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Thank you for your response!

Yes, each patient has its own folder, but inside these patient specific folders, there are symlink folders (namely fsaverage, lh.EC_average and rh.EC_average) pointing to folders with the same name under $FREESURFER_HOME/subjects. We were seeing same-titled files in both the patient specific folder and the common directory (i.e. FREESURFER_HOME/subjects) (e.g. aparc.a2009s+aseg.mgz), and thought that we're maybe overwriting to the common directory and copying the final product to the patient specific folder at the end. Is this not the case?

Kind regards

Douglas N. Greve <dgreve@mgh.harvard.edu>, 5 Eki 2020 Pzt, 16:57 tarihinde şunu yazdı:

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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