taglen = 132 (tag = 7, length =
4)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 116 (tag = 45, length =
27)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 77 (tag = 8, length =
48)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 17 (tag = -1, length =
1)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 4
Thank you for choosing SynthMorph. Please cite us!
SynthMorph: learning contrast-invariant registration without acquired images
Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV
IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022
https://doi.org/10.1109/TMI.2021.3116879
Anatomy-specific acquisition-agnostic affine registration learned from
fictitious images
Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution)
SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023
https://doi.org/10.1117/12.2653251
https://synthmorph.io/#papers (PDF)
Anatomy-aware and acquisition-agnostic joint registration with SynthMorph
Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution)
Imaging Neuroscience, 2, 1-33, 2024
https://doi.org/10.1162/imag_a_00197
Website: https://synthmorph.io
\n\nmri_warp_convert --inras
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz
--insrcgeom
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
--outm3z
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz
--vg-thresh 1e-5 --lta1-inv
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta
--lta2
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta
dev
--inras:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz
input RAS warp.
--insrcgeom:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz
atlas/source image (used for geometry).
--outm3z:
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz
output M3Z.
Setting vg_isEqual_Threshold to 0.000010
Applying LTAs to the GCAM
GCAMwrite(/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz)
[INFO] Warpfield::convert(): converting GCAM ...
[INFO] Warpfield::convert(): gcam [193 x 229 x 193]
[INFO] Warpfield::convert(): gcam image [256 x 256 x 256]
[INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193]
[INFO] Warpfield::convert(): total out of range voxel count: 0
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, -17.5000, 18.5000)
file :
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
volume geometry:
extent : (193, 229, 193)
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, -17.5000, 18.5000)
file :
/autofs/space/curv_001/users/fs-mni152-atlas/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz
mri_warp_convert successful.
\n\nmri_ca_register -invert-and-save
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz
INFO: using NIfTI-1 sform (sform_code=1)
Loading gcam
[DEBUG] Warpfield::read() gcam->status = GCAM_LABELED
setting orig areas to linear transform determinant scaled 1.00
Computing inverse of GCAM
Filling inverse of GCAM
Allocating inv_gcam...(256, 256, 256)
Saving inverse to
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz
GCAMwrite(/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz)
[INFO] Warpfield::convert(): converting GCAM ...
[INFO] Warpfield::convert(): gcam [256 x 256 x 256]
[INFO] Warpfield::convert(): gcam image [193 x 229 x 193]
[INFO] Warpfield::convert(): gcam atlas [256 x 256 x 256]
[INFO] Warpfield::convert(): total out of range voxel count: 0
volume geometry:
extent : (193, 229, 193)
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, -17.5000, 18.5000)
file :
/autofs/space/curv_001/users/fs-mni152-atlas/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz
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, -17.5000, 18.5000)
file :
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
mri_vol2vol --regheader --mov
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz
--targ
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz
movvol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz
targvol
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz
outvol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz
invert 0
tal 0
talres 2
regheader 1
noresample 0
interp trilinear (1)
precision float (3)
Gdiag_no -1
Synth 0
SynthSeed 1739655395
Computing registration based on scanner-to-scanner
Final tkRAS-to-tkRAS Matrix is:
1.00000 0.00000 0.00000 -0.50000;
0.00000 1.00000 0.00000 13.50000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox Matrix is:
1.00000 0.00000 0.00000 -20.00000;
0.00000 1.00000 0.00000 -20.00000;
0.00000 0.00000 1.00000 -2.00000;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_convert -rt nearest
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
-at
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz
mri_convert -rt nearest
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz
-at
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz
INFO: using NIfTI-1 sform (sform_code=1)
reading from
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: Reading transformation from file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz...
INFO: Applying transformation from file
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz...
Applying morph_3d ...
[DEBUG] Warpfield::read() gcam->status = GCAM_LABELED
setting orig areas to linear transform determinant scaled 1.00
morphing to atlas with resample type 0
writing to
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz...
mri_diff --po
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz
mri_diff --po
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz
diffcount 4338064
Volumes differ in pixel data
maxdiff 108.62528229 at 64 177 128 0
tkmeditfv -f
/Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz
-aux
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz
Started at Tue Feb 11 10:14:03 CST 2025
Ended at Tue Feb 11 10:31:41 CST 2025
Fs-Synthmorph-Reg-Run-Time-Sec 1058
Fs-Synthmorph-Reg-Run-Time-Min 17.63
Fs-Synthmorph-Reg-Run-Time-Hours 0.29
fs-synthmorph-reg Done
#--------------------------------------------
#@# Nu Intensity Correction Tue Feb 11 10:31:41 CST 2025
\n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm
--n 2 --ants-n4 \n
/usr/bin/bc
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
/Applications/freesurfer/8.0.0-beta/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
nIters 2
FreeSurferEnv.csh dev
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
Tue Feb 11 10:31:41 CST 2025
tmpdir is ./tmp.mri_nu_correct.mni.97202
cd
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o
./tmp.mri_nu_correct.mni.97202/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_binarize --i ./tmp.mri_nu_correct.mni.97202/nu0.mgz --min -1 --o
./tmp.mri_nu_correct.mni.97202/ones.mgz
dev
cwd
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.97202/nu0.mgz --min -1 --o
./tmp.mri_nu_correct.mni.97202/ones.mgz
sysname Darwin
hostname R5523400.local
machine arm64
user yanez-ramos.mariaguadalupe
input ./tmp.mri_nu_correct.mni.97202/nu0.mgz
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.97202/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Writing output to ./tmp.mri_nu_correct.mni.97202/ones.mgz
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.97202/ones.mgz --i orig.mgz
--sum ./tmp.mri_nu_correct.mni.97202/sum.junk --avgwf
./tmp.mri_nu_correct.mni.97202/input.mean.dat
dev
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.97202/ones.mgz --i
orig.mgz --sum ./tmp.mri_nu_correct.mni.97202/sum.junk --avgwf
./tmp.mri_nu_correct.mni.97202/input.mean.dat
sysname Darwin
hostname R5523400.local
machine arm64
user yanez-ramos.mariaguadalupe
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.97202/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.97202/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.97202/ones.mgz --i
./tmp.mri_nu_correct.mni.97202/nu0.mgz --sum
./tmp.mri_nu_correct.mni.97202/sum.junk --avgwf
./tmp.mri_nu_correct.mni.97202/output.mean.dat
dev
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.97202/ones.mgz --i
./tmp.mri_nu_correct.mni.97202/nu0.mgz --sum
./tmp.mri_nu_correct.mni.97202/sum.junk --avgwf
./tmp.mri_nu_correct.mni.97202/output.mean.dat
sysname Darwin
hostname R5523400.local
machine arm64
user yanez-ramos.mariaguadalupe
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.97202/ones.mgz
Loading ./tmp.mri_nu_correct.mni.97202/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.97202/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.97202/nu0.mgz
./tmp.mri_nu_correct.mni.97202/nu0.mgz mul 1.13345000013348604136
Packing
Done packing
Unpacking
Saving result to './tmp.mri_nu_correct.mni.97202/nu0.mgz' (type = MGH )
[ ok ]
#VMPC# mris_calc VmPeak 0
mri_convert ./tmp.mri_nu_correct.mni.97202/nu0.mgz nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.97202/nu0.mgz nu.mgz --like orig.mgz
reading from ./tmp.mri_nu_correct.mni.97202/nu0.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 1 seconds.
FIRST_PERCENTILE 0.010000
WM_PERCENTILE 0.900000
MAX_R 50.000000
i1 = 5, i2 = 71
#mri_make_uchar# mapping 12 167 to 3 110 : b -5.59015 m 0.691738 : thresh
8.08131 maxsat 376.718 : nzero 13848606 nsat 0
Tue Feb 11 10:32:26 CST 2025
mri_nu_correct.mni done
\n mri_add_xform_to_header -c
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/talairach.xfm
nu.mgz nu.mgz \n
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Tue Feb 11 10:32:26 CST 2025
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
\n mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz \n
using max gradient = 1.000
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from nu.mgz...
normalizing image...
NOT doing gentle normalization with control points/label
talairach transform
1.08684 0.08641 0.04272 -2.30562;
-0.05741 1.05093 -0.07044 -2.13585;
0.01811 -0.01467 1.21110 -3.66046;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 22
Starting OpenSpline(): npoints = 22
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 68 (68), valley at 32 (32)
csf peak at 10, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 68 (68), valley at 31 (31)
csf peak at 10, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 0 minutes and 44 seconds.
#--------------------------------------
\n#@# MCADura Segmentation Tue Feb 11 10:33:10 CST 2025
mri_mcadura_seg --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/mca-dura.mgz
--threads 1 --synthmorphdir
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm
Tue Feb 11 10:33:10 CST 2025
setenv SUBJECTS_DIR
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer
cd
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
/Applications/freesurfer/8.0.0-beta/bin/mri_mcadura_seg --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/mca-dura.mgz
--threads 1 --synthmorphdir
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm
-rwxr-xr-x 1 root wheel 13384 Nov 3 18:22
/Applications/freesurfer/8.0.0-beta/bin/mri_mcadura_seg
freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc
$Id$
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
pid 97373
~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373
~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri
mri_vol2vol --reg
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta
--mov
/Applications/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/mcadura.prior.lh.nii.gz
regio_read_register: loading lta
Matrix from regfile:
-1.13544 -0.08307 -0.06023 3.80927;
0.01077 -0.02236 1.28161 1.67021;
0.05069 -1.09134 0.13900 4.76448;
0.00000 0.00000 0.00000 1.00000;
Getting target volume geom from lta destination
movvol
/Applications/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz
outvol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/mcadura.prior.lh.nii.gz
regfile
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision float (3)
Gdiag_no -1
Synth 0
SynthSeed 1740127077
Final tkRAS-to-tkRAS Matrix is:
-1.13544 -0.08307 -0.06023 3.80927;
0.01077 -0.02236 1.28161 1.67021;
0.05069 -1.09134 0.13900 4.76448;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox Matrix is:
-1.13544 -0.06023 0.08307 235.10382;
0.05069 0.13900 1.09134 -54.23622;
-0.01077 -1.28161 -0.02236 266.45721;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_mask -T .001 -crop-to-fov-mm 80 80 80
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/mcadura.prior.lh.nii.gz
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/lh.crop.nii.gz
CropToFoVmm 80 80 80
DoAbs = 0
Found 5557 voxels in mask (pct= 0.03)
MRIcropToFoV(): thresh=0.001 FoV = (80,80,80)
nhits=5557 centroid = (161.479,159.884,163.755) min = (134,139,147) max =
(181,177,179) delta = (48,39,33)
Region 121 120 124 80 80 80
121 120 124 80 80 80
maskval=0, outval=0
Writing masked volume to
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/lh.crop.nii.gz...done.
mri_vol2vol --regheader --mov
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz
--targ
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/lh.crop.nii.gz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/invol.lh.crop.nii.gz
movvol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz
targvol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/lh.crop.nii.gz
outvol
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/invol.lh.crop.nii.gz
invert 0
tal 0
talres 2
regheader 1
noresample 0
interp trilinear (1)
precision float (3)
Gdiag_no -1
Synth 0
SynthSeed 1739719516
Computing registration based on scanner-to-scanner
Final tkRAS-to-tkRAS Matrix is:
1.00000 0.00000 0.00000 -33.00000;
0.00000 1.00000 0.00000 36.00000;
0.00000 0.00000 1.00000 -32.00000;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox Matrix is:
1.00000 0.00000 0.00000 121.00000;
0.00000 1.00000 0.00000 120.00000;
0.00000 0.00000 1.00000 124.00000;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_sclimbic_seg --model
/Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5
--ctab
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/dumca.lh.ctab
--keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile
mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/invol.lh.crop.nii.gz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/seg.lh.mgz
/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg --model
/Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5
--ctab
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/dumca.lh.ctab
--keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile
mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/invol.lh.crop.nii.gz
--o
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/seg.lh.mgz
Keeping anterior commissure in vols and stats
Using CPU
Using 1 thread(s)
Loaded lookup table
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/dumca.lh.ctab
Loaded population stats
/Applications/freesurfer/8.0.0-beta/models/sclimbic.volstats.csv
nb_labels 2
inshape (72, 72, 72) features 24
(None, 72, 72, 72, 1)
Loading weights from
/Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5
-----------------------
Done loading weights -----------------------
Loaded model weights
/Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5
Segmenting image 1/1
[DEBUG] FSNifti1Extension.read(): esize = 1520
[DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1508 (tag = 7, length =
4)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1492 (tag = 45, length =
27)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1453 (tag = 8, length =
48)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1393 (tag = 31, length =
131)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 1250 (tag = 3, length =
592)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 646 (tag = 3, length =
607)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 27 (tag = -1, length =
1)
[DEBUG] FSNifti1Extension.read(): remaining taglen = 14 (tag = 0, length =
0)
Loaded input image from
/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.97373/invol.lh.crop.nii.gz
ERROR:
Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22
PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64
recon-all -s sub-01 exited with ERRORS at Tue Feb 11 10:33:15 CST 2025
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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