External Email - Use Caution        

But this will take long time because I had another group with 300 patients 


On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Each subject needs to be processed separately. You will need submit 24 recon-all.

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 12:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

 

        External Email - Use Caution        

What if I had 24 subjects. Should I specify the name for each one in the line ?  

 

Dunia

 

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

This is your recon-all submitted

 

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

 

Add ‘-all’ to the line.

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 11:50 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

 

        External Email - Use Caution        

Could you please explain more ho to specify all in recon-all command ?

 

Dunia

 

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 10:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors in recon-all command

 

        External Email - Use Caution        

Hello Freesurfer Developers 

 

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

 

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

 

1) freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2) platform: bash terminal

3) log file


Tue Nov 21 15:50:35 GMT 2023
cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3
setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects
/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3
setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects
FREESURFER_HOME /Applications/freesurfer/7.4.1
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8176 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
descriptors  256
memorylocked unlimited
maxproc      1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

########################################
program versions used
7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460)
7.4.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
7.4.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
7.4.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
mri_motion_correct.fsl 7.4.1
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
#######################################
GCADIR /Applications/freesurfer/7.4.1/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/7.4.1/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3
\n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz \n
mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz
reading from /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii...
TR=8.98, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz...
#--------------------------------------------
#@# Qdec Cache preproc lh thickness fsaverage Tue Nov 21 15:50:39 GMT 2023
/Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf
\n mris_preproc --s I12250_MP-RAGE_20060321115220_3 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh \n
nsubjects = 1
ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf/lh.thickness
Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

recon-all -s I12250_MP-RAGE_20060321115220_3 exited with ERRORS at Tue Nov 21 15:50:39 GMT 2023

--

Dunia Ahmad Al-Hamad

PhD Student 

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road 

Sheffield

S10 2HQ

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