FSL

FSL is diffusion MRI software made by FMRIB, the Oxford Centre for Functional MRI of the Brain. "FSL" stands for "FMRIB Software Library" and it includes tools for image viewing, masking, segmentation, and registration, as well as diffusion tensor fitting, analysis, and tractography, both deterministic and probabilistic.

See the FSL website for more information about the tools included in FSL.

Getting Started

FSL is installed on the CS Linux machines, but your environment requires some setup before you can use it. The setup is different depending on which command-line shell you use. To check which shell you use, open up a terminal window and type echo $SHELL, then hit enter.

If your shell is csh or tcsh

1. Edit the file ".cshrc" in your home directory and add the following lines somewhere above the line that reads if ($?prompt == 0) exit:

   setenv FSLDIR /usr/share/fsl
   source ${FSLDIR}/etc/fslconf/fsl.csh
   setenv PATH ${FSLDIR}/bin:${PATH}
   setenv FSLTCLSH /usr/bin/tclsh
   setenv FSLWISH /usr/bin/wish

2. Save the file, exit your shell, and open a new shell.

If your shell is bash

1. Edit the file ".bashrc" in your home directory and add the following lines somewhere above the line that reads if [ -z "$PS1" ]; then:

   . /usr/share/fsl/etc/fslconf/fsl.sh

   Note that the above line of code begins with a dot and a space; these must be included!

2. Save the file, exit your shell, and open a new shell.

Running the FSL GUI

Once you've set up your shell as above, simply execute fsl on the command line to bring up the FSL GUI, which gives you access to interactive, graphical interfaces to most of FSL's tools.