1. make sure 'tcsh' is in her PATH 2. It looks like she has '/opt/cycle/jetpack/bin/' in her PATH. Is '/campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup' her Freesurfer install directory? I'm assuming she sourced Freesurfer environment correctly.
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux After sourcing Freesurfer environment correctly, 'echo $PATH' should show $FREESURFER_HOME/bin in the very beginning. Also, check if executables in $FREESURFER_HOME/bin have executable permissions. Yujing From: Roberto Scipioni <roberto.scipi...@redoakconsulting.co.uk> Sent: Tuesday, June 17, 2025 10:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes) External Email - Use Caution Dear Sir or Madam, I am an HPC admin who has been contacted by a user who has installed the Freesurfer in his local directory. However, she keeps getting errors in using the software., for instance: 1. tcsh ONLY works if it is actually present in /bin . This defeats the purpose of using the HPC and its module environment especially using the Cloud as compute nodes are ephemeral. 1. Update needed is searched in /opt/cycle/jetpack/bin/UpdateNeeded rather than in the Software folder /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin where it is. Is there any obvious reason why this may happen. The user is knowledgeable and she has already trying different environment options like those suggested in: https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads<https://secure-web.cisco.com/1MlpAewP0l0b-LfNakbZ011g7UhgKbNFb1Xo5kZEtuRQnXEAECu9FmWBZm65-GZQWdvjcO5hkdZoZkHg0wxkpxalrCyIv-Hz2MjKulkVmPp4Jgceh-yH1R8Su4ULTsjJWVmROXuxOFVdbKcfgN_ob42Yz6zYYYxTKSq1HEYGlHhnEHTACMaUXyZ8Tn-MlMhG91GrhSAZS5qi_ecW_7aMnqkB0VWXDgx0xkX3zEno1zcTX1HPWteHEPhzZ512aSjt6ZbiPBerZServOdUOh2ZTab8hINMTmeZn7G40uMxocANYL1X81bZ9lxS15OL_9VzsO723Ea2vQwI8OzZ7kOyfDQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads> Your help with this would be greatly appreciated. Kind regards Dr Roberto Scipioni Senior HPC specialist, Red Oak Consulting, UK
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