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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