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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