Current

From the FSL download page, after agreeing to the license, FSL provides a python installer script and directs you to an instruction page for the version you're installed.

Legacy

Custom FSL Installation (based on wiki, with FAQ troubleshooting)

Make sure the VM has been customized, especially setting the shell to tcsh, and changing the /usr/local permissions

Download the latest FSL distribution, and copy it to /usr/local
Extract: tar xzvf ...
Edit the shell script to set the environment variables: from home directory, gedit .tcshrc (the same file that has FreeSurfer variables)

setenv FSLDIR /usr/local/fsl
source ${FSLDIR}/etc/fslconf/fsl.csh
setenv PATH ${FSLDIR}/bin:${PATH}

start fsl (type "fsl" in terminal); if nothing happens, restart
Click View; if you get the error

/usr/local/fsl/bin/fslview_bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory

install libexpat0. System => Administration => Add/Remove Software, search for libexpat0, or compat-expat. Check, click Apply, enter root password.

If you get a similar error with libmng, this is available through the Add/Remove Software (search for libmng, and select the non-development option).

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