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