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Dear FreeSurfer Experts,
FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Secure Shell port of a high performance computer (HPC) accessed via Ubuntu 18.04 WSL
Having processed a cohort of 1mm^3 MRI images via the recon-all command, we have had issues processing the hippocampal subfield command as described: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Although we eventually want to run the command in array, we are currently attempting it on individual subjects to ensure a good output. Upon running the command we receive a "permission denied" error. The HPC is a shared cluster, and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot edit, and thus couldn't download the Matlab runtime to.
We initially thought this may be the issue, and so tried multiple workarounds, including copying the entirety of the FreeSurfer installation package from the shared directory to our own directory, within which we have editing permissions. This didn't help, even when setting our personal directory as the FREESURFER_HOME. As you can see from the end of the recon-all.log file, we tried numerous attempts with various workarounds and all have the same outcome.
I appreciate this may still be more of an issue with running FreeSurfer via a secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, but I'm sure you have many research labs asking questions regarding using HPC systems to run FreeSurfer, so any recommendations or thoughts would be welcome.
Kind Regards, Aleks Duvnjak