This means that the automatic correcting of the FSLDIR variable to point at the new location hasn’t worked because the installer doesn’t recognise the format of your shell setup file. Often this is because the FSL section of the setup files have been hand edited.
You need to check in your .bash_profile (or .cshrc or .tcshrc) for the lines that mention FSLDIR and either delete them and re-run the installer with the ‘-e’ option or change them yourself to point at the correct location for FSL (there will be three lines, one setting FSLDIR, one adding FSLDIR/bin to the PATH variable and one mentioning FSLDIR/etc/fslconf [this one won’t need changing if you are editing the file]).
Duncan
On 30 Aug 2014, at 09:13, gabriel robert <[log in to unmask]> wrote:
> Dear all,
>
> I am trying to re-install fsl on my Mac and the fsl installer provides the message "FSLDIR environment variable is corrupt" and then I am unable to run fsl tools,
>
> Many thanks for your help,
>
> Gabriel
--
Duncan Mortimer
Computing Officer, FMRIB Centre, University of Oxford
John Radcliffe Hospital, Oxford, UK
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