Hi,
On Tue, Mar 13, 2012 at 01:08:05PM -0500, Matt Glasser wrote:
> This is an Ubuntu FSL distribution bug where /etc/fsl/fsl.sh (FSL's config
> file) does not get sourced before launching FSLView from the launch panel
> (even if you have it properly set up in your .bashrc/.bash_profile.
I'd argue that the bug is more of a design problem in FSL. Relying on
the presence of various environment variables is a fragile setup. It
makes it really hard for other (mostly GUI) applications to use FSL.
They all have to guess where the relevant FSL configuration file could
be and source it. FSLView is only one of the victims. Mricron is
another, but there are more.
Desktop user expect to click on a button and get a working tool. It is
not possible to prepare a system environment that could achieve this
with a reasonably general validity. The reason being that the
environment would need to be globally modified. However, that puts FSL
into the system name space -- but it conflicts with other system tools
(e.g. immv). This approach can even ruin things completely. For example
when done for AFNI and Freesurfer (IIRC) on the same system you end up
with conflicting binaries from both. Depending who gets into the path
first, ruins the other.
A cleaner way of dealing with this problem would be a wrapper
binary/script. Git does that for example. The wrapper knows its
"commands", know the environment that needs to be created, ... Instead
of
fslmaths ...
it would be
fsl math ...
I wrote such a wrapper for the Debian package once, but in the end decided
that it would be useless with FSL itself using it. The fsl4.1-* commands
that get installed by the Debian package in addition are basically a
crippled version of such a wrapper
My 2ct,
Michael
--
Michael Hanke
http://mih.voxindeserto.de
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