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:
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)
above it does indicate that the FSF_OUTPUT_FORMAT is nii, but that is not the same as FSL, right?