MRI images upside-down in FSLVIEW
Totally out of my league here, but judging from a quick Google search, this seems to be a common problem in FSL. You've said this YouTube video helps, so that's good...but since it uses an applescript, I suppose it requires the Mac OS.

You say Freesurfer's mri_convert works in Linux using this code:

mri_convert 
--in_orientation [file's current storage order, e.g. LAS]
--out_orientation [desired storage order] 
&lt;in volume&gt;
&lt;out volume&gt;