= 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: * Main page: http://www.fmrib.ox.ac.uk/fsl * FAQ: http://www.fmrib.ox.ac.uk/fslfaq/ * FSL course notes: http://www.fmrib.ox.ac.uk/fslcourse/ 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 {{{ 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 $path) }}} If you want to use the loadsharing system, then replace the last line above with the following: {{{ set path = (${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. == ALIAS suggestions == Sometimes the FSL GUIs seem to freeze if launched with the '&' command from a terminal. A simple suggestion to avoid this from happening is to add a couple aliases in your .cshrc file. For example: {{{ #FSL Aliases alias fslview 'xterm -e fslview &' alias fsl 'xterm -e fsl &' }}} (remember to source the .cshrc file after editing it, by typing 'source ~/.cshrc') As a result of the aliases when you type 'fsl' in a terminal, it will open a new xterm (on the least busy machine, if you are using the loadbalancing scripts -- see above) and launch from there the FSL GUI. You will then be able to still use the terminal from which you launched the command without the GUI freezing. You can create any other alias command by replacing 'guiname' with whichever GUI you like in the following command: {{{ alias guiname 'xterm -e guiname &' }}}