Dear Jeff,
What do you get when you do the following in a terminal:
echo $FSLOUTPUTTYPE
This is the only variable that matters.
I normally set this type of environment variable up in my
~/.bash_profile or ~/.profile or ~/.bashrc (depending on
which one or ones you already have). If you try adding
the lines that set this variable into these files (near where
you set up the FSLDIR would be a good place) then this
should take effect globally for you.
All the best,
Mark
On 29 Aug 2011, at 23:53, Jeff Eriksen wrote:
> I have tried to set the default file to NIFTI (not NIFTI_GZ), but nothing seems to work. I have created an fsl.sh file under ~/.fslconf that has only this in it:
>
> FSLOUTPUTTYPE=NIFTI
> export FSLOUTPUTTYPE
>
> The above does not work, I still get .nii.gz outputs. I also modified the global fsl.sh as above, and still no good.
>
> /usr/local/fsl/etc/fslconf/ is where the central copy lives.
>
> below is what I get when invoking Terminal:
>
> -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /Applications/freesurfer
> FSFAST_HOME /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii
> SUBJECTS_DIR /Applications/freesurfer/subjects
> MNI_DIR /Applications/freesurfer/mni
> FSL_DIR /usr/local/fsl
>
> above it does indicate that the FSF_OUTPUT_FORMAT is nii, but that is not the same as FSL, right?
>
> Thanks,
> -Jeff
>
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