External Email - Use Caution
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