External Email - Use Caution        

Could explain more, as I am not very expert in freesurfer 
For e.g I had 300 subject and their NIFTI files are named by their number (1.nii) 
How to make a script to launch, do you mean in a txt file ? 

Thank you

On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
you can write a script to launch them, eg
foreach subject (your-list-of-subjects)
  recon-all -s $subject -all ...
end



On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

        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: