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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