[Condor-users] Using Freesurfer with Condor

["Shi, Bo" <bo.shi@xxxxxxxxxxxxxxxxxxxxx>]

Hi All - 

I'm exploring the possibility of using Condor to manage Freesurfer
(https://surfer.nmr.mgh.harvard.edu/fswiki) processes.  Installation of
Condor went smoothly on a RHEL4 system, but I've come across a possible
issue with how Freesurfer handles data files.

Freesurfer processes data located in a subject directory (2 levels deep)

In section 2.5.4.4,
> Therefore, the executing program must access input files without paths.
> Because all transferred files are placed into a single, flat directory,
> input files must be uniquely named to avoid collision when transferred.
> A collision causes the last file in the list to overwrite the earlier
> one.

Can Condor handle such a usage case?  Can I specify a whole directory as
program input?

Or even better, has anyone every used Freesurfer with Condor?


Thanks,
Bo