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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 *$FREESURFER_HOME/subjects* is being used by *recon-all* and other scripts in common. So, if we run our pipeline script in parallel, they'll call *recon-all* and other freesurfer scripts in parallel, possibly writing to and reading from this directory, eventually leading to a mix up in the patient data.
So, we feel that we need to run our script one by one for the patients. Am I right to be concerned about this?
Kind Regards, Gunes
No I don't think so. As long as each subject has its own name/folder, there will not be any problem. We do this kind of thing all the time with hundreds (or more) subjects running simultaneously.
On 10/5/2020 11:14 AM, gunes wrote:
External Email - Use Caution
Dear Freesurfer experts,
We have a pipeline script that uses *recon-all* and other executables (like applywarp, mri_convert, mri_em_register etc.) several times. We ran our script in parallel from different terminals to process the patients faster. However, it's come to our attention that the directory *$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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 *$FREESURFER_HOME/subjects. *We were seeing same-titled files in both the patient specific folder and the common directory (i.e. FREESURFER_HOME/subjects) (e.g. aparc.a2009s+aseg.mgz), and thought that we're maybe overwriting to the common directory and copying the final product to the patient specific folder at the end. Is this not the case?
Kind regards
Douglas N. Greve dgreve@mgh.harvard.edu, 5 Eki 2020 Pzt, 16:57 tarihinde şunu yazdı:
No I don't think so. As long as each subject has its own name/folder, there will not be any problem. We do this kind of thing all the time with hundreds (or more) subjects running simultaneously.
On 10/5/2020 11:14 AM, gunes wrote:
External Email - Use CautionDear Freesurfer experts,
We have a pipeline script that uses *recon-all* and other executables (like applywarp, mri_convert, mri_em_register etc.) several times. We ran our script in parallel from different terminals to process the patients faster. However, it's come to our attention that the directory *$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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No, you are not overwriting anything.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of gunes gunesbayir@gmail.com Sent: Monday, October 5, 2020 12:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Parallel Run of Multiple Patients
External Email - Use Caution
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.edumailto: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:
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Greve, Douglas N.,Ph.D.
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gunes