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Yup, That solved it!
Thank you for your help! I totally missed that. 
Misque 

On Jul 3, 2023, at 9:36 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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lta_convert looks fine in /Applications/freesurfer/7.4.1/.
 
Your ‘export FREESURFER_HOME=Applications/freesurfer/7.4.1’ doesn’t have the leading ‘/’.
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Misque Boswell
Sent: Monday, July 3, 2023 12:30 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error Help
 

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Thank you, Yujing. Here it is:
 
Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info 
7.4.1
 
ProgramName: lta_convert  ProgramArguments: /Applications/freesurfer/7.4.1/bin/lta_convert -all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/07/03-16:28:36-GMT  BuildTime: Jun 14 2023 00:15:19  BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: misqueboswell  Machine: Misques-MBP-3.local  Platform: Darwin  PlatformVersion: 22.2.0  CompilerName: Clang  CompilerVersion: 12.0.0
 
Misque 


On Jul 3, 2023, at 8:55 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
 

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Can you run the following at prompt?
 
‘Applications/freesurfer/7.4.1/bin/lta_convert -all-info’
 
I’m not a Mac user. Do you need ‘/’ in front of ‘Application’?
 
Yujing
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Misque Boswell
Sent: Monday, July 3, 2023 11:44 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error Help
 

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Hello Yujing, 
 
Thank you for your response. I followed the directions for setup and sourced SetUpFreeSurfer.sh as you stated. All goes as planned up to this point. 
 
Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1
Misques-MBP-3 / % source $FREESURFER_HOME/SetUpFreeSurfer.sh
 
-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   Applications/freesurfer/7.4.1
FSFAST_HOME       Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      Applications/freesurfer/7.4.1/subjects
MNI_DIR           Applications/freesurfer/7.4.1/mni
FSL_DIR           /Users/misqueboswell/fsl
 
 
Can you check where your recon-all is and if lta_convert is in the distribution?
1. which recon-all
 
Misques-MBP-3 / % which recon-all
Applications/freesurfer/7.4.1/bin/recon-all
 
2. ls -l <recon-all_path>/lta_convert
 
lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" (rwxr-xr-x  1 root  wheel   2613752 Jun 13 21:21 lta_convert) 
 
Thank you again for your help! 
Misque 



On Jul 3, 2023, at 6:26 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
 
Yujing
 
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