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:

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.

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

Your help with this would be greatly appreciated.

Kind regards

Dr Roberto Scipioni

Senior HPC specialist, Red Oak Consulting, UK