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. 2. 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://secure-web.cisco.com/1MlpAewP0l0b-LfNakbZ011g7UhgKbNFb1Xo5kZEtuRQnXE...
Your help with this would be greatly appreciated. Kind regards
Dr Roberto Scipioni Senior HPC specialist, Red Oak Consulting, UK
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.scipioni@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/rel6downloadshttps://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
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
Roberto Scipioni