No I don't think so. As long as each subject has its own name/folder, there will not be any problem. We do this kind of thing all the time with hundreds (or more) subjects running simultaneously.

On 10/5/2020 11:14 AM, gunes wrote:

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Dear Freesurfer experts,

We have a pipeline script that uses recon-all and other executables (like applywarp, mri_convert, mri_em_register etc.) several times. We ran our script in parallel from different terminals to process the patients faster. However, it's come to our attention that the directory $FREESURFER_HOME/subjects is being used by recon-all and other scripts in common. So, if we run our pipeline script in parallel, they'll call recon-all and other freesurfer scripts in parallel, possibly writing to and reading from this directory, eventually leading to a mix up in the patient data.

So, we feel that we need to run our script one by one for the patients. Am I right to be concerned about this?

Kind Regards,

Gunes
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