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FSL

Introduction

For reference FSL's homepage is located at http://www.fmrib.ox.ac.uk/fsl/ FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

FSL at TCHPC

Before running FSL on our TCHPC clusters, please become familiar with the methods for connecting to our systems, and for transferring files.

FSL for TBSS techniques

If using FSL for TBSS techniques, you may need to run on the TCIN mini-cluster. If unsure, please contact us for details.

Loading the FSL Environment

A module file has been created to set up your environment for FSL

module load tcin fsl/5.0.10

There are a number of older versions of FSL also installed:

fsl/4.1.4
fsl/4.1.6
fsl/4.1.6-jt
fsl/4.1.9
fsl/5.0.4
fsl/5.0.9
fsl/5.0.10

Requirements and notes

The FSL install at TCHPC has a customised 'fsl_sub' command for the TBSS tools in FSL. The TBSS steps should now also work on lonsdale, (previously they were configured to only work correctly on the TCIN minicluster). The customised script 'fsl_sub' will parallelise various parts of the workflow for TBSS work. Please visit http://www.fmrib.ox.ac.uk/fsl/fsl/sgesub.html for more information on which components can be parallelised.

Patch for fsl_sub to work with Slurm

A simple patch for fsl_sub is attached.

Please see the attached file (fsl_sub.patch.20180208.txt) for the latest patch. It offers two modes of operation with Slurm:

  1. if the 'staskfarm' module is available, then use it to submit the multiple tasks in fsl_sub as a single job with the Slurm multi-prog config (useful if nodes do not share jobs)
  2. otherwise, submit each of the multiple tasks in fsl_sub as individual jobs

For backwards compatibility, the original patch (fsl_sub.patch.20170613.txt) is also attached. It just employs the second mode of operation (submit single jobs).

We also attach a small patch to bedpostx, to allow it do be used with Slurm (bedpostx.patch.txt).