Hi Jeff
It sounds like you are using bash on Linux. (It's generally useful to
mention such things when asking for help.)
On Wed, Jan 27, 2010 at 10:48:22PM +0000, Jeff Eriksen wrote:
> I am trying to set the default output format to NIFTI, uncompressed. I have
> tried to edit the default fsl.sh but do not have permission to save, not even
> as a super user. I successfully created a secondary, local fsl.sh in my home
> directory as per the instructions below, but it has no effect. What am I
> missing? The following are the instructions from the FSL install page, which I
> believe I have followed correctly:
Perhaps you aren't sourcing the file properly. In bash, this is
achieved with
. ${FSLDIR}/etc/fsl/fsl.sh
Note that this is "period space dollar" and the FSLDIR variable needs
to be correctly set -- otherwise replace the whole path expression
with the actual path name on your system. Sourcing the default fsl.sh
also sources the one you've created in $HOME/.fslconf/
If I'm wrong and you're doing this already, check what FSLOUTPUTTYPE
is currently set to:
echo $FSLOUTPUTTYPE
and modify with
export FSLOUTPUTTYPE=NIFTI
This will stay in effect for the current bash session.
As superuser, you should definitely be able to modify the file
(although it is not recommended). If you can't, there must be a
deeper problem with your FSL or system installation.
See how it goes and let us know if you need more input.
Rolf
--
Rolf A Heckemann, MD PhD
Médecin chercheur
Fondation Neurodis
CERMEP - Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
59 Boulevard Pinel
69003 Lyon
France
1264633831
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