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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