External Email - Use Caution
Dear Freesurfer developers,
I realised some of my recon-alls been processed with the following error:
ERROR: input(s) cannot have multiple frames!
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames
(I have attached the recon-all.log)
I checked the mri info and I think the problem is the dimensions which is
256 x 256 x 211 x 2.
I'll attach the original commands I used with mri info in txt file in case
it would help you to see where I went wrong.
If anyone has been through this problem or if you know what I can do to fix
this, please let me know.
Best,
H
Thu Mar 3 09:44:42 KST 2022
cd /Users/mac_01/Desktop/1155_401
setenv SUBJECTS_DIR /Users/mac_01/Desktop
/Applications/freesurfer/7.2.0/bin/recon-all -s 1155_401 -i 1155_401.nii -all
-qcache
subjid 1155_401
setenv SUBJECTS_DIR /Users/mac_01/Desktop
FREESURFER_HOME /Applications/freesurfer/7.2.0
Actual FREESURFER_HOME /Applications/freesurfer/7.2.0
build-stamp.txt: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
Darwin mac-01.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51
PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101 arm64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8176 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 2560
memorylocked unlimited
maxproc 2666
PhysMem: 15G used (1437M wired), 93M unused.
########################################
program versions used
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
7.2.0
ProgramName: lta_convert ProgramArguments: lta_convert -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:42-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:43-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:43-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:43-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:43-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:43-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:44-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:44-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:44-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0
TimeStamp: 2022/03/03-00:44:44-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:45-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:45-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_concat ProgramArguments: mri_concat -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:45-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:45-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:45-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:46-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:46-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:46-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:46-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:46-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:47-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:47-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:47-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:47-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:47-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:48-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:48-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:48-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:48-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:48-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0
TimeStamp: 2022/03/03-00:44:48-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mri_relabel_hypointensities ProgramArguments:
mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp:
2022/03/03-00:44:49-GMT BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:49-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:49-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
7.2.0
ProgramName: mri_robust_register ProgramArguments: mri_robust_register
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:49-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
7.2.0
ProgramName: mri_robust_template ProgramArguments: mri_robust_template
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:50-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:50-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:50-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:50-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mris_convert ProgramArguments: mris_convert -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:50-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:50-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:51-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion:
7.2.0 TimeStamp: 2022/03/03-00:44:51-GMT BuildTime: Jul 13 2021 22:05:06
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root
Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName:
Clang CompilerVersion: 10.0.1
ProgramName: mris_divide_parcellation ProgramArguments:
mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp:
2022/03/03-00:44:51-GMT BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mri_segment ProgramArguments: mri_segment -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:51-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:52-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:52-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:52-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:52-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:52-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:53-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_left_right_register ProgramArguments:
mris_left_right_register -all-info ProgramVersion: 7.2.0 TimeStamp:
2022/03/03-00:44:53-GMT BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:53-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:53-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_register ProgramArguments: mris_register -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:54-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:54-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:54-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:54-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:54-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:55-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff
-all-info ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:55-GMT
BuildTime: Jul 13 2021 22:05:06 BuildStamp:
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b User: root Machine:
mac-01.local Platform: Darwin PlatformVersion: 20.3.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:55-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:55-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:55-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:56-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:56-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:56-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:56-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:56-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:57-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:57-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:57-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
mri_motion_correct.fsl 7.2.0
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info
ProgramVersion: 7.2.0 TimeStamp: 2022/03/03-00:44:57-GMT BuildTime: Jul 13
2021 22:05:06 BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
User: root Machine: mac-01.local Platform: Darwin PlatformVersion: 20.3.0
CompilerName: Clang CompilerVersion: 10.0.1
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu
(x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
#######################################
GCADIR /Applications/freesurfer/7.2.0/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/7.2.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/Users/mac_01/Desktop/1155_401
\n mri_convert /Users/mac_01/Desktop/1065-1281_nii/1155_401.nii
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz \n
mri_convert /Users/mac_01/Desktop/1065-1281_nii/1155_401.nii
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz
reading from /Users/mac_01/Desktop/1065-1281_nii/1155_401.nii...
TR=6.45, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0618165, -0.996563, -0.0551468)
j_ras = (0.0211862, 0.0565501, -0.998175)
k_ras = (-0.997863, -0.0605354, -0.0246105)
writing to /Users/mac_01/Desktop/1155_401/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Mar 3 09:45:02 KST 2022
Found 1 runs
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames
Darwin mac-01.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51
PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101 arm64
recon-all -s 1155_401 exited with ERRORS at Thu Mar 3 09:45:02 KST 2022
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
mac-01:Desktop root# cd /Users/mac_01/Desktop/1065-1281_nii
mac-01:1065-1281_nii root# ls 1155_401.nii | parallel --jobs 8 recon-all -s {.}
-i {} -all -qcache
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
Tange, O. (2021, June 22). GNU Parallel 20210622 ('Protasevich').
Zenodo. https://doi.org/10.5281/zenodo.5013933
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 39 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Subject Stamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
Current Stamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
INFO: SUBJECTS_DIR is /Users/mac_01/Desktop
Actual FREESURFER_HOME /Applications/freesurfer/7.2.0
Darwin mac-01.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51
PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101 arm64
/Users/mac_01/Desktop/1155_401
\n mri_convert /Users/mac_01/Desktop/1065-1281_nii/1155_401.nii
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz \n
mri_convert /Users/mac_01/Desktop/1065-1281_nii/1155_401.nii
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz
reading from /Users/mac_01/Desktop/1065-1281_nii/1155_401.nii...
TR=6.45, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0618165, -0.996563, -0.0551468)
j_ras = (0.0211862, 0.0565501, -0.998175)
k_ras = (-0.997863, -0.0605354, -0.0246105)
writing to /Users/mac_01/Desktop/1155_401/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Mar 3 09:45:02 KST 2022
Found 1 runs
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames
Darwin mac-01.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51
PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101 arm64
recon-all -s 1155_401 exited with ERRORS at Thu Mar 3 09:45:02 KST 2022
For more details, see the log file
/Users/mac_01/Desktop/1155_401/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
mac-01:1065-1281_nii root# freeview
------------------------------------------------------------------------------------------------------------------------------------------------------
mac-01:1065-1281_nii root# mri_info 1155_401.nii
Volume information for 1155_401.nii
type: nii
dimensions: 256 x 256 x 211 x 2
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -105.5, zend: 105.5
TR: 6.45 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 2
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = 0.0618, y_r = 0.0212, z_r = -0.9979, c_r = -5.0969
: x_a = -0.9966, y_a = 0.0566, z_a = -0.0605, c_a = 5.9937
: x_s = -0.0551, y_s = -0.9982, z_s = -0.0246, c_s = 27.5053
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
0.0618 0.0212 -0.9979 89.5533
-0.9966 0.0566 -0.0605 132.7018
-0.0551 -0.9982 -0.0246 164.9269
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
0.0618 -0.9966 -0.0551 135.8050
0.0212 0.0566 -0.9982 155.2242
-0.9979 -0.0605 -0.0246 101.4538
-0.0000 -0.0000 -0.0000 1.0000_______________________________________________
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