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setenv FSLDIR /imaging/local/linux/bin/fsl-3.3.11 setenv FSLDIR /imaging/local/linux/bin/fsl-4.1.2

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 MartinMonti.

Using the latest version of FSL

Before running fsl you need to run


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-4.1.2
source ${FSLDIR}/etc/fslconf/fsl.csh
set path = (${FSLDIR}/bin $path)

If you want to use the loadsharing system, then replace the last 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.

Recent Updates:

2008/12/15 Installed latest FSL



to use it[RC]

2008/10/6 small FSL patch requested by Mirjana

Ask her if you're curious [RC]

2008/9/15 FSL patches applied as requested by Eleftherios

You may now choose between the patched version


and the unpatched one



2008/9/1 and 2008/9/2 Installed FSL 4.1.0



to use it

Fixed, added load sharing wrappers, accidentally deleted fsl3.2, hope no-one need it.


2008/02/06 Added load balancing to FSL

All FSL 4.0.1 commands are now executed with load balancing.

Details... wrote python script /imaging/local/spm/loadshare/runfsl.py which launches an FSL command on the currently least busy machine. Then, /imaging/local/spm/loadshare/fslwrappers.py which makes symbolic links in /imaging/local/linux/bin/fsl-4.01/bin/loadshare/bin

This directory is now added by fsl_4.0.1_setup instead of the one with the actual commands in.

If you wish to run multiple scripts or jobs in parallel launch with separate xterms like this:

   xterm -e [your command 1] &
   xterm -e [your command 2] &
   e.g., xterm -e feat myscript.fsf &

[RC, MM]

2007/12/12 Added FSL 4.0.1

To use, type


at the Linux prompt

CbuImaging: FslInformation (last edited 2019-09-11 13:50:27 by MartaCorreia)