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:

On our system, the current version of FSL (that is, the version you get by typing 'fsl' at the command prompt) is the one pointed to by the link /imaging/local/linux/fsl. At the time of writing this is the slightly outdated 3.2 version.

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 MatthewBrett or RhodriCusack.

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)

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.

You can check which version of FSL you are getting by typing fsl at the unix prompt, and looking at the version number at the top of the FSL button window - for FSL 3.3.11 it should read FSL 3.3. Oddly, you can't check which version of FSL you are getting by typing which fsl in unix - because, the version that you actually get depends on the FSLDIR environment variable, which can be mis-set, without the fixes above.