Setting up FSL to use a SunGridEngine or computing cluster

De Grupo de Inteligencia Computacional (GIC)

Several of the more compute-intensive tools can now take advantage of cluster computing, via SunGridEngine (SGE):

   * 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.
   * BEDPOST (FDT) low-level diffusion processing will run all slices in parallel.
   * FSL-VBM 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. 

First step: install SGE

All the above tools interact with a compute cluster via a single central script fsl_sub; if no cluster is available then this script silently runs all the requested jobs in series. To customise FSL for your local compute cluster and clustering software, simply edit ${FSLDIR}/bin/fsl_sub - hopefully the comments in this file are sufficient to make this fairly painless, particularly for labs using SGE. For other clustering software than SGE, note that fsl_sub makes use of an SGE feature allowing the submission of a text file containing a list of commands (one per line) to be run in parallel.