FslInformation - MRC CBU Imaging Wiki

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FSL information

FSL is the FMRIB Software Library. It is a C / C++ / Tcl/Tk package written by the Oxford analysis group.

For more information see:

You can find the FSL example data set (http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html) in /imaging/local/fsl/feeds.

The data for the FSL course is in /imaging/local/fsl/fslcourse.

Any problems, report them to RhodriCusack.

Using the latest version of FSL

Before running fsl you need to run

fsl_4.1.2_setup

which is the latest version of fsl at the moment. By running this command you are also using load sharing with any fsl command. If you want to check if you are using the latest version try

which fsl

Using a specific version of FSL on the CBU systems

If you need to use a specific version, rather than the one pointed to by /imaging/local/linux/bin/fsl, then define the path to the version of FSL you want, and put something like this at the end of your ~/.cshrc file:

# FSL stuff
setenv FSLDIR /imaging/local/linux/bin/fsl-3.3.11
source ${FSLDIR}/etc/fslconf/fsl.csh
set path = (${FSLDIR}/bin $path)

If you want to use the loadsharing system, then replace the lst line above with the following:

set path = (${FSLDIR}/bin/loadshare/bin $path)

In order for this to work when you login across linux machines, you will (I'm afraid) also need to put the same lines in your ~/.login file. Put these lines somewhere between the lines #  Space for personal defaults and #  End space for personal defaults in the ~/.login file. By using this method load sharing is not used automatically.