Change your script to specify full path to 001.nii - “</your-filepath>${i}.nii”

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Wednesday, November 22, 2023 5:55 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

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Hi again..

I made the script but I got a problem 

I would like to mention that I am working on Linux system 

the message error I got is 

duniaa77@TENCC96E5342F26:/usr/local/freesurfer/7.4.1/subjects$ for i in {001..024}; do
> echo "Processing subject sub${i} with input ${i}.nii"
> recon-all -s sub${i} -i ${i}.nii -all
> done
Processing subject sub001 with input 001.nii
ERROR: 001.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub001 exited with ERRORS at Wed Nov 22 10:53:03 GMT 2023

For more details, see the log file
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Processing subject sub002 with input 002.nii
ERROR: 002.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub002 exited with ERRORS at Wed Nov 22 10:53:06 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub003 with input 003.nii
ERROR: 003.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub003 exited with ERRORS at Wed Nov 22 10:53:08 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub004 with input 004.nii
ERROR: 004.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub004 exited with ERRORS at Wed Nov 22 10:53:09 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub005 with input 005.nii
ERROR: 005.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub005 exited with ERRORS at Wed Nov 22 10:53:11 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub006 with input 006.nii
ERROR: 006.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub006 exited with ERRORS at Wed Nov 22 10:53:13 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub007 with input 007.nii
ERROR: 007.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub007 exited with ERRORS at Wed Nov 22 10:53:15 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub008 with input 008.nii
ERROR: 008.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub008 exited with ERRORS at Wed Nov 22 10:53:16 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub009 with input 009.nii
ERROR: 009.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub009 exited with ERRORS at Wed Nov 22 10:53:18 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub010 with input 010.nii
ERROR: 010.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub010 exited with ERRORS at Wed Nov 22 10:53:20 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub011 with input 011.nii
ERROR: 011.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub011 exited with ERRORS at Wed Nov 22 10:53:21 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub012 with input 012.nii
ERROR: 012.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub012 exited with ERRORS at Wed Nov 22 10:53:23 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub013 with input 013.nii
ERROR: 013.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub013 exited with ERRORS at Wed Nov 22 10:53:24 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub014 with input 014.nii
ERROR: 014.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub014 exited with ERRORS at Wed Nov 22 10:53:26 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub015 with input 015.nii
ERROR: 015.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub015 exited with ERRORS at Wed Nov 22 10:53:27 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub016 with input 016.nii
ERROR: 016.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub016 exited with ERRORS at Wed Nov 22 10:53:28 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub017 with input 017.nii
ERROR: 017.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub017 exited with ERRORS at Wed Nov 22 10:53:29 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub018 with input 018.nii
ERROR: 018.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub018 exited with ERRORS at Wed Nov 22 10:53:30 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub019 with input 019.nii
ERROR: 019.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub019 exited with ERRORS at Wed Nov 22 10:53:32 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub020 with input 020.nii
ERROR: 020.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub020 exited with ERRORS at Wed Nov 22 10:53:33 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub021 with input 021.nii
ERROR: 021.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub021 exited with ERRORS at Wed Nov 22 10:53:34 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub022 with input 022.nii
ERROR: 022.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub022 exited with ERRORS at Wed Nov 22 10:53:36 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub023 with input 023.nii
ERROR: 023.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub023 exited with ERRORS at Wed Nov 22 10:53:37 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Processing subject sub024 with input 024.nii
ERROR: 024.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub024 exited with ERRORS at Wed Nov 22 10:53:39 GMT 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

On Tue, 21 Nov 2023 at 17:57, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Assuming

1. NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
2. To name the subjects as sub1, sub2, …, sub300

In bash shell, you can do the batch submission as following at prompt:

for i in {1..300}; \

do \

echo “recon-all -all -s sub${i} -i ${i}.nii” \

recon-all -all -s sub${i} -i ${i}.nii \

done

Adjust recon-all command line options for any additional flags, and change the subject IDs for something more descriptive.

It is a good idea to submit one first to get familiar with Freesurfer recon-all output directory structure before doing the batch submission.

Best,

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 12:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

        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

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

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:

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Dunia Ahmad Al-Hamad

PhD Student 

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road 

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