[Freesurfer] FreeSurfer error when running Hippocampal Subfields

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Good morning,

I am a Biomedical Engineering Student at Universitat de Barcelona and I am creating a python script that has a Watchdog which detects new patients in a specific folder, and we want it to run FS and Hippocampal Subfields. The FS runs properly, but when the script arrives to the Hippocampal Subfields command, it breaks.

When using the FreeSurfer's Hippocampal Subfields from a python script after running FS recon-all right before, the processing is not performed due to the error shown in the attatched file. However, when running the Hippocampal Subfields from the terminal it does work.

We have even tried to create a watchdog only for the Hippocampal Subfields, and when we move a folder obtained after running FS to a specific folder, it also runs properly. It is only when it is concatenated with FS that it does not work.

We have contacted MathWorks Support, but they told us to reach you. The Matlab versions we have are Matlab_R2020a and Matlab_R2014b.

Thanks a lot,

Joana Collet