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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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