Hi - you should check whether FreeSurfer actually needs those variables
itself, or simply sets them up because it includes some FSL programs and
hence has to setup "it's" FSL environment, in which case I would think
that it's fine to overwrite those variables with the "real" FSL settings
by setting up FreeSurfer first (in your shell setup) and then setting up
FSL.
Cheers.
On Tue, 8 Nov 2005, Molly M Davies wrote:
> hello,
>
> Thanks so much for the reply. Turns out Freesurfer also has environmental variables for
> TCL_LIBRARY, TK_LIBRARY and the like. So far I've found that all the EVs in FSL's $FSLDIR/bin/tclsh
> and $FSLDIR/bin/wish conflict (ie freesurfer has EVs of the same name that are assigned freesurfer-
> specific values.)
> Commenting out the line I'd put in my profile to automatically source the freesurfer setup file upon
> login has apparently fixed the problem.
> Is there something simple I could do to ameliorate this conflict in a more fundamental way? Are these
> files unique to each software package (eg a specific image or custom code)? I'm unfamiliar with TIX
> and TCL, so I didn't know if I could simply change the values assigned to the various EVs in the FSL
> files mentioned above to correspond to those of freesurfer.
> More importantly, is there anything ominous I should watch out for in light of this conflict?
> It'll probably be easy enough to just not run FSL and tkmedit from the same terminal...
>
> Thanks again for your time,
> Molly
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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