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====== Using FSL ======


===== Requesting More Memory =====

If your jobs are killed because of insufficient memory, it means most likely that the portions run via SGE are hitting the default memory limit. To request more, do so via the [[using_ogs_sge#setting_default_options_for_all_scripts|.sqe_request file]] in your home directory.

**NOTE** however that this will make the request for **all** jobs your run, which is an inefficient use of memory for you and everyone else, so be careful to always change this file before running other jobs that don't need as much memory (e.g. simply comment-out or deactivate any lines by adding a hash mark (#) by itself at the beginning of the line in your .sge_request file). I'm hoping to work out a more flexible way to request more memory and will let everyone know if I work it out.

===== Commands that Use SGE =====

Several compute-intensive commands use SGE to run portions of the processing in parallel. They submit qsub jobs using your username.

These are the commands:

  FEAT    will run multiple first-level analyses in parallel if they are setup all together in one GUI setup. At second level, if full FLAME (stages 1+2) is selected then all the slices are processed in parallel.
  
  MELODIC will run multiple single-session analyses (or single-session preprocessing if a multi-session/subject analysis is being done) in parallel if they are setup all together in one GUI setup.
  
  TBSS    will run all registrations in parallel.
  
  BEDPOSTX (FDT) low-level diffusion processing will run all slices in parallel.
  
  FSLVBM  will run all registrations in parallel, both at the template-creation stage and at the final registrations stage.
  
  POSSUM  will process all slices in parallel.

If you get an error like this:

  denied: host "compute-0-6.local" is no submit host

tell the admin. This shouldn't happen as of May 2016.

==== Using FSL WITHOUT SGE ====

You may need to tell FSL to __not__ use SGE for one of the above commands. 

To tell FSL not to use SGE, you must clear the ''SGE_ROOT'' environment variable for your script. Add this line to your script, before you call an FSL command that normally uses SGE:

  unset SGE_ROOT
  
When the FSL scripts see that ''SGE_ROOT'' is not defined (i.e. it is unset), it will run its analysis portions on the same computer that the script was run from.

==== CPU Time Limit Issues ====

If your command gets killed because it takes too much CPU time running on chead, email the admin to learn how to work around this. This is very unlikely to be an issue.