External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to run recon-all on a T1.nii file on my M5 macbook pro. I have set my environment variables per documentation instructions:
export FREESURFER_HOME=/Applications/freesurfer/8.1.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=$FREESURFER_HOME/subjects export FS_LICENSE=$FREESURFER_HOME/license.txt
I am concerned if the issue is due to me trying to run freesurfer on an M5 macbook.
Also, I'm getting this recurring warning:
if: Empty if. then: Command not found.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: MacOSX Tahoe 26.2 (25C56) 3) uname -a: Darwin Ajays-MBP.attlocal.net 25.2.0 Darwin Kernel Version 25.2.0: Tue Nov 18 21:09:49 PST 2025; root:xnu-12377.61.12~1/RELEASE_ARM64_T8142 arm64 4) recon-all.log: see attached