Here are the steps to setup Freesurfer environment and run 'recon-all': 1. Source the correct Freesurfer environment needs to be sourced before running recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux 2. Set 'SUBJECTS_DIR' to point to directory outside the Freesurfer installation tree, and make sure you have write permission 3. Run recon-all https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all (ex. recon-all -all -s <> -i <>)

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Katherine Sawyer Sent: Friday, December 20, 2024 8:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Help

External Email - Use Caution Hello,

When trying to run recon-all I keep getting the following error message:

mri_convert: Command not found. ERROR: Executable 'mri_convert -all-info failed! Is it missing from the distribution?'

I just wondered what would be causing it and how to fix it?

When running initially, I got the error mris_fix_topology: Command not found. My IT department, deleted and reinstalled FreeSurfer and now I am getting the mri_convert error instead. They deleted 7.4.1 and installed 7.4.0 and this issue is now occurring. The commands seem to be missing from the FreeSurfer bin folder for some reason?

I am wondering what could be the cause and solution - or if I'm doing something incorrectly. I imagine it is a local problem for me rather than a wider issue.

Thank you.

Best wishes,

Katherine Sawyer